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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|16082692|ref|NP_395138.1| putative transposase (YPCD1.01) [Yersinia pestis CO92] 340 COG0113 1-338 -122.000 42  [L] COG4584 Transposase and inactivated derivatives
PDB0113 4-338 -23.000 9  4fcy_A mol:protein length:529 Transposase
PfamA26U 1-91 -17.100 9  PF01710.11; P74627_SYNY3/1-120; Transposase
4-328 -10.300 10  PF07592.6; B3EJR4_CHLPB/96-407; Rhodopirellula transposase DDE domain
121-295 -17.000 11  PF02914.10; TRA_HAEIN/267-485; Bacteriophage Mu transposase
SCOP175 1-42 -15.800 14  d1tc3c_ a.4.1.2 (C:) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}
1-83 -10.100 12  d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}
120-266 -21.600 14  d1cxqa_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Rous sarcoma virus RSV [TaxId: 11886]}
121-303 -15.600 12  d1bcoa2 c.55.3.3 (A:258-480) mu transposase, core domain {Bacteriophage mu [TaxId: 10677]}
2 gi|16082693|ref|NP_395139.1| transposase/IS protein (YPCD1.02) [Yersinia pestis CO92] 259 COG0113 7-229 -9.640 15  [P] COG1122 ABC-type cobalt transport system, ATPase component
54-252 -30.800 19  [L] COG1484 DNA replication protein
PDB0113 14-257 -14.300 14  2z4r_A mol:protein length:440 Chromosomal replication initiator protein dna
54-243 -56.200 16  2w58_A mol:protein length:202 PRIMOSOME COMPONENT (HELICASE LOADER)
PfamA26U 56-235 -83.800 31  PF01695.12; Y4IQ_RHISN/60-238; IstB-like ATP binding protein
SCOP175 66-231 -18.900 20  d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}
3 gi|16082696|ref|NP_395142.1| secretion chaperone (YPCD1.05c) [Yersinia pestis CO92] 130 COG0113 6-123 -10.500 9  [S] COG5465 Uncharacterized conserved protein
PDB0113 1-130 -62.600 98  1n5b_A mol:protein length:132 YOPE regulator
PfamA26U 6-118 -38.700 15  PF05932.8; Q2SNL0_HAHCH/10-127; Tir chaperone protein (CesT) family
SCOP175 2-118 -58.200 100  d1jyaa_ d.198.1.1 (A:) YopE chaperone SycE {Yersinia pestis [TaxId: 632]}
4 gi|16082697|ref|NP_395143.1| putative outer membrane virulence protein (YPCD1.06) [Yersinia pestis CO92] 219 COG0113 128-217 -5.450 8  [S] COG4718 Phage-related protein
PDB0113 17-85 -31.100 100  1l2w_I mol:protein length:69 Outer membrane virulence protein yopE
90-219 -71.800 100  1hy5_A mol:protein length:136 YERSINIA PESTIS VIRULENCE PROTEIN YOPE
PfamA26U 1-126 -49.600 92  PF09020.5; Q56931_YEREN/1-126; YopE, N terminal
127-195 -46.000 39  PF03545.8; A6YCJ6_AERHY/128-197; Yersinia virulence determinant (YopE)
SCOP175 22-78 -24.700 100  d1l2wi_ d.198.1.1 (I:) YopE chaperone SycE {Yersinia pestis [TaxId: 632]}
100-219 -70.900 100  d1hy5a_ a.24.11.1 (A:) YopE {Yersinia pestis [TaxId: 632]}
5 gi|16082698|ref|NP_395144.1| hypothetical protein (YPCD1.07) [Yersinia pestis CO92] 98 COG0113 39-98 -6.400 20  [S] COG4713 Predicted membrane protein
PDB0113 15-97 -5.780 10  1y1u_A mol:protein length:585 Signal transducer and activator of transcript
PfamA26U 23-73 -7.470 19  PF05279.6; ASPH_MOUSE/52-307; Aspartyl beta-hydroxylase N-terminal region
SCOP175 26-52 -5.700 22  d2jw6a1 g.85.1.1 (A:503-540) Zinc finger MYND domain-containing protein 2, MTG8 {Human (Homo sapiens) [TaxId: 9606]}
6 gi|16082699|ref|NP_395145.1| hypothetical protein (YPCD1.08c) [Yersinia pestis CO92] 99 COG0113 2-94 -54.700 31  [R] COG3668 Plasmid stabilization system protein
PDB0113 2-94 -52.600 30  3kxe_A mol:protein length:110 Toxin protein parE-1
PfamA26U 2-90 -36.200 20  PF05016.9; Q9Z4G4_9ZZZZ/4-92; Plasmid stabilisation system protein
SCOP175 2-89 -12.600 11  d1wmia1 d.298.1.2 (A:1-88) Hypothetical protein PHS013 {Pyrococcus horikoshii [TaxId: 53953]}
