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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|16758994|ref|NP_454611.1| thr operon leader peptide (STY0001) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 21 COG0113 1-20 -1.950 30  [T] KOG2417 Predicted G-protein coupled receptor
PDB0113 1-9 -2.120 44  2lqx_A mol:protein length:41 Trypsin inhibitor BWI-2c
PfamA26U 1-15 -3.920 33  PF07418.6; Q4YUM7_PLABA/1-292; Acidic phosphoprotein precursor PCEMA1
SCOP175 5-21 -2.080 47  d1xc3a2 c.55.1.10 (A:119-294) Putative fructokinase YhdR {Bacillus subtilis [TaxId: 1423]}
2 gi|16758995|ref|NP_454612.1| bifunctional aspartokinase I/homeserine dehydrogenase I (STY0002) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 820 COG0113 1-481 -96.200 27  [E] COG0527 Aspartokinases
456-820 -89.100 68  [E] COG0460 Homoserine dehydrogenase
PDB0113 1-481 -94.100 27  2cdq_A mol:protein length:510 ASPARTOKINASE
462-817 -75.400 31  1q7g_A mol:protein length:359 Homoserine dehydrogenase
PfamA26U 614-810 -34.000 28  PF00742.14; C1P978_BACCO/136-314; Homoserine dehydrogenase
SCOP175 1-300 -76.200 33  d2j0wa1 c.73.1.3 (A:3-294) Aspartokinase {Escherichia coli [TaxId: 562]}
303-395 -19.600 22  d2cdqa2 d.58.18.10 (A:329-419) Aspartokinase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}
396-462 -26.200 43  d2hmfa2 d.58.18.10 (A:404-470) Aspartokinase {Methanococcus jannaschii [TaxId: 2190]}
462-635 -43.500 26  d1ebfa1 c.2.1.3 (A:2-150,A:341-359) Homoserine dehydrogenase {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
614-798 -64.200 34  d1ebfa2 d.81.1.2 (A:151-340) Homoserine dehydrogenase {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
3 gi|16758996|ref|NP_454613.1| homoserine kinase (STY0003) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 309 COG0113 2-309 -104.000 70  [E] COG0083 Homoserine kinase
PDB0113 2-308 -97.400 30  1fwk_A mol:protein length:296 HOMOSERINE KINASE
PfamA26U 83-150 -18.500 25  PF00288.21; ISPE_BACSU/86-144; GHMP kinases N terminal domain
220-285 -15.800 15  PF08544.8; ISPE_HAEDU/194-263; GHMP kinases C terminal
SCOP175 2-167 -67.700 31  d1h72c1 d.14.1.5 (C:5-167) Homoserine kinase {Archaeon Methanococcus jannaschii [TaxId: 2190]}
170-308 -49.900 28  d1h72c2 d.58.26.1 (C:168-300) Homoserine kinase {Archaeon Methanococcus jannaschii [TaxId: 2190]}
4 gi|16758997|ref|NP_454614.1| threonine synthase (STY0004) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 428 COG0113 1-427 -112.000 30  [E] COG0498 Threonine synthase
PDB0113 1-428 -125.000 93  1vb3_A mol:protein length:428 Threonine synthase
PfamA26U 84-379 -5.780 12  PF00291.20; A0Z504_9GAMM/17-322; Pyridoxal-phosphate dependent enzyme
SCOP175 1-428 -125.000 93  d1vb3a1 c.79.1.1 (A:1-428) Threonine synthase {Escherichia coli [TaxId: 562]}
5 gi|16758998|ref|NP_454615.1| hypothetical protein (STY0005) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 257 COG0113 1-257 -124.000 86  [S] COG3022 Uncharacterized protein conserved in bacteria
PDB0113 112-220 -6.300 22  2ofc_A mol:protein length:142 Sclerotium rolfsii lectin
PfamA26U 1-245 -118.000 60  PF03883.9; Y1338_ALCBS/1-245; Protein of unknown function (DUF328 topsan)
