Query 008270
Match_columns 571
No_of_seqs 141 out of 272
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 21:40:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008270.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008270hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01936 NYN: NYN domain; Int 99.8 3.2E-20 7E-25 162.9 6.1 133 29-169 1-144 (146)
2 cd06167 LabA_like LabA_like pr 99.6 1.5E-15 3.2E-20 135.7 8.9 135 29-167 2-146 (149)
3 TIGR00288 conserved hypothetic 99.3 1.8E-11 4E-16 116.0 13.3 135 24-170 19-155 (160)
4 COG1432 Uncharacterized conser 97.7 0.00025 5.5E-09 68.1 9.5 147 27-175 5-165 (181)
5 PF04263 TPK_catalytic: Thiami 81.1 6.2 0.00013 36.3 7.1 76 70-151 39-121 (123)
6 COG4634 Uncharacterized protei 79.3 8.9 0.00019 35.7 7.4 72 77-157 8-80 (113)
7 KOG0260 RNA polymerase II, lar 76.6 1.3E+02 0.0027 38.1 17.5 16 122-137 1323-1338(1605)
8 cd05013 SIS_RpiR RpiR-like pro 73.2 52 0.0011 28.2 10.3 94 65-169 14-110 (139)
9 KOG0260 RNA polymerase II, lar 72.9 1.2E+02 0.0027 38.1 16.3 9 123-131 1352-1360(1605)
10 PRK00124 hypothetical protein; 69.6 15 0.00033 35.5 6.7 81 31-138 2-82 (151)
11 cd05014 SIS_Kpsf KpsF-like pro 66.0 25 0.00053 30.7 6.9 93 66-170 2-98 (128)
12 COG1671 Uncharacterized protei 58.3 43 0.00093 32.7 7.4 80 30-138 2-81 (150)
13 PLN02714 thiamin pyrophosphoki 54.1 64 0.0014 32.5 8.3 82 70-155 57-148 (229)
14 COG0794 GutQ Predicted sugar p 52.9 70 0.0015 32.4 8.3 107 49-169 27-136 (202)
15 cd05005 SIS_PHI Hexulose-6-pho 52.3 1.2E+02 0.0025 28.6 9.3 91 65-171 34-127 (179)
16 TIGR01378 thi_PPkinase thiamin 51.1 90 0.0019 30.7 8.6 89 60-156 33-128 (203)
17 PF07283 TrbH: Conjugal transf 49.1 42 0.00091 31.4 5.6 54 104-157 4-61 (121)
18 TIGR03127 RuMP_HxlB 6-phospho 48.1 1.3E+02 0.0028 28.2 8.9 91 64-170 30-123 (179)
19 PF08497 Radical_SAM_N: Radica 47.4 24 0.00051 37.8 4.2 42 110-154 7-56 (302)
20 TIGR00393 kpsF KpsF/GutQ famil 45.8 71 0.0015 31.5 7.1 94 65-170 1-98 (268)
21 COG0796 MurI Glutamate racemas 43.9 1.3E+02 0.0028 31.8 8.8 85 43-153 13-99 (269)
22 PRK11557 putative DNA-binding 42.9 1.6E+02 0.0035 29.4 9.2 94 65-169 129-225 (278)
23 PRK05628 coproporphyrinogen II 42.9 2.6E+02 0.0057 29.7 11.1 105 44-148 72-191 (375)
24 PRK11337 DNA-binding transcrip 42.1 2E+02 0.0043 29.2 9.7 94 66-170 142-238 (292)
25 PF02590 SPOUT_MTase: Predicte 40.3 2E+02 0.0044 27.7 8.9 41 133-173 84-127 (155)
26 cd07995 TPK Thiamine pyrophosp 38.7 1.7E+02 0.0038 28.6 8.4 88 58-153 35-129 (208)
27 cd05008 SIS_GlmS_GlmD_1 SIS (S 38.6 1.9E+02 0.0041 25.1 7.8 48 121-169 46-96 (126)
28 PRK11543 gutQ D-arabinose 5-ph 38.6 1.7E+02 0.0036 29.9 8.7 94 65-170 43-140 (321)
29 PRK11302 DNA-binding transcrip 38.4 2.7E+02 0.0059 27.8 10.0 94 65-170 129-225 (284)
30 cd08502 PBP2_NikA_DppA_OppA_li 37.5 33 0.00071 36.8 3.5 34 488-521 254-287 (472)
31 PRK00414 gmhA phosphoheptose i 36.7 2.9E+02 0.0063 26.9 9.6 49 120-169 110-161 (192)
32 PF09419 PGP_phosphatase: Mito 36.7 3.2E+02 0.007 26.8 9.8 113 29-151 41-164 (168)
33 COG1737 RpiR Transcriptional r 36.6 2.8E+02 0.0062 28.4 9.9 90 69-169 133-227 (281)
34 PF09314 DUF1972: Domain of un 35.8 3.8E+02 0.0082 26.7 10.3 103 41-151 12-124 (185)
35 KOG1610 Corticosteroid 11-beta 35.6 52 0.0011 35.5 4.6 45 120-164 26-73 (322)
36 PRK15482 transcriptional regul 35.1 3.9E+02 0.0085 27.1 10.6 95 65-170 136-233 (285)
37 PLN02625 uroporphyrin-III C-me 34.9 1.9E+02 0.0041 29.4 8.2 88 8-98 21-128 (263)
38 PF10450 POC1: POC1 chaperone; 34.4 24 0.00052 37.1 1.9 72 452-536 186-262 (273)
39 PRK15473 cbiF cobalt-precorrin 33.4 2.7E+02 0.0058 28.2 9.0 88 8-98 14-116 (257)
40 COG3233 Predicted deacetylase 32.4 1E+02 0.0022 32.1 5.9 23 130-152 52-74 (233)
41 COG1576 Uncharacterized conser 32.3 2.4E+02 0.0053 27.7 8.1 42 132-173 83-126 (155)
42 cd05006 SIS_GmhA Phosphoheptos 31.8 4.4E+02 0.0095 24.8 10.3 50 120-170 100-152 (177)
43 PRK10014 DNA-binding transcrip 31.4 4.8E+02 0.01 26.1 10.4 100 48-152 35-151 (342)
44 TIGR02417 fruct_sucro_rep D-fr 30.8 5.3E+02 0.011 25.7 10.6 99 49-152 32-147 (327)
45 PF06073 DUF934: Bacterial pro 30.3 1.1E+02 0.0024 28.3 5.2 52 41-99 27-79 (110)
46 TIGR01675 plant-AP plant acid 30.1 1.9E+02 0.0042 29.6 7.4 70 81-153 127-203 (229)
47 PF05991 NYN_YacP: YacP-like N 29.9 1.5E+02 0.0032 28.5 6.2 44 88-137 65-109 (166)
48 PRK10294 6-phosphofructokinase 29.7 4.2E+02 0.0092 26.7 9.8 44 50-96 40-83 (309)
49 PF02602 HEM4: Uroporphyrinoge 29.2 2.3E+02 0.0049 27.2 7.4 73 67-151 74-146 (231)
50 PRK13883 conjugal transfer pro 29.1 1.1E+02 0.0024 29.8 5.2 53 103-155 31-87 (151)
51 PRK07334 threonine dehydratase 28.9 1.6E+02 0.0035 31.8 7.0 94 45-151 307-402 (403)
52 PRK14828 undecaprenyl pyrophos 28.6 1.4E+02 0.003 31.2 6.1 67 34-101 80-155 (256)
53 PF07582 AP_endonuc_2_N: AP en 28.6 51 0.0011 27.0 2.5 19 52-70 3-21 (55)
54 PRK13835 conjugal transfer pro 28.6 1.3E+02 0.0028 29.3 5.5 50 101-150 35-87 (145)
55 PF10965 DUF2767: Protein of u 28.2 1.1E+02 0.0023 26.6 4.4 53 458-510 11-66 (69)
56 PRK01254 hypothetical protein; 27.9 1E+02 0.0022 36.6 5.5 41 111-154 31-79 (707)
57 TIGR02764 spore_ybaN_pdaB poly 27.5 5.3E+02 0.012 24.4 9.7 100 45-151 74-187 (191)
58 PRK14101 bifunctional glucokin 27.0 4.3E+02 0.0093 30.4 10.2 93 65-169 469-564 (638)
59 cd08491 PBP2_NikA_DppA_OppA_li 26.9 46 0.00099 35.7 2.5 31 490-520 239-269 (473)
60 PF10740 DUF2529: Protein of u 26.6 1.9E+02 0.0041 28.9 6.4 102 51-169 28-133 (172)
61 PRK11303 DNA-binding transcrip 26.5 5.8E+02 0.012 25.4 10.0 99 49-152 33-148 (328)
62 cd08496 PBP2_NikA_DppA_OppA_li 26.5 49 0.0011 35.1 2.6 29 491-519 243-271 (454)
63 PRK01045 ispH 4-hydroxy-3-meth 26.0 2.2E+02 0.0047 30.4 7.2 43 50-95 15-58 (298)
64 PF02739 5_3_exonuc_N: 5'-3' e 25.9 1E+02 0.0022 29.7 4.4 60 84-153 93-152 (169)
65 TIGR00441 gmhA phosphoheptose 25.9 4.7E+02 0.01 24.4 8.6 51 120-171 78-131 (154)
66 PRK08599 coproporphyrinogen II 25.7 6.9E+02 0.015 26.5 10.9 53 45-97 65-117 (377)
67 PRK09058 coproporphyrinogen II 25.6 7.3E+02 0.016 27.4 11.4 53 43-96 126-179 (449)
68 PRK11382 frlB fructoselysine-6 25.4 6.7E+02 0.015 26.5 10.7 107 52-171 33-144 (340)
69 KOG2236 Uncharacterized conser 25.1 4.5E+02 0.0098 30.1 9.6 19 304-323 416-434 (483)
70 PRK10401 DNA-binding transcrip 24.7 4.4E+02 0.0096 26.6 8.9 112 31-148 141-263 (346)
71 smart00645 Pept_C1 Papain fami 24.5 91 0.002 29.6 3.8 54 457-510 26-79 (174)
72 PF00496 SBP_bac_5: Bacterial 24.4 65 0.0014 32.6 2.9 30 491-520 211-240 (374)
73 cd01174 ribokinase Ribokinase 23.3 5.4E+02 0.012 25.3 9.0 44 50-96 38-82 (292)
74 cd08492 PBP2_NikA_DppA_OppA_li 23.2 75 0.0016 33.8 3.3 28 492-519 261-288 (484)
75 cd08519 PBP2_NikA_DppA_OppA_li 23.1 59 0.0013 34.8 2.4 33 488-520 248-280 (469)
76 cd00995 PBP2_NikA_DppA_OppA_li 22.8 63 0.0014 33.7 2.5 30 491-520 248-277 (466)
77 PRK09997 hydroxypyruvate isome 22.6 6.7E+02 0.014 24.8 9.5 76 50-130 17-107 (258)
78 cd08517 PBP2_NikA_DppA_OppA_li 22.4 66 0.0014 34.1 2.6 29 492-520 257-285 (480)
