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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|13507740|ref|NP_109689.1| DNA polymerase III beta subunit MPN001 [Mycoplasma pneumoniae M129] 380 PfamA26U 1-121 -45.300 19  PF00712.14; DPO3B_BACSU/1-127; DNA polymerase III beta subunit, N-terminal domain
135-256 -39.800 13  PF02767.11; DPO3B_PROMI/129-244; DNA polymerase III beta subunit, central domain
258-380 -54.000 23  PF02768.10; DPO3B_BACSU/253-376; DNA polymerase III beta subunit, C-terminal domain
2 gi|13507741|ref|NP_109690.1| DnaJ domain-containing protein MPN002 [Mycoplasma pneumoniae M129] 309 PfamA26U 2-61 -34.900 43  PF00226.26; Q22028_CAEEL/17-79; DnaJ domain
147-217 -13.600 PF00684.14; DNAJ1_CORGL/147-211; DnaJ central domain
182-282 -11.300 16  PF01556.13; A2FIH5_TRIVA/258-337; DnaJ C terminal domain
3 gi|13507742|ref|NP_109691.1| DNA gyrase subunit B MPN003 [Mycoplasma pneumoniae M129] 650 PfamA26U 43-143 -9.890 20  PF13589.1; A5G4D8_GEOUR/22-165; Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
228-408 -75.700 40  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
4 gi|13507743|ref|NP_109692.1| DNA gyrase subunit A MPN004 [Mycoplasma pneumoniae M129] 839 PfamA26U 44-474 -94.600 28  PF00521.15; A1ZXC5_9BACT/29-447; DNA gyrase/topoisomerase IV, subunit A
620-665 -10.900 28  PF03989.8; GYRA_HAEIN/641-686; DNA gyrase C-terminal domain, beta-propeller
5 gi|13507744|ref|NP_109693.1| seryl-tRNA synthetase MPN005 [Mycoplasma pneumoniae M129] 420 PfamA26U 1-104 -34.800 22  PF02403.17; Q8GE42_HELMO/1-107; Seryl-tRNA synthetase N-terminal domain
169-338 -96.400 49  PF00587.20; SYS_BACSU/173-344; tRNA synthetase class II core domain (G, H, P, S and T)
6 gi|13507745|ref|NP_109694.1| thymidylate kinase MPN006 [Mycoplasma pneumoniae M129] 210 PfamA26U 9-197 -87.800 34  PF02223.12; KTHY_BACSU/8-199; Thymidylate kinase
7 gi|13507746|ref|NP_109695.1| DNA polymerase III subunit delta' MPN007 [Mycoplasma pneumoniae M129] 253 PfamA26U 2-143 -70.700 27  PF13177.1; B3XQR6_LACRE/12-172; DNA polymerase III, delta subunit
5-185 -30.800 11  PF06068.8; Q9GZH2_CAEEL/17-408; TIP49 C-terminus
5-218 -11.300 PF05621.6; Q48383_KLEAE/1-302; Bacterial TniB protein
8 gi|13507747|ref|NP_109696.1| tRNA modification GTPase TrmE MPN008 [Mycoplasma pneumoniae M129] 442 PfamA26U 6-121 -54.500 34  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 -38.800 29  PF01926.18; DER_CHLCV/3-119; 50S ribosome-binding GTPase
368-439 -28.500 15  PF12631.2; B7IBI3_ACIB5/331-403; Catalytic cysteine-containing C-terminus of GTPase, MnmE
9 gi|13507748|ref|NP_109697.1| hydrolase MPN009 [Mycoplasma pneumoniae M129] 261 PfamA26U 4-260 -96.200 29  PF01026.16; Y454_HAEIN/4-256; TatD related DNase
10 gi|13507749|ref|NP_109698.1| hypothetical protein MPN010 [Mycoplasma pneumoniae M129] 131 PfamA26U 38-130 -13.500 44  PF01519.11; Y145_MYCPN/37-164; Protein of unknown function DUF16 topsan
11 gi|13507750|ref|NP_109699.1|(removed signal:1-26) hypothetical protein MPN011 [Mycoplasma pneumoniae M129] 205 PfamA26U 1-82 -34.500 32  PF00938.12; Y646_MYCPN/28-114; Lipoprotein