SCOP175 118-227 -6.600 14  d1f6fb2 b.1.2.1 (B:101-203) Prolactin receptor {Rat (Rattus norvegicus) [TaxId: 10116]}
6 gi|16758999|ref|NP_454616.1| putative amino-acid transport protein (STY0006) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 476 COG0113 1-471 -138.000 43  [E] COG1115 Na+/alanine symporter
PDB0113 52-430 -14.900 12  3gi8_C mol:protein length:444 Uncharacterized protein MJ0609
PfamA26U 40-458 -127.000 48  PF01235.12; Y183_HAEIN/53-467; Sodium:alanine symporter family
SCOP175 59-431 -10.600 13  d2a65a1 f.54.1.1 (A:5-513) Na(+):neurotransmitter symporter homologue LeuT {Aquifex aeolicus [TaxId: 63363]}
7 gi|16759000|ref|NP_454617.1| transaldolase B (STY0007) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 317 COG0113 1-317 -128.000 87  [G] COG0176 Transaldolase
PDB0113 1-317 -126.000 94  3cwn_A mol:protein length:337 Transaldolase B
PfamA26U 14-313 -115.000 57  PF00923.14; Q966C7_CAEEL/13-315; Transaldolase
SCOP175 2-317 -125.000 94  d1onra_ c.1.10.1 (A:) Transaldolase {Escherichia coli [TaxId: 562]}
8 gi|16759001|ref|NP_454618.1| molybdenum cofactor biosynthesis protein MogA (STY0008) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 196 COG0113 2-191 -92.200 75  [H] COG0521 Molybdopterin biosynthesis enzymes
PDB0113 1-195 -91.900 91  1di6_A mol:protein length:195 MOLYBDENUM COFACTOR BIOSYNTHETIC ENZYME
PfamA26U 8-144 -20.300 21  PF00994.19; CINAL_DESPS/4-169; Probable molybdopterin binding domain
SCOP175 2-191 -91.700 93  d1di6a_ c.57.1.1 (A:) MogA {Escherichia coli [TaxId: 562]}
9 gi|16759002|ref|NP_454619.1| hypothetical protein (STY0009) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 188 COG0113 3-184 -98.800 65  [S] COG1584 Predicted membrane protein
PDB0113 4-175 -7.320 11  1dg3_A mol:protein length:592 PROTEIN (INTERFERON-INDUCED GUANYLATE-BINDING
PfamA26U 3-187 -88.900 31  PF01184.14; A7TND9_VANPO/71-281; GPR1/FUN34/yaaH family
SCOP175 47-75 -5.670 25  d1g4ia_ a.133.1.2 (A:) Phospholipase A2 {Cow (Bos taurus), pancreas [TaxId: 9913]}
10 gi|16759003|ref|NP_454620.1| hypothetical protein (STY0010) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 237 COG0113 1-237 -92.900 87  [S] COG4735 Uncharacterized protein conserved in bacteria
PDB0113 8-125 -6.930 11  2clb_A mol:protein length:188 DPS-LIKE PROTEIN
PfamA26U 5-39 -12.100 40  PF13099.1; D0W7K2_NEILA/3-37; Domain of unknown function (DUF3944 topsan)
SCOP175 2-143 -6.690 11  d1nf4a_ a.25.1.1 (A:) Bacterioferritin (cytochrome b1) {Desulfovibrio desulfuricans [TaxId: 876]}
11 gi|16759004|ref|NP_454621.1|(removed signalp:1-23) hypothetical protein (STY0011) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 111 COG0113 1-97 -6.630 9  [R] COG4455 Protein of avirulence locus involved in temperature-dependent protein secretion
PDB0113 30-98 -8.030 10  4dxt_A mol:protein length:198 SUN domain-containing protein 2
PfamA26U 1-111 -74.200 79  PF10807.3; A6T4F3_KLEP7/1-134; Protein of unknown function (DUF2541 topsan)
SCOP175 18-107 -8.290 12  d1y6kr1 b.1.2.1 (R:2-100) Interleukin-10 receptor 1, IL-10R1 {Human (Homo sapiens) [TaxId: 9606]}
12 gi|16759005|ref|NP_454622.1| molecular chaperone DnaK (STY0012) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 638 COG0113 1-638 -182.000 56  [O] COG0443 Molecular chaperone