79 PRK05904 coproporphyrinogen II 22.4 7.8E+02 0.017 26.4 10.6 54 42-97 67-120 (353)
80 PRK14814 NADH dehydrogenase su 22.1 94 0.002 31.3 3.4 26 449-477 137-162 (186)
81 cd08498 PBP2_NikA_DppA_OppA_li 21.8 74 0.0016 34.0 2.9 29 492-520 259-287 (481)
82 PRK10727 DNA-binding transcrip 21.7 6.6E+02 0.014 25.4 9.5 114 29-148 139-263 (343)
83 KOG2972 Uncharacterized conser 21.5 3.2E+02 0.007 29.1 7.2 27 123-149 204-231 (276)
84 PF10096 DUF2334: Uncharacteri 21.4 2.1E+02 0.0046 29.0 5.8 24 131-154 54-77 (243)
85 COG1564 THI80 Thiamine pyropho 21.4 4.2E+02 0.0091 27.1 7.9 89 58-155 37-132 (212)
86 TIGR01231 lacC tagatose-6-phos 21.3 6.8E+02 0.015 25.2 9.5 43 50-96 37-80 (309)
87 PRK09989 hypothetical protein; 21.2 6.5E+02 0.014 24.9 9.2 37 56-95 22-58 (258)
88 PRK14820 NADH dehydrogenase su 21.1 93 0.002 31.1 3.2 28 449-479 137-164 (180)
89 cd06578 HemD Uroporphyrinogen- 20.7 4.3E+02 0.0092 24.9 7.4 64 81-151 87-151 (239)
90 COG2247 LytB Putative cell wal 20.6 4.8E+02 0.01 28.7 8.4 87 65-157 75-164 (337)
91 cd08489 PBP2_NikA The substrat 20.5 72 0.0016 34.1 2.5 30 490-519 249-278 (488)
92 cd08512 PBP2_NikA_DppA_OppA_li 20.4 74 0.0016 33.8 2.5 32 488-519 259-290 (476)
93 cd08493 PBP2_DppA_like The sub 20.2 76 0.0017 33.9 2.6 28 492-519 264-291 (482)
No 1
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=99.80 E-value=3.2e-20 Score=162.85 Aligned_cols=133 Identities=33% Similarity=0.500 Sum_probs=93.7
Q ss_pred ceEEEEEccCCCCCCC---CChhhHHHHHHHHHHhcCccCce-EEEEEecCCCC-ChhHHHHhhhcCCceeeccC-----
Q 008270 29 KTSVWWDIENCQVPKN---CDPHTIAQNISSALVKMNYCGPV-SISAYGDTNRI-PASVQHALSSTGIALNHVPA----- 98 (571)
Q Consensus 29 kTaVFWDIENCPVP~G---~da~~Va~NIr~AL~klGY~GpV-TIrAYGD~s~i-p~~vl~aLsSSGISLihVPa----- 98 (571)
+|+||||+|||..+.. +++..+...|+. .|++ .+++|+++..- ...++++|...||.+.+++.
T Consensus 1 rvavfvD~eN~~~~~~~~~~~~~~l~~~i~~-------~~~~~~~~~y~~~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~ 73 (146)
T PF01936_consen 1 RVAVFVDGENLYIPLKRWDIDFERLLEEIRK-------YGPLVRIRAYGNWDDPNQKSFQEALQRAGIKVRHFPLRKRGG 73 (146)
T ss_dssp EEEEEEEHHHHHHHHHSS-B-HHHHHHHHTT-------TEEEEEEEEEE----HHHHHHHHHHHHHT-EEEE------S-
T ss_pred CEEEEEEhHhCchhhCCCCCCHHHHHHHHHh-------cCCeEEEEEEeeccccchhhHHHHHHhCeeeEEeeecccccc
Confidence 6899999999999765 565555555443 4667 79999995432 35577899999999999986
Q ss_pred CCccchhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEec-cCCCChhHHhhcCeEEE
Q 008270 99 GVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWL 169 (571)
Q Consensus 99 G~KnAADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq-P~~AS~~L~aaAd~vWl 169 (571)
+.|+++|.+|.+||+.|+.+++. +++||||||.||.+++..|+.+|++|.++. +..++..|..+|+.++.
T Consensus 74 ~~k~~~D~~l~~d~~~~~~~~~~-d~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~~~~~s~~L~~~ad~f~~ 144 (146)
T PF01936_consen 74 GGKKGVDVALAVDILELAYENPP-DTIVLVSGDSDFAPLVRKLRERGKRVIVVGAEDSASEALRSAADEFIS 144 (146)
T ss_dssp --S---HHHHHHHHHHHG--GG--SEEEEE---GGGHHHHHHHHHH--EEEEEE-GGGS-HHHHHHSSEEEE
T ss_pred cccCCcHHHHHHHHHHHhhccCC-CEEEEEECcHHHHHHHHHHHHcCCEEEEEEeCCCCCHHHHHhcCEEEe
Confidence 57899999999999999988766 999999999999999999999999998888 56789999999998764
No 2
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=99.61 E-value=1.5e-15 Score=135.68 Aligned_cols=135 Identities=24% Similarity=0.217 Sum_probs=107.7
Q ss_pred ceEEEEEccCCCCCCCCCh--hhHHHHHHHHHHhcCccCc-eEEEEEecCCC--CChhHHHHhhhcCCceeeccC----C
Q 008270 29 KTSVWWDIENCQVPKNCDP--HTIAQNISSALVKMNYCGP-VSISAYGDTNR--IPASVQHALSSTGIALNHVPA----G 99 (571)
Q Consensus 29 kTaVFWDIENCPVP~G~da--~~Va~NIr~AL~klGY~Gp-VTIrAYGD~s~--ip~~vl~aLsSSGISLihVPa----G 99 (571)
+++||||.||+..-..... ..-...+...+... +. ...++|+++.. ......++|...|+.+++++. +
T Consensus 2 r~~ifiD~~Nl~~~~~~~~~~~~d~~~l~~~~~~~---~~~~~~r~y~~~~~~~~~~~~~~~L~~~g~~~~~~~~~~~~~ 78 (149)
T cd06167 2 RVAVFIDGENLYYSLRDLGGKRFDYRKLLEFLRDG---GEIVLARAYGNWTSPERQRGFLDALRRLGFEPIQKPLRTRGS 78 (149)
T ss_pred eEEEEEeHHHHHHHHHHhcCCCcCHHHHHHHHHhC---CeEEEEEEEEecCCchhHHHHHHHHHHCCcEEEEEcceecCC
Confidence 6899999999975321110 11122233333322 44 46899999874 456788999999999999984 6
Q ss_pred CccchhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEeccC-CCChhHHhhcCeE
Q 008270 100 VKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSV 167 (571)
Q Consensus 100 ~KnAADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~-~AS~~L~aaAd~v 167 (571)
.|+++|.+|.+||+.++.++ .++.|||||||.||.+++..|+++|++|+++.+. ..+..|..+|+.+
T Consensus 79 ~~~~~D~~l~~d~~~~~~~~-~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d~f 146 (149)
T cd06167 79 GKKGVDVALAIDALELAYKR-RIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSRELRKAADRF 146 (149)
T ss_pred cccCccHHHHHHHHHHhhhc-CCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCCcc
Confidence 78999999999999999988 8899999999999999999999999999999977 7889999998854
No 3
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=99.33 E-value=1.8e-11 Score=115.98 Aligned_cols=135 Identities=16% Similarity=0.148 Sum_probs=106.5
Q ss_pred hhcCCceEEEEEccCCCCCCCCChhhHHHHHHHHHHhcCccCceE-EEEEecCCCCChhHHHHhhhcCCceeeccCCCcc
Q 008270 24 QYVTAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVS-ISAYGDTNRIPASVQHALSSTGIALNHVPAGVKD 102 (571)
Q Consensus 24 rya~AkTaVFWDIENCPVP~G~da~~Va~NIr~AL~klGY~GpVT-IrAYGD~s~ip~~vl~aLsSSGISLihVPaG~Kn 102 (571)
+-..-+++||-|.+|.. +..+. .. ...|...|.+ .|.++ -++||++.. ...+++.|...|++.+.+ |+
T Consensus 19 ~~~~~riAvfID~~Nv~-~~~~~-~d-~~~i~~~ls~---~G~i~~~R~Y~~a~a-~~~l~~~l~~~Gf~pv~~----kG 87 (160)
T TIGR00288 19 RKGEKKIGLLVDGPNML-RKEFN-ID-LDEIREILSE---YGDIKIGKVLLNQYA-SDKLIEAVVNQGFEPIIV----AG 87 (160)
T ss_pred cCCCCcEEEEEeCCccC-hhhhc-cC-HHHHHHHHHh---cCCeEEEEEEechhc-cHHHHHHHHHCCceEEEe----cC
Confidence 33356799999999996 32221 11 3456666665 47665 589999643 346788999999998754 55
Q ss_pred chhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEec-cCCCChhHHhhcCeEEEe
Q 008270 103 ASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 103 AADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq-P~~AS~~L~aaAd~vWlW 170 (571)
+.|..|.+|+|..++ .+..+.++|+|||.||.+++.+||++|..|+++. +..++.+|..+|+.++.-
T Consensus 88 ~~Dv~laIDame~~~-~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~acd~FI~L 155 (160)
T TIGR00288 88 DVDVRMAVEAMELIY-NPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNSADIAIIL 155 (160)
T ss_pred cccHHHHHHHHHHhc-cCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHhcCeEEeC
Confidence 899999999999886 4788999999999999999999999999999998 556888999999987654
No 4
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=97.65 E-value=0.00025 Score=68.06 Aligned_cols=147 Identities=20% Similarity=0.151 Sum_probs=97.8
Q ss_pred CCceEEEEEccCCCCCCCCChhhHHHHHHHHHHhcCccCce-EEEEEe---cCCCCChhHHH--HhhhcCCceeeccC--
Q 008270 27 TAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPV-SISAYG---DTNRIPASVQH--ALSSTGIALNHVPA-- 98 (571)
Q Consensus 27 ~AkTaVFWDIENCPVP~G~da~~Va~NIr~AL~klGY~GpV-TIrAYG---D~s~ip~~vl~--aLsSSGISLihVPa-- 98 (571)
...+++|-|++|-+.-.. ....+.-.....|++......+ ....|. +...+..-... ++...|+.++-.+.
