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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|108885075|ref|NP_072661.2| DNA polymerase III, beta subunit (MG_001) [Mycoplasma genitalium G37] 380 COG0113 1-380 -88.200 18  [L] COG0592 DNA polymerase sliding clamp subunit (PCNA homolog)
PDB0113 1-380 -96.800 21  1vpk_A mol:protein length:378 DNA polymerase III, beta subunit
PfamA26U 1-121 -45.800 20  PF00712.14; DPO3B_BACSU/1-127; DNA polymerase III beta subunit, N-terminal domain
135-256 -39.300 13  PF02767.11; DPO3B_PROMI/129-244; DNA polymerase III beta subunit, central domain
258-380 -53.800 29  PF02768.10; DPO3B_BACSU/253-376; DNA polymerase III beta subunit, C-terminal domain
SCOP175 1-121 -48.300 21  d1vpka1 d.131.1.1 (A:1-120) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]}
129-257 -41.700 14  d1ok7a2 d.131.1.1 (A:123-244) DNA polymerase III, beta subunit {Escherichia coli [TaxId: 562]}
258-380 -51.500 23  d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]}
2 gi|108885076|ref|NP_072662.2| DnaJ domain-containing protein (MG_002) [Mycoplasma genitalium G37] 310 COG0113 2-309 -104.000 17  [O] COG0484 DnaJ-class molecular chaperone with C-terminal Zn finger domain
PDB0113 2-309 -84.000 16  3lz8_A mol:protein length:329 Putative chaperone DnaJ
PfamA26U 2-61 -39.600 46  PF00226.26; Q22028_CAEEL/17-79; DnaJ domain
151-218 -21.600 14  PF00684.14; DNAJ1_CORGL/147-211; DnaJ central domain
SCOP175 2-70 -44.100 30  d1wjza_ a.2.3.1 (A:) CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK) {Mouse (Mus musculus) [TaxId: 10090]}
135-223 -26.800 11  d1exka_ g.54.1.1 (A:) Cysteine-rich domain of the chaperone protein DnaJ {Escherichia coli [TaxId: 562]}
187-266 -21.300 13  d1nlta1 b.4.1.1 (A:110-138,A:213-257) Mitochondrial protein import protein mas5 (Hsp40, Ydj1), C-terminal domain {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
277-310 -10.900 14  d1c3ga2 b.4.1.1 (A:260-349) Heat shock protein 40 Sis1 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
3 gi|12044853|ref|NP_072663.1| DNA gyrase subunit B (MG_003) [Mycoplasma genitalium G37] 650 COG0113 3-650 -144.000 47  [L] COG0187 Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit
PDB0113 9-409 -120.000 40  1kij_A mol:protein length:390 DNA GYRASE SUBUNIT B
398-650 -108.000 50  3foe_C mol:protein length:268 DNA topoisomerase 4 subunit B
PfamA26U 43-143 -9.930 18  PF13589.1; A5G4D8_GEOUR/22-165; Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
228-408 -75.800 39  PF00204.20; Q9R3E4_ACISP/115-285; DNA gyrase B
576-639 -45.700 57  PF00986.16; Q6MRR8_BDEBA/731-795; DNA gyrase B subunit, carboxyl terminus
SCOP175 7-227 -84.800 47  d1ei1a2 d.122.1.2 (A:2-220) DNA gyrase B {Escherichia coli [TaxId: 562]}
228-409 -78.000 34  d1ei1a1 d.14.1.3 (A:221-392) DNA gyrase B {Escherichia coli [TaxId: 562]}
423-640 -26.600 28  d1bjta_ e.11.1.1 (A:) DNA topoisomerase II, C-terminal fragment (residues 410-1202) {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