PDB0113 1-605 -188.000 97  2kho_A mol:protein length:605 Heat shock protein 70
1-638 -141.000 25  3d2e_A mol:protein length:675 Heat shock protein homolog SSE1
PfamA26U 4-604 -182.000 58  PF00012.15; HSP77_YEAST/32-633; Hsp70 protein
SCOP175 2-184 -85.100 55  d1bupa1 c.55.1.1 (A:4-188) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]}
185-383 -75.100 45  d1bupa2 c.55.1.1 (A:189-381) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]}
389-506 -77.000 96  d1dkza2 b.130.1.1 (A:389-506) DnaK {Escherichia coli [TaxId: 562]}
507-602 -38.100 96  d1dkza1 a.8.4.1 (A:507-603) DnaK {Escherichia coli [TaxId: 562]}
13 gi|16759006|ref|NP_454623.1| chaperone protein DnaJ (STY0013) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 379 COG0113 1-375 -144.000 58  [O] COG0484 DnaJ-class molecular chaperone with C-terminal Zn finger domain
PDB0113 1-359 -107.000 40  3lz8_A mol:protein length:329 Putative chaperone DnaJ
PfamA26U 5-67 -40.300 55  PF00226.26; Q22028_CAEEL/17-79; DnaJ domain
145-347 -9.690 12  PF02335.10; NRFA_BACFN/56-493; Cytochrome c552
147-207 -31.300 44  PF00684.14; DNAJ1_CORGL/147-211; DnaJ central domain
265-343 -27.500 22  PF01556.13; A2FIH5_TRIVA/258-337; DnaJ C terminal domain
SCOP175 2-76 -48.000 96  d1xbla_ a.2.3.1 (A:) DnaJ chaperone, N-terminal (J) domain {Escherichia coli [TaxId: 562]}
2-110 -39.200 18  d1gh6a_ a.2.3.1 (A:) Large T antigen, the N-terminal J domain {Simian virus 40, Sv40 [TaxId: 10633]}
134-212 -41.400 96  d1exka_ g.54.1.1 (A:) Cysteine-rich domain of the chaperone protein DnaJ {Escherichia coli [TaxId: 562]}
181-257 -21.300 18  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]}
259-345 -30.700 26  d1c3ga2 b.4.1.1 (A:260-349) Heat shock protein 40 Sis1 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
14 gi|16759007|ref|NP_454624.1| putative regulatory protein (STY0014) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 315 COG0113 7-313 -31.300 14  [K] COG0583 Transcriptional regulator
PDB0113 2-313 -95.100 19  1utb_A mol:protein length:315 LYSR-TYPE REGULATORY PROTEIN
PfamA26U 16-70 -13.200 20  PF00126.22; Q8EIK0_SHEON/8-63; Bacterial regulatory helix-turn-helix protein, lysR family
95-312 -10.300 10  PF03466.15; Q98I60_RHILO/88-294; LysR substrate binding domain
SCOP175 7-96 -42.800 26  d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}
90-315 -58.000 16  d1utha_ c.94.1.1 (A:) LysR-type regulatory protein DntR {Burkholderia sp. [TaxId: 36773]}
15 gi|16759008|ref|NP_454625.1| hypothetical protein (STY0015) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 114 COG0113 18-94 -10.300 13  [D] COG0239 Integral membrane protein possibly involved in chromosome condensation
PDB0113 21-98 -7.130 10  2los_A mol:protein length:121 Transmembrane protein 14C
PfamA26U 3-107 -17.100 10  PF05106.7; B1JD04_PSEPW/4-103; Phage holin family (Lysis protein S)
SCOP175 2-87 -6.060 5  d1kqfc_ f.21.1.1 (C:) Formate dehydrogenase N, cytochrome (gamma) subunit {Escherichia coli [TaxId: 562]}
16 gi|16759009|ref|NP_454626.1| hypothetical protein (STY0016) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 177 COG0113 1-177 -78.400 25  [R] COG3926 Putative secretion activating protein