T Consensus 5 ~~~i~~~id~~n~~~~~~-~~~~~~~d~~~ll~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~ 83 (181)
T COG1432 5 VDRIALFIDGKNLYASQR-KNLGILIDYRKLLRKELKRIYLYEAAPYTAEYGDIEIQEVFLNEYELRSDGFTVVTSNLDG 83 (181)
T ss_pred ccceeEEeehhhhHHHHH-HhcCcccCHHHHHHHHhcCceEEEEeehhhccccchhhhheecHHHHhhcCcEEEeccccc
Confidence 347899999998654221 1111222233444443333333 233332 22333333322 66667776665443
Q ss_pred -----CCccchhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEeccC-CCChhHHhhcCeEEEech
Q 008270 99 -----GVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSVWLWTS 172 (571)
Q Consensus 99 -----G~KnAADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~-~AS~~L~aaAd~vWlWeS 172 (571)
-.|..-|..|.+||+..+ +++.-.+++|+|||.||.+++..++.+|..|+++.-. ..|..|..+|+.+..-.+
T Consensus 84 ~~~~~~~k~~vDv~la~D~~~l~-~~~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~~s~~L~~~aD~~i~L~~ 162 (181)
T COG1432 84 FTDLRITKGDVDVELAVDAMELA-DKKNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAADYYIDLKS 162 (181)
T ss_pred cCcccccccCcchhhHHHHHHhh-cccCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCCcCHHHHHHhhcceEEchh
Confidence 234567889999999987 5678899999999999999999999999999998743 577889999998887776
Q ss_pred hhc
Q 008270 173 LVA 175 (571)
Q Consensus 173 LLa 175 (571)
+..
T Consensus 163 ~~~ 165 (181)
T COG1432 163 LEE 165 (181)
T ss_pred hhh
Confidence 554
No 5
>PF04263 TPK_catalytic: Thiamin pyrophosphokinase, catalytic domain; InterPro: IPR007371 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0005524 ATP binding, 0009229 thiamine diphosphate biosynthetic process; PDB: 2F17_B 1IG3_B 3S4Y_B 2OMK_B 1IG0_A 3MEL_B 3CQ9_A 3LM8_B 3K94_B 3L8M_B ....
Probab=81.10 E-value=6.2 Score=36.30 Aligned_cols=76 Identities=25% Similarity=0.460 Sum_probs=49.8
Q ss_pred EEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEe--CCc---chHH--HHHHHH
Q 008270 70 SAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS--GDR---DFSN--ALHQLR 142 (571)
Q Consensus 70 rAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLIS--GDr---DFS~--aL~~LR 142 (571)
-+.||...+..++++.+.+.|+.+++.| .||..|-.+.++.+ ... .+..|+|+- |-| -++. +|.+++
T Consensus 39 ~iiGDfDSi~~~~~~~~~~~~~~~~~~p--~kD~TD~e~Al~~~---~~~-~~~~i~v~Ga~GgR~DH~lanl~~l~~~~ 112 (123)
T PF04263_consen 39 LIIGDFDSISPEVLEFYKSKGVEIIHFP--EKDYTDLEKALEYA---IEQ-GPDEIIVLGALGGRFDHTLANLNLLYKYK 112 (123)
T ss_dssp EEEC-SSSS-HHHHHHHHHCTTEEEEE---STTS-HHHHHHHHH---HHT-TTSEEEEES-SSSSHHHHHHHHHHHHHHH
T ss_pred EEEecCCCCChHHHHHHHhhccceeccc--ccccCHHHHHHHHH---HHC-CCCEEEEEecCCCcHHHHHHHHHHHHHHH
Confidence 4789999998899999999999999999 68888887766655 333 344555543 322 2333 344455
Q ss_pred hCCCeEEEe
Q 008270 143 MRRYNILLA 151 (571)
Q Consensus 143 ~RGYNILLA 151 (571)
+++.+|+|+
T Consensus 113 ~~~~~i~li 121 (123)
T PF04263_consen 113 KRGIKIVLI 121 (123)
T ss_dssp TTTSEEEEE
T ss_pred HcCCeEEEE
Confidence 679999886
No 6
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.29 E-value=8.9 Score=35.68 Aligned_cols=72 Identities=25% Similarity=0.359 Sum_probs=50.1
Q ss_pred CCChhHHHHhhhcCCceeecc-CCCccchhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEeccCC
Q 008270 77 RIPASVQHALSSTGIALNHVP-AGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHK 155 (571)
Q Consensus 77 ~ip~~vl~aLsSSGISLihVP-aG~KnAADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~~ 155 (571)
++|..+.+-|..+||+-+|+. -|-+|+.|..|+ .+|. -.+.||+|.|.||.. |..+...-..|+.+.-.+
T Consensus 8 ~Lp~rlad~l~~~g~e~~h~r~lg~~da~D~EI~----a~A~----~~~~iivTkDsDF~~-la~~~G~Ppki~wLr~gN 78 (113)
T COG4634 8 QLPPRLADWLPMAGIEAVHWRDLGLRDATDIEIW----AYAR----RNNRIIVTKDSDFAD-LALTLGSPPKIVWLRCGN 78 (113)
T ss_pred CCChHHHHHhhhcccceeeecccCcCCCccHHHH----HHHH----hcCcEEEEcCccHHH-HHHHcCCCCeEEEEEecC
Confidence 467788889999999888886 366777765433 3343 357899999999943 444444556777776556
Q ss_pred CC
Q 008270 156 AS 157 (571)
Q Consensus 156 AS 157 (571)
.+
T Consensus 79 vs 80 (113)
T COG4634 79 VS 80 (113)
T ss_pred CC
Confidence 55
No 7
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=76.56 E-value=1.3e+02 Score=38.10 Aligned_cols=16 Identities=25% Similarity=0.127 Sum_probs=9.6
Q ss_pred CceEEEEeCCcchHHH
Q 008270 122 PSNYLLISGDRDFSNA 137 (571)
Q Consensus 122 PANIMLISGDrDFS~a 137 (571)
+.-.++|+.|..+...
T Consensus 1323 ~e~~~vi~f~gsyVny 1338 (1605)
T KOG0260|consen 1323 RELLNVISFDGSYVNY 1338 (1605)
T ss_pred hhhhheEeecccchhH
Confidence 3445677777766553
No 8
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=73.20 E-value=52 Score=28.21 Aligned_cols=94 Identities=15% Similarity=0.110 Sum_probs=55.6
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCCc---chHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDR---DFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGDr---DFS~aL~~L 141 (571)
.+|-+.+.|....+-..+...|...|.....++... ....++ ..-.+-+-+++||-.. +...++..+
T Consensus 14 ~~i~i~g~g~s~~~a~~~~~~l~~~~~~~~~~~~~~------~~~~~~----~~~~~~~~~i~iS~~g~~~~~~~~~~~a 83 (139)
T cd05013 14 RRIYIFGVGSSGLVAEYLAYKLLRLGKPVVLLSDPH------LQLMSA----ANLTPGDVVIAISFSGETKETVEAAEIA 83 (139)
T ss_pred CEEEEEEcCchHHHHHHHHHHHHHcCCceEEecCHH------HHHHHH----HcCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 556666666644444556667777777655543210 111111 1123456677788543 466778888
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
+++|-.|+++..... .+|...++.++.