7 gi|40548796|ref|NP_395146.2| hypothetical protein (YPCD1.09c) [Yersinia pestis CO92] 80 COG0113 1-79 -32.000 29  [K] COG3609 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain
PDB0113 1-77 -38.300 29  3kxe_C mol:protein length:88 Antitoxin protein parD-1
PfamA26U 1-79 -40.800 36  PF03693.9; PARD_MYCBO/1-81; Uncharacterised protein family (UPF0156 topsan)
SCOP175 3-48 -17.400 32  d2hzaa1 a.43.1.3 (A:1-48) Nickel responsive regulator NikR, N-terminal domain {Escherichia coli [TaxId: 562]}
8 gi|16082702|ref|NP_395148.1| plasmid-partitioning protein (YPCD1.12c) [Yersinia pestis CO92] 320 COG0113 24-157 -23.100 12  [L] KOG3388 Predicted transcription regulator/nuclease, contains ParB domain
61-320 -48.700 10  [K] COG1475 Predicted transcriptional regulators
PDB0113 31-257 -48.500 19  1vz0_A mol:protein length:230 CHROMOSOME PARTITIONING PROTEIN PARB
146-317 -51.200 41  3mky_B mol:protein length:189 Protein sopB
PfamA26U 74-156 -27.100 24  PF02195.13; PARB_CHLTR/12-105; ParB-like nuclease domain
157-317 -20.100 9  PF07506.6; Q9F5B9_AGRRH/157-326; RepB plasmid partitioning protein
SCOP175 65-212 -28.300 16  d1vk1a_ d.268.1.2 (A:) Hypothetical protein PF0380 {Pyrococcus furiosus [TaxId: 2261]}
74-159 -32.700 25  d1vz0a2 d.268.1.1 (A:23-115) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}
159-257 -22.600 17  d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}
9 gi|16082703|ref|NP_395149.1| plasmid-partitioning protein SopA (YPCD1.13c) [Yersinia pestis CO92] 388 COG0113 75-370 -28.600 16  [D] COG0455 ATPases involved in chromosome partitioning
105-374 -68.800 18  [D] COG1192 ATPases involved in chromosome partitioning
PDB0113 2-386 -76.000 20  3ez7_A mol:protein length:398 Plasmid partition protein A
PfamA26U 107-375 -50.800 15  PF06564.7; A6TFD7_KLEP7/1-243; YhjQ protein
109-340 -62.300 19  PF01656.18; P72976_SYNY3/5-262; CobQ/CobB/MinD/ParA nucleotide binding domain
SCOP175 105-372 -55.400 16  d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}
10 gi|40548797|ref|NP_954989.1| hypothetical protein (YPCD1.14n) [Yersinia pestis CO92] 65 COG0113 1-65 -25.500 20  [L] COG2801 Transposase and inactivated derivatives
PDB0113 1-65 -8.440 7  1c6v_A mol:protein length:164 PROTEIN (SIV INTEGRASE)
PfamA26U 1-64 -36.900 17  PF13683.1; Q7DB06_CAUCR/199-265; Integrase core domain
SCOP175 13-65 -8.740 13  d1bcoa2 c.55.3.3 (A:258-480) mu transposase, core domain {Bacteriophage mu [TaxId: 10677]}
11 gi|16082705|ref|NP_395151.1| hypothetical protein (YPCD1.15c) [Yersinia pestis CO92] 152 COG0113 1-152 -46.800 15  [L] COG2801 Transposase and inactivated derivatives
PDB0113 1-152 -17.400 11  4fcy_A mol:protein length:529 Transposase
PfamA26U 23-79 -24.600 21  PF13276.1; Q1WUI0_LACS1/209-271; HTH-like domain
105-149 -24.200 20  PF13610.1; B5WJN4_9BURK/77-216; DDE domain
SCOP175 100-152 -14.000 13  d1bcoa2 c.55.3.3 (A:258-480) mu transposase, core domain {Bacteriophage mu [TaxId: 10677]}
12 gi|16082706|ref|NP_395152.1| hypothetical protein (YPCD1.16c) [Yersinia pestis CO92] 107 COG0113 7-107 -50.500 28  [L] COG2963 Transposase and inactivated derivatives
PDB0113 7-107 -45.200 22  2rn7_A mol:protein length:108 IS629 orfA
PfamA26U 8-93 -32.600 24  PF01527.15; O50654_BURGL/7-89; Transposase
SCOP175 8-95 -41.700 18  d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}
13 gi|16082708|ref|NP_395154.1| Yop targeting protein (YPCD1.19c) [Yersinia pestis CO92] 182 COG0113 12-181 -7.340 12  [K] KOG4577 Transcription factor LIM3, contains LIM and HOX domains
PDB0113 28-180 -6.910 10  1uap_A mol:protein length:154 Procollagen C-proteinase enhancer protein
PfamA26U 58-128 -7.020 23  PF11065.3; A4JK10_BURVG/20-84; Protein of unknown function (DUF2866 topsan)