PDB0113 1-177 -82.300 34  2is5_A mol:protein length:166 Hypothetical protein
PfamA26U 3-88 -50.200 30  PF05838.7; Q7ME33_VIBVY/17-107; Glycosyl hydrolase 108
91-176 -34.700 23  PF09374.5; Q8EDS2_SHEON/119-186; Predicted Peptidoglycan domain
SCOP175 1-177 -82.500 34  d2ikba1 d.2.1.9 (A:1-163) Hypothetical protein NMB1012 {Neisseria meningitidis [TaxId: 487]}
17 gi|16759010|ref|NP_454627.1| hypothetical protein (STY0017) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 147 COG0113 2-129 -45.000 15  [K] COG3710 DNA-binding winged-HTH domains
PDB0113 2-106 -35.700 15  1gxp_A mol:protein length:106 PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY
17-141 -15.000 10  2fez_A mol:protein length:388 Probable regulatory protein embR
PfamA26U 25-102 -31.700 14  PF00486.23; O85058_PROST/114-189; Transcriptional regulatory protein, C terminal
SCOP175 2-106 -35.600 15  d1gxqa_ a.4.6.1 (A:) PhoB {Escherichia coli [TaxId: 562]}
18 gi|16759011|ref|NP_454628.1| putative chitinase (STY0018) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 699 COG0113 1-512 -121.000 97  [G] COG3325 Chitinase
28-699 -36.900 9  [R] COG3858 Predicted glycosyl hydrolase
PDB0113 2-514 -97.800 38  3oa5_A mol:protein length:574 Chi1
50-546 -83.000 19  1e15_A mol:protein length:499 CHITINASE B
643-698 -12.800 35  2d49_A mol:protein length:53 chitinase C
PfamA26U 53-465 -84.300 27  PF00704.23; Q9WFU7_9ABAC/159-544; Glycosyl hydrolases family 18
SCOP175 42-400 -73.100 23  d1itxa1 c.1.8.5 (A:33-337,A:410-451) Chitinase A1 {Bacillus circulans [TaxId: 1397]}
49-448 -69.900 22  d1w9pa1 c.1.8.5 (A:39-298,A:361-433) Chitinase 1 {Aspergillus fumigatus [TaxId: 5085]}
51-506 -68.200 20  d1goia2 c.1.8.5 (A:3-291,A:380-446) Chitinase B, catalytic domain {Serratia marcescens [TaxId: 615]}
631-698 -11.900 18  d1aiwa_ b.72.2.1 (A:) Cellulose-binding domain of endoglucanase Z {Erwinia chrysanthemi [TaxId: 556]}
19 gi|16759012|ref|NP_454629.1| hypothetical protein (STY0019) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 383 COG0113 272-363 -5.510 15  [S] COG4704 Uncharacterized protein conserved in bacteria
PDB0113 23-148 -6.430 8  1xb6_A mol:protein length:128 Azurin
PfamA26U 2-43 -7.860 25  PF02208.11; SRBS2_MOUSE/167-216; Sorbin homologous domain
SCOP175 23-149 -5.290 6  d2ccwa1 b.6.1.1 (A:1-129) Azurin {Alcaligenes xylosoxidans, NCIMB (11015), different isoforms [TaxId: 85698]}
20 gi|16759013|ref|NP_454630.1| hypothetical protein (STY0020) [Salmonella enterica subsp. enterica serovar Typhi str. CT18] 620 COG0113 110-405 -6.390 14  [G] COG5297 Cellobiohydrolase A (1,4-beta-cellobiosidase A)
PDB0113 255-547 -8.820 13  4a05_A mol:protein length:364 CELLOBIOHYDROLASE FAMILY 6
PfamA26U 253-517 -8.580 14  PF01341.12; Q0TVM0_PHANO/58-351; Glycosyl hydrolases family 6
SCOP175 188-522 -8.880 14  d1dysa_ c.6.1.1 (A:) Cellobiohydrolase II (Cel6) {Humicola insolens, Cel6b [TaxId: 34413]}

FFAS is supported by the NIH grant R01-GM087218-01
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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.

Robinson-Rechavi M, Godzik A. Structural Genomics of Thermotoga maritima Proteins Shows that Contact Order Is a Major Determinant of Protein Thermostability. Structure (Camb). 2005 Jun;13(6):857-60.