T Consensus 84 ~~~g~~iv~iT~~~~-~~l~~~~d~~i~ 110 (139)
T cd05013 84 KERGAKVIAITDSAN-SPLAKLADIVLL 110 (139)
T ss_pred HHcCCeEEEEcCCCC-ChhHHhcCEEEE
Confidence 999999998876433 456666665544
No 9
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=72.95 E-value=1.2e+02 Score=38.13 Aligned_cols=9 Identities=11% Similarity=0.302 Sum_probs=4.7
Q ss_pred ceEEEEeCC
Q 008270 123 SNYLLISGD 131 (571)
Q Consensus 123 ANIMLISGD 131 (571)
.++|+|+.+
T Consensus 1352 g~lm~itRh 1360 (1605)
T KOG0260|consen 1352 GHLMAITRH 1360 (1605)
T ss_pred cceeeeecc
Confidence 455555544
No 10
>PRK00124 hypothetical protein; Validated
Probab=69.57 E-value=15 Score=35.47 Aligned_cols=81 Identities=19% Similarity=0.207 Sum_probs=50.0
Q ss_pred EEEEEccCCCCCCCCChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHH
Q 008270 31 SVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILV 110 (571)
Q Consensus 31 aVFWDIENCPVP~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLv 110 (571)
-||-|-+-|| |..-|.++.++.| +.++.+++.++.. .-=.+..|+.+.|+.| .|++|..|+.
T Consensus 2 ~I~VDADACP---------Vk~~i~r~a~r~~----i~v~~Vas~n~~~----~~~~~~~v~~v~V~~g-~D~AD~~Iv~ 63 (151)
T PRK00124 2 KIYVDADACP---------VKDIIIRVAERHG----IPVTLVASFNHFL----RVPYSPFIRTVYVDAG-FDAADNEIVQ 63 (151)
T ss_pred EEEEECCCCc---------HHHHHHHHHHHHC----CeEEEEEeCCccc----CCCCCCceEEEEeCCC-CChHHHHHHH
Confidence 3899999998 3445555555543 3445566554421 0012346888889764 7788887764
Q ss_pred HHHHhhhcCCCCceEEEEeCCcchHHHH
Q 008270 111 DMLFWAVDNPAPSNYLLISGDRDFSNAL 138 (571)
Q Consensus 111 DML~WAlDNPpPANIMLISGDrDFS~aL 138 (571)
.+-. .=+|||.|.-++..+
T Consensus 64 ~~~~---------gDiVIT~Di~LAa~~ 82 (151)
T PRK00124 64 LAEK---------GDIVITQDYGLAALA 82 (151)
T ss_pred hCCC---------CCEEEeCCHHHHHHH
Confidence 4322 238899998766543
No 11
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=66.01 E-value=25 Score=30.69 Aligned_cols=93 Identities=19% Similarity=0.220 Sum_probs=54.3
Q ss_pred ceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcC-CCCceEEEEeCC---cchHHHHHHH
Q 008270 66 PVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGD---RDFSNALHQL 141 (571)
Q Consensus 66 pVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDN-PpPANIMLISGD---rDFS~aL~~L 141 (571)
+|-|.+.|....+-..+...|...|+....+... +.+.+...+ .+-+.+++||-. ++...++..+
T Consensus 2 ~I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~~-----------~~~~~~~~~~~~~d~vi~iS~sG~t~~~~~~~~~a 70 (128)
T cd05014 2 KVVVTGVGKSGHIARKIAATLSSTGTPAFFLHPT-----------EALHGDLGMVTPGDVVIAISNSGETDELLNLLPHL 70 (128)
T ss_pred eEEEEeCcHhHHHHHHHHHHhhcCCCceEEcccc-----------hhhccccCcCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 3444444433333344555666667766654221 111111112 334667777754 5788899999
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
|++|-.|+++..... .+|...|+..+..
T Consensus 71 ~~~g~~vi~iT~~~~-s~la~~ad~~l~~ 98 (128)
T cd05014 71 KRRGAPIIAITGNPN-STLAKLSDVVLDL 98 (128)
T ss_pred HHCCCeEEEEeCCCC-CchhhhCCEEEEC
Confidence 999999998875443 4577777766665
No 12
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.34 E-value=43 Score=32.66 Aligned_cols=80 Identities=21% Similarity=0.275 Sum_probs=52.1
Q ss_pred eEEEEEccCCCCCCCCChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHH
Q 008270 30 TSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKIL 109 (571)
Q Consensus 30 TaVFWDIENCPVP~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkML 109 (571)
+-||-|-+.|| |..-|.++.+++|. +|++ .++....+ +.+..|+.+.|-+ ..|++|..|+
T Consensus 2 ~~I~VDADACP---------Vk~~i~r~A~r~~~--~v~~--Van~~~~~------~~~~~i~~v~V~~-g~DaaD~~Iv 61 (150)
T COG1671 2 MTIWVDADACP---------VKDEIYRVAERMGL--KVTF--VANFPHRV------PPSPEIRTVVVDA-GFDAADDWIV 61 (150)
T ss_pred ceEEEeCCCCc---------hHHHHHHHHHHhCC--eEEE--EeCCCccC------CCCCceeEEEecC-CcchHHHHHH
Confidence 46899999998 45567777777665 3444 44443321 1445677777744 4788888776
Q ss_pred HHHHHhhhcCCCCceEEEEeCCcchHHHH
Q 008270 110 VDMLFWAVDNPAPSNYLLISGDRDFSNAL 138 (571)
Q Consensus 110 vDML~WAlDNPpPANIMLISGDrDFS~aL 138 (571)
..+ -..=++||.|.-++..|
T Consensus 62 ~~a---------~~gDlVVT~Di~LA~~l 81 (150)
T COG1671 62 NLA---------EKGDLVVTADIPLASLL 81 (150)
T ss_pred HhC---------CCCCEEEECchHHHHHH
Confidence 432 22338899998887655
No 13
>PLN02714 thiamin pyrophosphokinase
Probab=54.06 E-value=64 Score=32.53 Aligned_cols=82 Identities=20% Similarity=0.225 Sum_probs=51.6
Q ss_pred EEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCC-----ceEEEEe--CCc---chHHHHH
Q 008270 70 SAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAP-----SNYLLIS--GDR---DFSNALH 139 (571)
Q Consensus 70 rAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpP-----ANIMLIS--GDr---DFS~aL~ 139 (571)
.+.||...+..+.++.+.+.|+.++..|. .||..|-.+.+ .||.++.+. ..|+|+- |.| -|+.+..
T Consensus 57 ~iiGDfDSi~~e~~~~~~~~~~~i~~~~~-eKD~TD~e~Al---~~~~~~~~~~~~~~~~I~v~Ga~GGRlDH~laNi~~ 132 (229)
T PLN02714 57 VIKGDMDSIRPEVLDFYSNLGTKIVDESH-DQDTTDLHKCI---AYIRDSTPDLDKSNLCILVLGALGGRFDHEAGNINV 132 (229)
T ss_pred EEEeeccCCCHHHHHHHHHCCCEEEECCC-CcccCHHHHHH---HHHHHhccccccCCceEEEEcccCCchHHHHHHHHH
Confidence 47899999999999999999999887765 57777776654 444443221 2344432 322 3444433
Q ss_pred HHHhCCCeEEEeccCC
Q 008270 140 QLRMRRYNILLAQPHK 155 (571)
Q Consensus 140 ~LR~RGYNILLAqP~~ 155 (571)
.++..+.+|.|+...+
T Consensus 133 L~~~~~~~i~lid~~~ 148 (229)
T PLN02714 133 LYRFPDLRIVLLSDDC 148 (229)
T ss_pred HHhcCCceEEEEcCCc
Confidence 3343566777775444
No 14
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=52.93 E-value=70 Score=32.43 Aligned_cols=107 Identities=18% Similarity=0.187 Sum_probs=71.9
Q ss_pred hHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEE
Q 008270 49 TIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI 128 (571)
Q Consensus 49 ~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLI 128 (571)
.+.+.++..++. .|+|.+...|..-.+-+.+-..|.+.|...+.|-.+.-.--|--|+ .+-+-+++|
T Consensus 27 ~~~~a~~~i~~~---~gkv~V~G~GkSG~Igkk~Aa~L~s~G~~a~fv~p~ea~hgdlg~i----------~~~Dvviai 93 (202)
T COG0794 27 DFVRAVELILEC---KGKVFVTGVGKSGLIGKKFAARLASTGTPAFFVGPAEALHGDLGMI----------TPGDVVIAI 93 (202)
T ss_pred HHHHHHHHHHhc---CCcEEEEcCChhHHHHHHHHHHHHccCCceEEecCchhccCCccCC----------CCCCEEEEE
Confidence 444555555543 6889998888888887778888999999988884211000011111 234778899
Q ss_pred eCCc---chHHHHHHHHhCCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 129 SGDR---DFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 129 SGDr---DFS~aL~~LR~RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
|+.. ....++..+|++|-.|+.+..... +.|...||.++.
T Consensus 94 S~SGeT~el~~~~~~aK~~g~~liaiT~~~~-SsLak~aDvvl~ 136 (202)
T COG0794 94 SGSGETKELLNLAPKAKRLGAKLIAITSNPD-SSLAKAADVVLV 136 (202)
T ss_pred eCCCcHHHHHHHHHHHHHcCCcEEEEeCCCC-ChHHHhcCeEEE
Confidence 9864 567788888999999988874333 357788887665
No 15
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=52.29 E-value=1.2e+02 Score=28.61 Aligned_cols=91 Identities=15% Similarity=0.160 Sum_probs=57.1
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (571)
.+|-|.+.|....+-..+...|...|+.+..+... .+..-.+-+.+++||-. ++...++..+
T Consensus 34 ~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~---------------~~~~~~~~D~vI~iS~sG~t~~~i~~~~~a 98 (179)
T cd05005 34 KRIFVYGAGRSGLVAKAFAMRLMHLGLNVYVVGET---------------TTPAIGPGDLLIAISGSGETSSVVNAAEKA 98 (179)
T ss_pred CeEEEEecChhHHHHHHHHHHHHhCCCeEEEeCCC---------------CCCCCCCCCEEEEEcCCCCcHHHHHHHHHH
Confidence 45666666654433444556677778876665210 01122345677888854 4677788888
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEEec
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWlWe 171 (571)
+++|..|+++..... .+|...|+..+...