12 gi|13507751|ref|NP_109700.1|(removed signal:1-21) hypothetical protein MPN012 [Mycoplasma pneumoniae M129] 214 PfamA26U 1-88 -37.400 33  PF00938.12; Y646_MYCPN/28-114; Lipoprotein
13 gi|13507752|ref|NP_109701.1| hypothetical protein MPN013 [Mycoplasma pneumoniae M129] 257 PfamA26U 27-144 -15.500 PF04929.7; VG59_EHV2/8-414; Herpes DNA replication accessory factor
42-115 -26.400 17  PF02948.10; Q2HYD7_CHAVD/8-189; Amelogenin
166-256 -16.000 19  PF01519.11; Y145_MYCPN/37-164; Protein of unknown function DUF16 topsan
14 gi|13507753|ref|NP_109702.1| hypothetical protein MPN014 [Mycoplasma pneumoniae M129] 212 PfamA26U 2-101 -43.300 15  PF08275.6; Q64P92_BACFR/123-254; DNA primase catalytic core, N-terminal domain
108-195 -42.300 27  PF13155.1; C5EJG0_9FIRM/258-343; Toprim-like
15 gi|13507754|ref|NP_109703.1| hypothetical protein MPN015 [Mycoplasma pneumoniae M129] 285 PfamA26U 4-273 -48.500 12  PF05770.6; Q9AYJ2_ORYSJ/16-320; Inositol 1, 3, 4-trisphosphate 5/6-kinase
92-271 -65.900 17  PF08443.6; RIMK_HAEIN/105-293; RimK-like ATP-grasp domain
16 gi|13507755|ref|NP_109704.1| ribosomal S6 modification protein MPN016 [Mycoplasma pneumoniae M129] 288 PfamA26U 12-287 -43.800 10  PF05770.6; Q9AYJ2_ORYSJ/16-320; Inositol 1, 3, 4-trisphosphate 5/6-kinase
90-287 -67.500 25  PF08443.6; RIMK_HAEIN/105-293; RimK-like ATP-grasp domain
17 gi|13507756|ref|NP_109705.1| 5,10-methylene-tetrahydrofolate dehydrogenase MPN017 [Mycoplasma pneumoniae M129] 269 PfamA26U 2-111 -56.300 30  PF00763.18; FOLD_SHIFL/4-121; Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
114-265 -77.000 25  PF02882.14; Q9ZVI8_ARATH/182-349; Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
18 gi|13507757|ref|NP_109706.1|(removed signal:1-25) transport ATP-binding protein MPN018 [Mycoplasma pneumoniae M129] 598 PfamA26U 8-249 -15.800 PF13748.1; B6R989_9RHOB/9-243; ABC transporter transmembrane region
168-589 -25.600 10  PF09818.4; Q2C6W1_9GAMM/1-438; Predicted ATPase of the ABC class
19 gi|13507758|ref|NP_109707.1| transport ATP-binding protein MPN019 [Mycoplasma pneumoniae M129] 634 PfamA26U 43-329 -31.400 PF13748.1; B6R989_9RHOB/9-243; ABC transporter transmembrane region
228-634 -21.600 12  PF09818.4; Q2C6W1_9GAMM/1-438; Predicted ATPase of the ABC class
20 gi|13507759|ref|NP_109708.1| helicases MPN020 [Mycoplasma pneumoniae M129] 1030 PfamA26U 289-571 -11.200 12  PF08455.5; A4J9J5_DESRM/246-626; Bacterial SNF2 helicase associated
558-854 -49.700 24  PF00176.18; RAD54_YEAST/274-621; SNF2 family N-terminal domain
797-1030 -21.600 12  PF11496.3; Q6FSK5_CANGA/26-299; Class II histone deacetylase complex subunits 2 and 3


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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.

Plewczynski D, Tkacz A, Wyrwicz LS, Godzik A, Kloczkowski A, Rychlewski L. Support-vector-machine classification of linear functional motifs in proteins. J Mol Model 2006 Aug;12(4):453-61. Epub 2005 Dec 10.