4 gi|12044854|ref|NP_072664.1| DNA gyrase subunit A (MG_004) [Mycoplasma genitalium G37] 836 COG0113 16-836 -197.000 38  [L] COG0188 Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit
PDB0113 1-500 -144.000 53  2xco_A mol:protein length:726 DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
42-756 -144.000 32  1zvu_A mol:protein length:716 Topoisomerase IV subunit A
512-817 -62.700 38  1zi0_A mol:protein length:307 DNA gyrase subunit A
PfamA26U 44-474 -95.400 29  PF00521.15; A1ZXC5_9BACT/29-447; DNA gyrase/topoisomerase IV, subunit A
620-665 -11.300 37  PF03989.8; GYRA_HAEIN/641-686; DNA gyrase C-terminal domain, beta-propeller
SCOP175 42-498 -135.000 52  d1ab4a_ e.11.1.1 (A:) DNA Gyrase A {Escherichia coli [TaxId: 562]}
514-815 -60.300 27  d1suua_ b.68.10.1 (A:) DNA gyrase A C-terminal domain {Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139]}
5 gi|12044855|ref|NP_072665.1| seryl-tRNA synthetase (MG_005) [Mycoplasma genitalium G37] 417 COG0113 1-413 -130.000 42  [J] COG0172 Seryl-tRNA synthetase
PDB0113 1-417 -131.000 43  2dq3_A mol:protein length:425 Seryl-tRNA synthetase
PfamA26U 1-104 -35.100 24  PF02403.17; Q8GE42_HELMO/1-107; Seryl-tRNA synthetase N-terminal domain
169-338 -96.800 48  PF00587.20; SYS_BACSU/173-344; tRNA synthetase class II core domain (G, H, P, S and T)
SCOP175 1-109 -37.600 22  d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}
113-417 -118.000 37  d1seta2 d.104.1.1 (A:111-421) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}
6 gi|12044856|ref|NP_072666.1| thymidylate kinase (MG_006) [Mycoplasma genitalium G37] 210 COG0113 3-209 -89.900 31  [F] COG0125 Thymidylate kinase
PDB0113 1-204 -93.200 29  3v9p_A mol:protein length:227 Thymidylate kinase
PfamA26U 9-197 -86.600 33  PF02223.12; KTHY_BACSU/8-199; Thymidylate kinase
SCOP175 3-207 -89.200 30  d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}
7 gi|12044857|ref|NP_072667.1| DNA polymerase III subunit delta' (MG_007) [Mycoplasma genitalium G37] 254 COG0113 2-254 -79.300 16  [L] COG2812 DNA polymerase III, gamma/tau subunits
PDB0113 2-205 -87.100 20  1njf_A mol:protein length:250 DNA polymerase III subunit gamma
2-254 -84.300 17  3glf_B mol:protein length:395 DNA polymerase III subunit tau
PfamA26U 2-144 -72.800 23  PF13177.1; B3XQR6_LACRE/12-172; DNA polymerase III, delta subunit
2-186 -30.700 11  PF06068.8; Q9GZH2_CAEEL/17-408; TIP49 C-terminus
7-219 -10.900 PF05621.6; Q48383_KLEAE/1-302; Bacterial TniB protein
194-254 -10.200 PF12169.3; Q11B01_MESSB/247-389; DNA polymerase III subunits gamma and tau domain III
SCOP175 2-205 -89.300 20  d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}
8 gi|12044858|ref|NP_072668.1| tRNA modification GTPase TrmE (MG_008) [Mycoplasma genitalium G37] 442 COG0113 1-442 -124.000 28  [R] COG0486 Predicted GTPase
PDB0113 1-442 -130.000 28  3geh_A mol:protein length:462 tRNA modification GTPase mnmE
PfamA26U 6-121 -54.400 27  PF10396.4; MNME_PSEA6/12-126; GTP-binding protein TrmE N-terminus
178-420 -18.100 12  PF05049.8; Q9DCE9_MOUSE/50-412; Interferon-inducible GTPase (IIGP)
219-332 -38.900 26  PF01926.18; DER_CHLCV/3-119; 50S ribosome-binding GTPase