T Consensus 99 k~~g~~iI~IT~~~~-s~la~~ad~~l~~~ 127 (179)
T cd05005 99 KKAGAKVVLITSNPD-SPLAKLADVVVVIP 127 (179)
T ss_pred HHCCCeEEEEECCCC-CchHHhCCEEEEeC
Confidence 999999998875433 45777777766543
No 16
>TIGR01378 thi_PPkinase thiamine pyrophosphokinase. This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis, previously designated YloS.
Probab=51.08 E-value=90 Score=30.74 Aligned_cols=89 Identities=18% Similarity=0.307 Sum_probs=56.1
Q ss_pred hcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEE--eCCc---ch
Q 008270 60 KMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI--SGDR---DF 134 (571)
Q Consensus 60 klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLI--SGDr---DF 134 (571)
++|+. =-.+.||...+..+.++.+.+.|+.+...|. .||..|-.+.+ .||.++. +..|+|+ +|.| -+
T Consensus 33 ~~gi~---Pd~iiGDfDSi~~~~~~~~~~~~~~~~~~~~-eKD~TD~e~Al---~~~~~~~-~~~i~i~Ga~GgR~DH~l 104 (203)
T TIGR01378 33 KLGLT---PDLIVGDFDSIDEEELDFYKKAGVKIIVFPP-EKDTTDLELAL---KYALERG-ADEITILGATGGRLDHTL 104 (203)
T ss_pred HCCCC---CCEEEeCcccCCHHHHHHHHHcCCceEEcCC-CCCCCHHHHHH---HHHHHCC-CCEEEEEcCCCCcHHHHH
Confidence 45553 2346799999999999999889999887766 48888876655 4554443 3445554 3433 23
Q ss_pred HHH--HHHHHhCCCeEEEeccCCC
Q 008270 135 SNA--LHQLRMRRYNILLAQPHKA 156 (571)
Q Consensus 135 S~a--L~~LR~RGYNILLAqP~~A 156 (571)
+.+ |.+++.++.+|.|+...+.
T Consensus 105 ani~~L~~~~~~~~~i~l~d~~~~ 128 (203)
T TIGR01378 105 ANLNLLLEYAKRGIKVRLIDEQNV 128 (203)
T ss_pred HHHHHHHHHHhcCCeEEEEcCCcE
Confidence 432 2233345778888765443
No 17
>PF07283 TrbH: Conjugal transfer protein TrbH; InterPro: IPR010837 This entry represents TrbH, a bacterial conjugal transfer protein approximately 150 residues long. TrbH contains a putative membrane lipoprotein lipid attachment site [].
Probab=49.09 E-value=42 Score=31.44 Aligned_cols=54 Identities=24% Similarity=0.367 Sum_probs=36.8
Q ss_pred hhhHHHHHHHHhhhcCCCC-ce-EEEEeCC-cchHHH-HHHHHhCCCeEEEeccCCCC
Q 008270 104 SDKKILVDMLFWAVDNPAP-SN-YLLISGD-RDFSNA-LHQLRMRRYNILLAQPHKAS 157 (571)
Q Consensus 104 ADkkMLvDML~WAlDNPpP-AN-IMLISGD-rDFS~a-L~~LR~RGYNILLAqP~~AS 157 (571)
.+..|..||.......-+| .| |.|--.| ..|..+ +..||.+||-|+-..+....
T Consensus 4 ~~~~iA~D~v~qL~~~ypPA~Tt~~L~q~~~d~Fg~aL~~~LR~~GYaV~e~~~~~~~ 61 (121)
T PF07283_consen 4 DAQAIAGDMVSQLAEQYPPAKTTFELKQKDPDPFGQALENALRAKGYAVIEDDPPDNS 61 (121)
T ss_pred HHHHHHHHHHHHHHHhcCCCccEEEEEcCCCChHHHHHHHHHHhcCcEEEecCCcccc
Confidence 4567889999877665443 33 5552334 468765 57799999999988876543
No 18
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=48.08 E-value=1.3e+02 Score=28.16 Aligned_cols=91 Identities=11% Similarity=0.064 Sum_probs=57.1
Q ss_pred cCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHH
Q 008270 64 CGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQ 140 (571)
Q Consensus 64 ~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~ 140 (571)
.++|-|.+.|....+-..+...|...|+....+... . ...-.+-+-+++||.. ++...++..
T Consensus 30 a~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~-------------~--~~~~~~~Dv~I~iS~sG~t~~~i~~~~~ 94 (179)
T TIGR03127 30 AKRIFVAGAGRSGLVGKAFAMRLMHLGFNVYVVGET-------------T--TPSIKKGDLLIAISGSGETESLVTVAKK 94 (179)
T ss_pred CCEEEEEecCHHHHHHHHHHHHHHhCCCeEEEeCCc-------------c--cCCCCCCCEEEEEeCCCCcHHHHHHHHH
Confidence 355666666654434445566677778766654221 0 0112345667778854 467778888
Q ss_pred HHhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 141 LR~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
++++|-.|+++..... .+|...|+.++.-
T Consensus 95 ak~~g~~ii~IT~~~~-s~la~~ad~~l~~ 123 (179)
T TIGR03127 95 AKEIGATVAAITTNPE-STLGKLADVVVEI 123 (179)
T ss_pred HHHCCCeEEEEECCCC-CchHHhCCEEEEe
Confidence 9999999999875444 4577777766654
No 19
>PF08497 Radical_SAM_N: Radical SAM N-terminal; InterPro: IPR013704 This domain tends to occur to the N terminus of PF04055 from PFAM radical SAM domain in hypothetical bacterial proteins. Proteins in this entry are radical SAM proteins, they catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=47.38 E-value=24 Score=37.76 Aligned_cols=42 Identities=29% Similarity=0.547 Sum_probs=30.0
Q ss_pred HHHHHhhhcCCCCceEEEEeCCc-----chHHHH--HHHHhCCCeE-EEeccC
Q 008270 110 VDMLFWAVDNPAPSNYLLISGDR-----DFSNAL--HQLRMRRYNI-LLAQPH 154 (571)
Q Consensus 110 vDML~WAlDNPpPANIMLISGDr-----DFS~aL--~~LR~RGYNI-LLAqP~ 154 (571)
.||....++. .-|+|||||- .|..+| +-|..+||.| |++||.
T Consensus 7 ~em~~rGWd~---lDvilVtGDAYVDHPsFG~AiIgR~Le~~GyrVgIiaQPd 56 (302)
T PF08497_consen 7 EEMKARGWDE---LDVILVTGDAYVDHPSFGAAIIGRVLEAHGYRVGIIAQPD 56 (302)
T ss_pred HHHHHcCCcc---ccEEEEeCcccccCcchhHHHHHHHHHHcCCeEEEEeCCC
Confidence 3555555553 4589999993 576654 5577899999 788886
No 20
>TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.
Probab=45.84 E-value=71 Score=31.50 Aligned_cols=94 Identities=18% Similarity=0.174 Sum_probs=59.0
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcC-CCCceEEEEeCC---cchHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGD---RDFSNALHQ 140 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDN-PpPANIMLISGD---rDFS~aL~~ 140 (571)
|+|-|.+.|....+-..+...|...|+.+.++.. .++..+...+ .+-+-+++||-. ++-..++..
T Consensus 1 ~rI~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~-----------~~~~~~~~~~~~~~d~~i~iS~sG~t~~~~~~~~~ 69 (268)
T TIGR00393 1 GKLVIVGIGKSGLIGKKIVATFASTGTPSFFLHP-----------TEAMHGDLGMVEPNDVVLMISYSGESLELLNLIPH 69 (268)
T ss_pred CcEEEEecChHHHHHHHHHHHHHhcCCceEEeCH-----------hHHhhcccCCCCCCCEEEEEeCCCCCHHHHHHHHH
Confidence 5666666674444445566678788887776521 1122222222 344667778754 467788889
Q ss_pred HHhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 141 LR~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
++++|..|+.+..... .+|...|+..+.+
T Consensus 70 a~~~g~~ii~iT~~~~-s~l~~~~d~~l~~ 98 (268)
T TIGR00393 70 LKRLSHKIIAFTGSPN-SSLARAADYVLDI 98 (268)
T ss_pred HHHcCCcEEEEECCCC-CcccccCCEEEEc
Confidence 9999999998876443 3466667776665
No 21
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=43.94 E-value=1.3e+02 Score=31.84 Aligned_cols=85 Identities=20% Similarity=0.280 Sum_probs=60.6
Q ss_pred CCCChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccc-hhhHHHHHHHHhhhcCCC
Q 008270 43 KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDA-SDKKILVDMLFWAVDNPA 121 (571)
Q Consensus 43 ~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnA-ADkkMLvDML~WAlDNPp 121 (571)
+|+-+-.|...|++.|=. -.|..|||.-++| .|.|.. .-+....+++.|..++.