SCOP175 51-169 -7.640 15  d1ee8a2 b.113.1.1 (A:1-121) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]}
14 gi|16082709|ref|NP_395155.1| Yop targeted effector (YPCD1.20) [Yersinia pestis CO92] 322 COG0113 78-290 -9.940 10  [R] COG3271 Predicted double-glycine peptidase
PDB0113 128-315 -46.200 18  1ukf_A mol:protein length:188 Avirulence protein AVRPPH3
PfamA26U 103-320 -81.400 100  PF03543.9; YOPT_YERPE/103-320; Yersinia/Haemophilus virulence surface antigen
SCOP175 128-315 -46.200 18  d1ukfa_ d.3.1.10 (A:) Avirulence protein Avrpph3 {Pseudomonas syringae pv. phaseolicola [TaxId: 319]}
15 gi|16082710|ref|NP_395156.1| YopT chaperone (YPCD1.21) [Yersinia pestis CO92] 132 COG0113 88-131 -5.920 20  [S] COG5509 Uncharacterized small protein containing a coiled-coil domain
PDB0113 1-132 -72.600 98  2bho_A mol:protein length:130 CHAPERONE PROTEIN SYCT
PfamA26U 7-114 -17.200 16  PF05932.8; Q2SNL0_HAHCH/10-127; Tir chaperone protein (CesT) family
SCOP175 3-114 -35.600 20  d1jyaa_ d.198.1.1 (A:) YopE chaperone SycE {Yersinia pestis [TaxId: 632]}
16 gi|16082711|ref|NP_395157.1| hypothetical protein (YPCD1.22c) [Yersinia pestis CO92] 129 COG0113 9-129 -6.160 9  [K] KOG4134 DNA-dependent RNA polymerase I
PDB0113 97-129 -6.040 43  3bc9_A mol:protein length:599 Alpha amylase, catalytic region
PfamA26U 98-124 -6.820 22  PF09871.4; Q8THJ6_METAC/31-124; Uncharacterized protein conserved in archaea (DUF2098 topsan)
SCOP175 96-120 -6.330 32  d2hqya1 d.108.1.4 (A:135-298) Hypothetical protein BT3689 {Bacteroides thetaiotaomicron [TaxId: 818]}
17 gi|16082712|ref|NP_395158.1| hypothetical protein (YPCD1.23) [Yersinia pestis CO92] 139 COG0113 14-91 -6.960 19  [A] KOG0106 Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily)
PDB0113 11-91 -8.640 16  2cpj_A mol:protein length:99 Non-POU domain-containing octamer-binding pro
PfamA26U 8-122 -6.560 24  PF01698.11; Q6XPU5_IDASC/1-385; Floricaula / Leafy protein
SCOP175 11-91 -7.930 16  d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}
18 gi|16082715|ref|NP_395161.1| secreted effector protein (YPCD1.26c) [Yersinia pestis CO92] 409 COG0113 4-409 -46.200 19  [T] KOG4641 FOG: Toll/interleukin receptor and related proteins containing LRR and TIR repeats
PDB0113 1-409 -75.800 94  1g9u_A mol:protein length:454 OUTER PROTEIN YOPM
PfamA26U 153-207 -9.480 20  PF13855.1; C4PX53_SCHMA/92-151; Leucine rich repeat
SCOP175 19-386 -74.100 92  d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}
19 gi|16082716|ref|NP_395162.1| secreted effector protein (YPCD1.28c) [Yersinia pestis CO92] 306 COG0113 7-296 -13.200 6  [YU] KOG4460 Nuclear pore complex, Nup88/rNup84 component
PDB0113 153-298 -11.700 8  1jch_A mol:protein length:551 COLICIN E3
PfamA26U 7-296 -12.200 6  PF10168.4; Q707M9_XENLA/4-726; Nuclear pore component
41-306 -57.900 42  PF05844.7; Q5XL01_AERHY/1-296; YopD protein
SCOP175 160-297 -7.120 6  d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]}
20 gi|16082717|ref|NP_395163.1| secreted effector protein (YPCD1.29c) [Yersinia pestis CO92] 401 COG0113 1-401 -112.000 100  [S] COG5613 Uncharacterized conserved protein
PDB0113 116-160 -6.160 17  3ryc_E mol:protein length:143 Stathmin-4
PfamA26U 106-398 -74.800 49  PF04888.7; Q699Q8_AERHY/103-387; Secretion system effector C (SseC) like family
SCOP175 116-160 -6.190 17  d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]}

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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.

Ye Y, Osterman A, Overbeek R, Godzik A. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics. 2005 Jun 1;21 Suppl 1:i478-i486.