368-439 -27.800 18  PF12631.2; B7IBI3_ACIB5/331-403; Catalytic cysteine-containing C-terminus of GTPase, MnmE
SCOP175 5-121 -58.200 42  d1xzpa3 d.250.1.2 (A:1-117) TrmE formyl-THF-binding domain {Thermotoga maritima [TaxId: 2336]}
122-442 -40.200 23  d1xzpa1 a.24.25.1 (A:118-211,A:372-450) TrmE connector domain {Thermotoga maritima [TaxId: 2336]}
217-362 -56.700 32  d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}
9 gi|12044859|ref|NP_072669.1| TatD family deoxyribonuclease (MG_009) [Mycoplasma genitalium G37] 262 COG0113 1-261 -101.000 27  [L] COG0084 Mg-dependent DNase
PDB0113 1-261 -99.400 23  1zzm_A mol:protein length:259 putative deoxyribonuclease yjjV
PfamA26U 4-260 -96.500 29  PF01026.16; Y454_HAEIN/4-256; TatD related DNase
SCOP175 1-261 -99.700 31  d1j6oa_ c.1.9.12 (A:) Hypothetical protein TM0667 {Thermotoga maritima [TaxId: 2336]}
10 gi|12044860|ref|NP_072670.1| DNA primase-related protein (MG_010) [Mycoplasma genitalium G37] 218 COG0113 1-217 -64.400 17  [L] COG0358 DNA primase (bacterial type)
PDB0113 1-216 -76.800 18  4e2k_A mol:protein length:329 DNA primase
PfamA26U 1-106 -36.100 15  PF08275.6; Q64P92_BACFR/123-254; DNA primase catalytic core, N-terminal domain
114-201 -40.100 25  PF13155.1; C5EJG0_9FIRM/258-343; Toprim-like
SCOP175 2-217 -74.800 19  d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]}
11 gi|12044861|ref|NP_072671.1| hypothetical protein (MG_011) [Mycoplasma genitalium G37] 287 COG0113 1-285 -55.600 11  [HJ] COG0189 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase)
PDB0113 22-278 -67.800 15  1uc8_A mol:protein length:280 lysine biosynthesis enzyme
PfamA26U 1-275 -47.900 10  PF05770.6; Q9AYJ2_ORYSJ/16-320; Inositol 1, 3, 4-trisphosphate 5/6-kinase
94-273 -63.600 19  PF08443.6; RIMK_HAEIN/105-293; RimK-like ATP-grasp domain
SCOP175 10-96 -19.300 12  d1uc8a1 c.30.1.6 (A:1-88) Lysine biosynthesis enzyme LysX, N-terminal domain {Thermus thermophilus [TaxId: 274]}
97-278 -60.300 16  d1uc8a2 d.142.1.7 (A:89-280) Lysine biosynthesis enzyme LysX ATP-binding domain {Thermus thermophilus [TaxId: 274]}
12 gi|12044862|ref|NP_072672.1| alpha-L-glutamate ligase (MG_012) [Mycoplasma genitalium G37] 287 COG0113 1-287 -49.800 19  [HJ] COG0189 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase)
PDB0113 4-287 -71.400 19  1uc8_A mol:protein length:280 lysine biosynthesis enzyme
PfamA26U 1-287 -46.300 PF05770.6; Q9AYJ2_ORYSJ/16-320; Inositol 1, 3, 4-trisphosphate 5/6-kinase
90-287 -66.800 22  PF08443.6; RIMK_HAEIN/105-293; RimK-like ATP-grasp domain
SCOP175 4-92 -17.700 14  d1uc8a1 c.30.1.6 (A:1-88) Lysine biosynthesis enzyme LysX, N-terminal domain {Thermus thermophilus [TaxId: 274]}
93-287 -64.300 22  d1uc8a2 d.142.1.7 (A:89-280) Lysine biosynthesis enzyme LysX ATP-binding domain {Thermus thermophilus [TaxId: 274]}
13 gi|108885077|ref|NP_072673.2| methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase (MG_013) [Mycoplasma genitalium G37] 273 COG0113 2-266 -111.000 28  [H] COG0190 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase
PDB0113 2-267 -118.000 30  3p2o_A mol:protein length:285 Bifunctional protein folD
PfamA26U 2-111 -55.300 32  PF00763.18; FOLD_SHIFL/4-121; Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
114-265 -78.800 23  PF02882.14; Q9ZVI8_ARATH/182-349; Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
SCOP175 2-112 -56.100 33  d1b0aa2 c.58.1.2 (A:2-122) Tetrahydrofolate dehydrogenase/cyclohydrolase {Escherichia coli [TaxId: 562]}
113-267 -79.600 24  d1a4ia1 c.2.1.7 (A:127-296) Methylenetetrahydrofolate dehydrogenase/cyclohydrolase {Human (Homo sapiens) [TaxId: 9606]}
14 gi|12044864|ref|NP_072674.1|(removed signalp:1-25) ABC transporter, ATP-binding/permease protein (MG_014) [Mycoplasma genitalium G37] 598 COG0113 2-590 -90.900 23  [V] COG1132 ABC-type multidrug transport system, ATPase and permease components
PDB0113 1-596 -146.000 29  3qf4_A mol:protein length:587 ABC transporter, ATP-binding protein
PfamA26U 1-249 -15.800 10  PF13748.1; B6R989_9RHOB/9-243; ABC transporter transmembrane region
168-589 -25.300 PF09818.4; Q2C6W1_9GAMM/1-438; Predicted ATPase of the ABC class
SCOP175 2-325 -40.700 16  d2hyda2 f.37.1.1 (A:1-323) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}
309-596 -58.500 21  d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}
340-591 -76.700 31  d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}
15 gi|12044865|ref|NP_072675.1|(removed signalp:1-25) ABC transporter, ATP-binding/permease protein (MG_015) [Mycoplasma genitalium G37] 564 COG0113 4-564 -113.000 18  [CO] COG4988 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
PDB0113 3-564 -145.000 34  3qf4_B mol:protein length:598 Uncharacterized ABC transporter ATP-binding p
PfamA26U 3-259 -28.400 11  PF13748.1; B6R989_9RHOB/9-243; ABC transporter transmembrane region
158-564 -22.500 11  PF09818.4; Q2C6W1_9GAMM/1-438; Predicted ATPase of the ABC class
SCOP175 3-311 -61.400 15  d2hyda2 f.37.1.1 (A:1-323) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}
327-564 -84.800 36  d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}
16 gi|108885078|ref|NP_072678.2| SNF2 family helicase putative (MG_018) [Mycoplasma genitalium G37] (Range:1-500) 500 COG0113 10-82 -7.510 25  [S] COG5431 Uncharacterized metal-binding protein
PDB0113 63-152 -7.390 14  2l03_A mol:protein length:74 Ly-6/neurotoxin-like protein 1
PfamA26U 46-85 -23.800 42  PF04434.12; Y020_MYCPN/46-86; SWIM zinc finger
SCOP175 70-125 -7.490 10  d1hfia_ g.18.1.1 (A:) Factor H, 15th and 16th modules {Human (Homo sapiens) [TaxId: 9606]}
17 gi|108885078|ref|NP_072678.2| SNF2 family helicase putative (MG_018) [Mycoplasma genitalium G37] (Range:251-750) 500 COG0113 39-500 -56.100 21  [KL] COG0553 Superfamily II DNA/RNA helicases, SNF2 family
PDB0113 98-493 -9.790 11  2y3t_A mol:protein length:1033 TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
300-500 -60.300 38  1z63_A mol:protein length:500 Helicase of the snf2/rad54 family
PfamA26U 29-321 -20.100 12  PF08455.5; A4J9J5_DESRM/246-626; Bacterial SNF2 helicase associated
311-500 -55.200 23  PF00176.18; RAD54_YEAST/274-621; SNF2 family N-terminal domain