T Consensus 13 SGVGGLsVlrei~~~LP~------e~~iY~~D~a~~P------------------YG~ks~e~I~~~~~~i~~~l~~~~- 67 (269)
T COG0796 13 SGVGGLSVLREIRRQLPD------EDIIYVGDTARFP------------------YGEKSEEEIRERTLEIVDFLLERG- 67 (269)
T ss_pred CCCCcHHHHHHHHHHCCC------CcEEEEecCCCCC------------------CCCCCHHHHHHHHHHHHHHHHHcC-
Confidence 688888899988877743 3566789987764 333321 12334566777777666
Q ss_pred CceEEEEeCCcchHHHHHHHHhC-CCeEEEecc
Q 008270 122 PSNYLLISGDRDFSNALHQLRMR-RYNILLAQP 153 (571)
Q Consensus 122 PANIMLISGDrDFS~aL~~LR~R-GYNILLAqP 153 (571)
..++||..+.-.+.+|..||++ ...|+.+.|
T Consensus 68 -ik~lVIACNTASa~al~~LR~~~~iPVvGviP 99 (269)
T COG0796 68 -IKALVIACNTASAVALEDLREKFDIPVVGVIP 99 (269)
T ss_pred -CCEEEEecchHHHHHHHHHHHhCCCCEEEecc
Confidence 7889999999899999999975 677777665
No 22
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=42.93 E-value=1.6e+02 Score=29.44 Aligned_cols=94 Identities=15% Similarity=0.121 Sum_probs=56.1
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (571)
.+|-|.+.|....+-..+...|...|+..... .|..++...+. .-.+.+-+++||-. ++...++..+
T Consensus 129 ~~I~i~G~G~s~~~A~~~~~~l~~~g~~~~~~-------~d~~~~~~~~~---~~~~~Dv~I~iS~sg~~~~~~~~~~~a 198 (278)
T PRK11557 129 RRIILTGIGASGLVAQNFAWKLMKIGINAVAE-------RDMHALLATVQ---ALSPDDLLLAISYSGERRELNLAADEA 198 (278)
T ss_pred CeEEEEecChhHHHHHHHHHHHhhCCCeEEEc-------CChHHHHHHHH---hCCCCCEEEEEcCCCCCHHHHHHHHHH
Confidence 45566666644334445666777788876543 12222222211 23455677777754 3556778888
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
+++|..|+++..... .+|...|+.++.
T Consensus 199 k~~ga~iI~IT~~~~-s~la~~ad~~l~ 225 (278)
T PRK11557 199 LRVGAKVLAITGFTP-NALQQRASHCLY 225 (278)
T ss_pred HHcCCCEEEEcCCCC-CchHHhCCEEEE
Confidence 999999999985443 446667776654
No 23
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=42.92 E-value=2.6e+02 Score=29.65 Aligned_cols=105 Identities=11% Similarity=0.047 Sum_probs=55.9
Q ss_pred CCChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccC-CCccc--------hhhHHHHHHHH
Q 008270 44 NCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPA-GVKDA--------SDKKILVDMLF 114 (571)
Q Consensus 44 G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPa-G~KnA--------ADkkMLvDML~ 114 (571)
-+++..+..-|+.+-+..+....+.|+..++-..+..+.++.|...|+.-+++.- +..+. ....-+.+.+.
T Consensus 72 ~l~~~~l~~ll~~i~~~~~~~~~~e~t~e~~p~~i~~e~l~~l~~~G~~rvslGvQS~~~~~L~~l~R~~s~~~~~~a~~ 151 (375)
T PRK05628 72 LLGAEGLARVLDAVRDTFGLAPGAEVTTEANPESTSPEFFAALRAAGFTRVSLGMQSAAPHVLAVLDRTHTPGRAVAAAR 151 (375)
T ss_pred cCCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCCCCHHHHHHHHHcCCCEEEEecccCCHHHHHHcCCCCCHHHHHHHHH
Confidence 3444444443333222234433456777888777888899999999998777741 11100 01112334445
Q ss_pred hhhcCCCC-ceEEEEeC---C--cchHHHHHHHHhCCCeE
Q 008270 115 WAVDNPAP-SNYLLISG---D--RDFSNALHQLRMRRYNI 148 (571)
Q Consensus 115 WAlDNPpP-ANIMLISG---D--rDFS~aL~~LR~RGYNI 148 (571)
.+....-+ -++-||.| . .+|...|..+.+.+..-
T Consensus 152 ~l~~~g~~~v~~dli~GlPgqt~~~~~~tl~~~~~l~~~~ 191 (375)
T PRK05628 152 EARAAGFEHVNLDLIYGTPGESDDDWRASLDAALEAGVDH 191 (375)
T ss_pred HHHHcCCCcEEEEEeccCCCCCHHHHHHHHHHHHhcCCCE
Confidence 55444333 45555654 1 35666666655555433
No 24
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=42.05 E-value=2e+02 Score=29.15 Aligned_cols=94 Identities=17% Similarity=0.153 Sum_probs=56.5
Q ss_pred ceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHHH
Q 008270 66 PVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQLR 142 (571)
Q Consensus 66 pVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~LR 142 (571)
+|-|.++|....+-..+...|...|+....+. |..++..... .-.+-+-+++||.. ++...++..++
T Consensus 142 ~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~-------d~~~~~~~~~---~~~~~Dl~I~iS~sG~t~~~~~~~~~ak 211 (292)
T PRK11337 142 QRDLYGAGGSAAIARDVQHKFLRIGVRCQAYD-------DAHIMLMSAA---LLQEGDVVLVVSHSGRTSDVIEAVELAK 211 (292)
T ss_pred eEEEEEecHHHHHHHHHHHHHhhCCCeEEEcC-------CHHHHHHHHh---cCCCCCEEEEEeCCCCCHHHHHHHHHHH
Confidence 45566666544344445566777787766542 2222211111 12345667888854 45677788889
Q ss_pred hCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 143 MRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 143 ~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
.+|-.|+++..... .+|...|+.++.-
T Consensus 212 ~~g~~ii~IT~~~~-s~la~~ad~~l~~ 238 (292)
T PRK11337 212 KNGAKIICITNSYH-SPIAKLADYVICS 238 (292)
T ss_pred HCCCeEEEEeCCCC-ChhHHhCCEEEEc
Confidence 99999999975443 4577777776653
No 25
>PF02590 SPOUT_MTase: Predicted SPOUT methyltransferase; InterPro: IPR003742 This family of proteins are predicted to be SPOUT methyltransferases []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1VH0_E 4FAK_A 1TO0_G 1O6D_A 1NS5_B.
Probab=40.33 E-value=2e+02 Score=27.68 Aligned_cols=41 Identities=12% Similarity=0.167 Sum_probs=27.9
Q ss_pred chHHHHHHHHhCCC-eEEE-ec-cCCCChhHHhhcCeEEEechh
Q 008270 133 DFSNALHQLRMRRY-NILL-AQ-PHKASAPLVAAAKSVWLWTSL 173 (571)
Q Consensus 133 DFS~aL~~LR~RGY-NILL-Aq-P~~AS~~L~aaAd~vWlWeSL 173 (571)
+|+..|..+...|. +|.+ +. +...+..+...|+..|....|
T Consensus 84 ~fA~~l~~~~~~g~~~i~F~IGG~~G~~~~~~~~a~~~lSLS~m 127 (155)
T PF02590_consen 84 EFAKKLERWMNQGKSDIVFIIGGADGLSEEVRKRADEKLSLSKM 127 (155)
T ss_dssp HHHHHHHHHHHTTS-EEEEEE-BTTB--HHHHHH-SEEEES-SS
T ss_pred HHHHHHHHHHhcCCceEEEEEecCCCCCHHHHhhcCceEEEecC
Confidence 79999999999887 7644 44 555778899889977766544
No 26
>cd07995 TPK Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Probab=38.70 E-value=1.7e+02 Score=28.58 Aligned_cols=88 Identities=23% Similarity=0.345 Sum_probs=55.5
Q ss_pred HHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEe--CCc---
Q 008270 58 LVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS--GDR--- 132 (571)
Q Consensus 58 L~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLIS--GDr--- 132 (571)
|.++|+.- -.+.||...+..+.++.+.+.|+.+++.|. .||..|-.+.+. +|.+... ..|+++- |.|
T Consensus 35 l~~~gi~P---d~iiGDfDSi~~~~~~~~~~~~~~~~~~p~-~KD~TD~e~Al~---~~~~~~~-~~i~i~Ga~GgR~DH 106 (208)
T cd07995 35 LLDLGIVP---DLIIGDFDSISPEVLEYYKSKGVEIIHFPD-EKDFTDFEKALK---LALERGA-DEIVILGATGGRLDH 106 (208)
T ss_pred HHHcCCCC---CEEEecCcCCCHHHHHHHHhcCCeEEECCC-CCCCCHHHHHHH---HHHHcCC-CEEEEEccCCCcHHH
Confidence 44455542 246799999988999999999999999987 677788766544 4444322 4555544 332
Q ss_pred chHHH--HHHHHhCCCeEEEecc
Q 008270 133 DFSNA--LHQLRMRRYNILLAQP 153 (571)
Q Consensus 133 DFS~a--L~~LR~RGYNILLAqP 153 (571)
-++.+ |.+++..+.+|.++..
T Consensus 107 ~lani~~l~~~~~~~~~~~l~d~ 129 (208)
T cd07995 107 TLANLNLLLKYAKDGIKIVLIDE 129 (208)
T ss_pred HHHHHHHHHHHHhcCCeEEEEcC
Confidence 23332 2233335777877754
No 27
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=38.58 E-value=1.9e+02 Score=25.10 Aligned_cols=48 Identities=17% Similarity=0.086 Sum_probs=33.9
Q ss_pred CCceEEEEeCC---cchHHHHHHHHhCCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 121 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 121 pPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
+.+-+++||-. ++-..++..++++|..|+.+.... ..+|...|+..+.
T Consensus 46 ~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~~-~s~la~~ad~~l~ 96 (126)
T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVV-GSTLAREADYVLY 96 (126)
T ss_pred CCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECCC-CChHHHhCCEEEE
Confidence 44567778754 356677888899999999887543 3467777776554
No 28
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=38.57 E-value=1.7e+02 Score=29.94 Aligned_cols=94 Identities=23% Similarity=0.248 Sum_probs=61.8
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhh-hcCCCCceEEEEeCC---cchHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWA-VDNPAPSNYLLISGD---RDFSNALHQ 140 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WA-lDNPpPANIMLISGD---rDFS~aL~~ 140 (571)
++|-|.+.|....+-..+...|...|+...++.. .+++.+. ..-.+.+-+++||.. .+...++..
T Consensus 43 ~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~-----------~~~~~~~~~~~~~~d~~i~iS~sG~t~~~~~~~~~ 111 (321)
T PRK11543 43 GKVVVSGIGKSGHIGKKIAATLASTGTPAFFVHP-----------AEALHGDLGMIESRDVMLFISYSGGAKELDLIIPR 111 (321)
T ss_pred CcEEEEecChhHHHHHHHHHHHHcCCCceeecCh-----------HHHhhCCcCccCCCCEEEEEeCCCCcHHHHHHHHH
Confidence 4577777775555556667788888887776521 1122111 122455778888865 466778888
Q ss_pred HHhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 141 LR~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
++++|-.|+.+..... .+|...|+.++.-
T Consensus 112 ak~~g~~vI~iT~~~~-s~la~~ad~~l~~ 140 (321)
T PRK11543 112 LEDKSIALLAMTGKPT-SPLGLAAKAVLDI 140 (321)
T ss_pred HHHcCCeEEEEECCCC-ChhHHhCCEEEEc
Confidence 8999999999886444 4588888877654
No 29
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=38.42 E-value=2.7e+02 Score=27.76 Aligned_cols=94 Identities=12% Similarity=0.151 Sum_probs=54.3
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (571)
.+|.|.+.|....+-..+...|...|+...... |..+. . +. +..-.+-+.+++||-- .+...++...
T Consensus 129 ~~I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~-------~~~~~-~-~~-~~~~~~~D~vI~iS~sG~t~~~~~~~~~a 198 (284)
T PRK11302 129 KKISFFGLGASAAVAHDAQNKFFRFNVPVVYFD-------DIVMQ-R-MS-CMNSSDGDVVVLISHTGRTKSLVELAQLA 198 (284)
T ss_pred CeEEEEEcchHHHHHHHHHHHHHhcCCceEecC-------CHHHH-H-HH-HHhCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 345555555333332334445666787666431 11111 1 11 1122345677888854 3567778888
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
+++|-.|+++.. . ..+|...|+.++.-
T Consensus 199 k~~g~~vI~IT~-~-~s~l~~~ad~~l~~ 225 (284)
T PRK11302 199 RENGATVIAITS-A-GSPLAREATLALTL 225 (284)
T ss_pred HHcCCeEEEECC-C-CChhHHhCCEEEec
Confidence 999999999985 3 45688888877654
No 30
>cd08502 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=37.51 E-value=33 Score=36.75 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=29.0
Q ss_pred hhcCCCCCCChhHHHHHHHHHHHhHHHHhhcCce
Q 008270 488 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGAL 521 (571)
Q Consensus 488 ir~gd~k~~~~dv~kal~~aie~~~v~~~~~g~~ 521 (571)
+...++-+.+.+|||||..||-.+.|+++.+|-.
T Consensus 254 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g~ 287 (472)
T cd08502 254 FNHLQPPFDNPKIRRAVLAALDQEDLLAAAVGDP 287 (472)
T ss_pred EcCCCCCCcCHHHHHHHHHhcCHHHHHHHHhCCC
Confidence 4445777899999999999999999999988654
No 31
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=36.73 E-value=2.9e+02 Score=26.93 Aligned_cols=49 Identities=12% Similarity=0.093 Sum_probs=35.2
Q ss_pred CCCceEEEEeCC---cchHHHHHHHHhCCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 120 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 120 PpPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
.+.+-+++||.. ++-..++..++.+|-.|+.+..... .+|...++.++.
T Consensus 110 ~~~Dv~I~iS~SG~t~~~i~~~~~ak~~g~~iI~iT~~~~-s~l~~~ad~~l~ 161 (192)
T PRK00414 110 REGDVLLGISTSGNSGNIIKAIEAARAKGMKVITLTGKDG-GKMAGLADIEIR 161 (192)
T ss_pred CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCC-ChhHHhCCEEEE
Confidence 445677888865 4677788888999999998875433 457777776654
No 32
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=36.69 E-value=3.2e+02 Score=26.80 Aligned_cols=113 Identities=22% Similarity=0.282 Sum_probs=57.6
Q ss_pred ceEEEEEccCCCCCCCCC--hhhHHHHHHHHHHhcCccCceEEEEEecC----CCCC-hhHHHHhhhcCCce-eeccCCC
Q 008270 29 KTSVWWDIENCQVPKNCD--PHTIAQNISSALVKMNYCGPVSISAYGDT----NRIP-ASVQHALSSTGIAL-NHVPAGV 100 (571)
Q Consensus 29 kTaVFWDIENCPVP~G~d--a~~Va~NIr~AL~klGY~GpVTIrAYGD~----s~ip-~~vl~aLsSSGISL-ihVPaG~ 100 (571)
--+|..|.+||=++.+-+ ...+...++...+. +....|.| +-+. .+.. .++...-...||.+ .|. ..
T Consensus 41 ik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~-~~~~~v~I--vSNsaGs~~d~~~~~a~~~~~~lgIpvl~h~--~k 115 (168)
T PF09419_consen 41 IKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQ-FGKDRVLI--VSNSAGSSDDPDGERAEALEKALGIPVLRHR--AK 115 (168)
T ss_pred ceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHH-CCCCeEEE--EECCCCcccCccHHHHHHHHHhhCCcEEEeC--CC
Confidence 358899999998764333 12344444433322 21112433 3332 1111 22222234458884 453 12
Q ss_pred ccchhhHHHHHHHHhhhcC---CCCceEEEEeCCcchHHHHHHHHhCCCeEEEe
Q 008270 101 KDASDKKILVDMLFWAVDN---PAPSNYLLISGDRDFSNALHQLRMRRYNILLA 151 (571)
Q Consensus 101 KnAADkkMLvDML~WAlDN---PpPANIMLISGDrDFS~aL~~LR~RGYNILLA 151 (571)
|-... .+++.|...+ -.|.. +++-||+=|...|-.-++--|.|++-
T Consensus 116 KP~~~----~~i~~~~~~~~~~~~p~e-iavIGDrl~TDVl~gN~~G~~tilv~ 164 (168)
T PF09419_consen 116 KPGCF----REILKYFKCQKVVTSPSE-IAVIGDRLFTDVLMGNRMGSYTILVT 164 (168)
T ss_pred CCccH----HHHHHHHhhccCCCCchh-EEEEcchHHHHHHHhhccCceEEEEe
Confidence 33222 2444443333 12444 44559999999998888777888764
No 33
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=36.62 E-value=2.8e+02 Score=28.45 Aligned_cols=90 Identities=18% Similarity=0.197 Sum_probs=57.4
Q ss_pred EEEEe--cCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHHHh
Q 008270 69 ISAYG--DTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQLRM 143 (571)
Q Consensus 69 IrAYG--D~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~LR~ 143 (571)
|..|| -..-+-.++...|..-|+.+..+. |..++. | .+....+-+-+++||-. ++...++...++
T Consensus 133 I~~~G~g~S~~vA~~~~~~l~~ig~~~~~~~-------d~~~~~-~--~~~~~~~~Dv~i~iS~sG~t~e~i~~a~~ak~ 202 (281)
T COG1737 133 IYFFGLGSSGLVASDLAYKLMRIGLNVVALS-------DTHGQL-M--QLALLTPGDVVIAISFSGYTREIVEAAELAKE 202 (281)
T ss_pred EEEEEechhHHHHHHHHHHHHHcCCceeEec-------chHHHH-H--HHHhCCCCCEEEEEeCCCCcHHHHHHHHHHHH
Confidence 44455 333345667778888999888763 333444 2 22334455667777754 366778888899
Q ss_pred CCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 144 RRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 144 RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
+|..||.+..... .+|...|+.++.