SCOP175 317-500 -72.600 41  d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}
18 gi|108885078|ref|NP_072678.2| SNF2 family helicase putative (MG_018) [Mycoplasma genitalium G37] (Range:501-1000) 500 COG0113 1-500 -92.700 33  [KL] COG0553 Superfamily II DNA/RNA helicases, SNF2 family
58-500 -96.500 28  [L] KOG1002 Nucleotide excision repair protein RAD16
PDB0113 50-500 -129.000 36  1z63_A mol:protein length:500 Helicase of the snf2/rad54 family
PfamA26U 64-354 -70.900 25  PF00176.18; RAD54_YEAST/274-621; SNF2 family N-terminal domain
297-500 -28.300 11  PF11496.3; Q6FSK5_CANGA/26-299; Class II histone deacetylase complex subunits 2 and 3
SCOP175 66-296 -89.900 39  d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}
298-500 -77.600 36  d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}
19 gi|108885078|ref|NP_072678.2| SNF2 family helicase putative (MG_018) [Mycoplasma genitalium G37] (Range:751-1031) 281 COG0113 1-281 -68.600 30  [L] KOG1002 Nucleotide excision repair protein RAD16
PDB0113 27-281 -102.000 34  1z5z_A mol:protein length:271 Helicase of the snf2/rad54 family
PfamA26U 1-104 -20.700 28  PF00176.18; RAD54_YEAST/274-621; SNF2 family N-terminal domain
47-281 -35.100 11  PF11496.3; Q6FSK5_CANGA/26-299; Class II histone deacetylase complex subunits 2 and 3
SCOP175 1-46 -11.900 37  d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}
48-281 -97.500 35  d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}
20 gi|12044869|ref|NP_072679.1| chaperone protein DnaJ (MG_019) [Mycoplasma genitalium G37] 389 COG0113 3-388 -129.000 32  [O] COG0484 DnaJ-class molecular chaperone with C-terminal Zn finger domain
PDB0113 1-377 -100.000 23  3lz8_A mol:protein length:329 Putative chaperone DnaJ
PfamA26U 7-74 -39.800 52  PF00226.26; Q22028_CAEEL/17-79; DnaJ domain
162-369 -10.700 12  PF02335.10; NRFA_BACFN/56-493; Cytochrome c552
164-229 -34.100 32  PF00684.14; DNAJ1_CORGL/147-211; DnaJ central domain
285-365 -25.400 18  PF01556.13; A2FIH5_TRIVA/258-337; DnaJ C terminal domain
SCOP175 1-113 -40.400 19  d1gh6a_ a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Simian virus 40, Sv40 [TaxId: 10633]}
2-83 -47.300 31  d1wjza_ a.2.3.1 (A:) CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK) {Mouse (Mus musculus) [TaxId: 10090]}
151-234 -37.000 31  d1exka_ g.54.1.1 (A:) Cysteine-rich domain of the chaperone protein DnaJ {Escherichia coli [TaxId: 562]}
203-277 -20.400 13  d1nlta1 b.4.1.1 (A:110-138,A:213-257) Mitochondrial protein import protein mas5 (Hsp40, Ydj1), C-terminal domain {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
279-367 -30.600 15  d1c3ga2 b.4.1.1 (A:260-349) Heat shock protein 40 Sis1 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}


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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Awobuluyi M, Yang J, Ye Y, Chatterton JE, Godzik A, Lipton SA, Zhang D. Subunit-specific roles of glycine-binding domains in activation of NR1/NR3N-methyl-D-aspartate receptors. Mol Pharmacol. 2007 Jan;71(1):112-22. Epub 2006 Oct 17.