T Consensus 203 ~ga~vIaiT~~~~-spla~~Ad~~L~ 227 (281)
T COG1737 203 RGAKVIAITDSAD-SPLAKLADIVLL 227 (281)
T ss_pred CCCcEEEEcCCCC-CchhhhhceEEe
Confidence 9999999975433 457777765544
No 34
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=35.80 E-value=3.8e+02 Score=26.68 Aligned_cols=103 Identities=20% Similarity=0.361 Sum_probs=62.0
Q ss_pred CCCCCCh-hhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHH--hhh
Q 008270 41 VPKNCDP-HTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLF--WAV 117 (571)
Q Consensus 41 VP~G~da-~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~--WAl 117 (571)
||+.+.+ +..++++..-|.+.| +..++||-....+.. .-.=.|+.|+++|...... -..|+-|++. +|+
T Consensus 12 IPa~YGGfET~ve~L~~~l~~~g----~~v~Vyc~~~~~~~~---~~~y~gv~l~~i~~~~~g~-~~si~yd~~sl~~al 83 (185)
T PF09314_consen 12 IPARYGGFETFVEELAPRLVSKG----IDVTVYCRSDYYPYK---EFEYNGVRLVYIPAPKNGS-AESIIYDFLSLLHAL 83 (185)
T ss_pred CCcccCcHHHHHHHHHHHHhcCC----ceEEEEEccCCCCCC---CcccCCeEEEEeCCCCCCc-hHHHHHHHHHHHHHH
Confidence 7877775 467888888887644 356677765443211 1122699999998654332 3456666543 444
Q ss_pred c----CCCCceEEEEeCCc---chHHHHHHHHhCCCeEEEe
Q 008270 118 D----NPAPSNYLLISGDR---DFSNALHQLRMRRYNILLA 151 (571)
Q Consensus 118 D----NPpPANIMLISGDr---DFS~aL~~LR~RGYNILLA 151 (571)
. +.--.-+++|-+-. -|...+..|+.+|..|++-
T Consensus 84 ~~~~~~~~~~~ii~ilg~~~g~~~~~~~r~~~~~g~~v~vN 124 (185)
T PF09314_consen 84 RFIKQDKIKYDIILILGYGIGPFFLPFLRKLRKKGGKVVVN 124 (185)
T ss_pred HHHhhccccCCEEEEEcCCccHHHHHHHHhhhhcCCcEEEC
Confidence 2 21122366666643 3566777888888777764
No 35
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=35.64 E-value=52 Score=35.54 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=34.4
Q ss_pred CCCceEEEEeC-CcchHHHHHH-HHhCCCeEEEeccCC-CChhHHhhc
Q 008270 120 PAPSNYLLISG-DRDFSNALHQ-LRMRRYNILLAQPHK-ASAPLVAAA 164 (571)
Q Consensus 120 PpPANIMLISG-DrDFS~aL~~-LR~RGYNILLAqP~~-AS~~L~aaA 164 (571)
+.....||||| |..|...|.+ |-++||+|+..+... ..+.|...+
T Consensus 26 ~~~~k~VlITGCDSGfG~~LA~~L~~~Gf~V~Agcl~~~gae~L~~~~ 73 (322)
T KOG1610|consen 26 SLSDKAVLITGCDSGFGRLLAKKLDKKGFRVFAGCLTEEGAESLRGET 73 (322)
T ss_pred ccCCcEEEEecCCcHHHHHHHHHHHhcCCEEEEEeecCchHHHHhhhh
Confidence 45788999997 8899997755 889999999999543 335566544
No 36
>PRK15482 transcriptional regulator MurR; Provisional
Probab=35.05 E-value=3.9e+02 Score=27.06 Aligned_cols=95 Identities=12% Similarity=0.097 Sum_probs=57.6
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (571)
.+|-|.+.|....+-..+...|...|..+.... |..+...+ +..-.+-+-+++||-. ++...++..+
T Consensus 136 ~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~-------d~~~~~~~---~~~~~~~Dv~i~iS~sg~t~~~~~~~~~a 205 (285)
T PRK15482 136 PFIQITGLGGSALVGRDLSFKLMKIGYRVACEA-------DTHVQATV---SQALKKGDVQIAISYSGSKKEIVLCAEAA 205 (285)
T ss_pred CeeEEEEeChhHHHHHHHHHHHHhCCCeeEEec-------cHhHHHHH---HhcCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 446666666544444445666777787665432 12222111 2222345778888865 4667788888
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
+++|-.|+++..... .+|...|+..+.-
T Consensus 206 ~~~g~~iI~IT~~~~-s~la~~ad~~l~~ 233 (285)
T PRK15482 206 RKQGATVIAITSLAD-SPLRRLAHFTLDT 233 (285)
T ss_pred HHCCCEEEEEeCCCC-CchHHhCCEEEEc
Confidence 899999998875443 4577777766654
No 37
>PLN02625 uroporphyrin-III C-methyltransferase
Probab=34.90 E-value=1.9e+02 Score=29.40 Aligned_cols=88 Identities=17% Similarity=0.117 Sum_probs=51.1
Q ss_pred ccccCCCCCCcchhhhhhcCCceEEEEEc----------cCCCC---C--CCC---ChhhHHHHHHHHHHhcCccCceEE
Q 008270 8 TVTASVSAPMASTAERQYVTAKTSVWWDI----------ENCQV---P--KNC---DPHTIAQNISSALVKMNYCGPVSI 69 (571)
Q Consensus 8 ~~~~~~~~~~~~~a~~rya~AkTaVFWDI----------ENCPV---P--~G~---da~~Va~NIr~AL~klGY~GpVTI 69 (571)
|+|-|++..-|-++......+.+.+..+. .++.+ . .+. .-..+...|...+++ | ..|.+
T Consensus 21 G~GpGdp~~LTl~a~~~l~~ADvI~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-g--~~Vvv 97 (263)
T PLN02625 21 GTGPGDPDLLTLKALRLLQTADVVLYDRLVSPDILDLVPPGAELLYVGKRGGYHSRTQEEIHELLLSFAEA-G--KTVVR 97 (263)
T ss_pred EeCCCChHHhHHHHHHHHhcCCEEEEeCcCCHHHHHhcCCCCEEEecCCcCCccccCHHHHHHHHHHHHHC-C--CeEEE
Confidence 55667777788888888888888887653 11110 0 001 112233334443332 2 35777
Q ss_pred EEEecCCCC--ChhHHHHhhhcCCceeeccC
Q 008270 70 SAYGDTNRI--PASVQHALSSTGIALNHVPA 98 (571)
Q Consensus 70 rAYGD~s~i--p~~vl~aLsSSGISLihVPa 98 (571)
-+.||-.-+ ...+.+.|...|+.+.-+|.
T Consensus 98 l~~GDP~~ys~~~~l~~~l~~~~~~veiiPG 128 (263)
T PLN02625 98 LKGGDPLVFGRGGEEMDALRKNGIPVTVVPG 128 (263)
T ss_pred EcCCCchhhhhHHHHHHHHHHCCCCEEEECC
Confidence 788986433 23355667777887777775
No 38
>PF10450 POC1: POC1 chaperone; InterPro: IPR018855 This entry represents fungal proteosome chaperone 1, a chaperone of the 20S proteasome which functions in early 20S proteasome assembly [].
Probab=34.38 E-value=24 Score=37.14 Aligned_cols=72 Identities=32% Similarity=0.470 Sum_probs=52.8
Q ss_pred CCCchhhhHHHHHHHHHHhhhhcc----ccCCCCcccchhhhcCCCCCCChhHHHHHHHHHHHhHHHHhhcC-ceeeeec
Q 008270 452 LTPSEYVQGLIGVILLALNTLKIE----RVVPSEANITDCIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLG-ALPLYVP 526 (571)
Q Consensus 452 ~~p~~~~qgli~vil~al~~lk~e----~~~pte~ni~dcir~gd~k~~~~dv~kal~~aie~~~v~~~~~g-~~~ly~~ 526 (571)
.+|-|.|-|.+|-||.+|..-+.. -|+|.|..+ |=-|+.+..+ +.+| -|+++.|| .-.-|+-
T Consensus 186 L~PPeFITG~~asvlsqL~~~~~~~~~~lVv~SEGp~------GfEK~~~~~i----~dl~---~v~~~~l~~~~~~Y~~ 252 (273)
T PF10450_consen 186 LQPPEFITGFIASVLSQLLSKEVPVFTALVVPSEGPI------GFEKLDLDTI----VDLI---DVCGQVLGFDSEEYVK 252 (273)
T ss_pred cCCccHhHhHHHHHHHHhhccCCCceeEEEecCCCCC------CceecCHHHH----HHHH---HHHHHHhCCChHHHHH
Confidence 378899999999999999443333 578999887 6666655433 3333 36778888 4456998
Q ss_pred CCCccceeec
Q 008270 527 KNEKLWNCEN 536 (571)
Q Consensus 527 kn~~lw~cvn 536 (571)
.=-++|||--
T Consensus 253 ~~~r~wk~~~ 262 (273)
T PF10450_consen 253 ECYRLWKLDG 262 (273)
T ss_pred HHHHHhhhcc
Confidence 8889999976
No 39
>PRK15473 cbiF cobalt-precorrin-4 C(11)-methyltransferase; Provisional
Probab=33.40 E-value=2.7e+02 Score=28.21 Aligned_cols=88 Identities=14% Similarity=0.177 Sum_probs=54.4
Q ss_pred ccccCCCCCCcchhhhhhcCCceEEEEE-------ccCCCC-----C-CCCChhhHHHHHHHHHHhcCccCceEEEEEec
Q 008270 8 TVTASVSAPMASTAERQYVTAKTSVWWD-------IENCQV-----P-KNCDPHTIAQNISSALVKMNYCGPVSISAYGD 74 (571)
Q Consensus 8 ~~~~~~~~~~~~~a~~rya~AkTaVFWD-------IENCPV-----P-~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD 74 (571)
|+|-|++-.-|-++......+.+.+..+ .+-++. . ...+...+...|+..+++ | ..|.+-+-||
T Consensus 14 G~GpG~~~~lT~~A~~~L~~advv~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~-g--~~Vv~L~sGD 90 (257)
T PRK15473 14 GAGPGDKELITLKGYRLLQQAQVVIYAGSLINTELLDYCPAQAECHDSAELHLEQIIDLMEAGVKA-G--KTVVRLQTGD 90 (257)
T ss_pred EeCCCChHHhhHHHHHHHHhCCEEEEecccCCHHHHhhcCCCCEEEecCCCCHHHHHHHHHHHHHC-C--CeEEEEeCcC
Confidence 5566666678888888888999988876 221211 0 011223445555555543 1 2577777898
Q ss_pred CCCCC--hhHHHHhhhcCCceeeccC
Q 008270 75 TNRIP--ASVQHALSSTGIALNHVPA 98 (571)
Q Consensus 75 ~s~ip--~~vl~aLsSSGISLihVPa 98 (571)
-.-+. ..+.++|...||.+.-+|.
T Consensus 91 P~~yg~~~~l~~~l~~~~i~veiiPG 116 (257)
T PRK15473 91 VSLYGSIREQGEELTKRGIDFQVVPG 116 (257)
T ss_pred chhhhhHHHHHHHHHHCCCCEEEeCC
Confidence 65432 3566778778888877775
No 40
>COG3233 Predicted deacetylase [General function prediction only]
Probab=32.40 E-value=1e+02 Score=32.06 Aligned_cols=23 Identities=17% Similarity=0.224 Sum_probs=20.4
Q ss_pred CCcchHHHHHHHHhCCCeEEEec
Q 008270 130 GDRDFSNALHQLRMRRYNILLAQ 152 (571)
Q Consensus 130 GDrDFS~aL~~LR~RGYNILLAq 152 (571)
.|..|+..|++++++||.++|=.
T Consensus 52 ~d~rf~~~l~~r~e~Gdel~lHG 74 (233)
T COG3233 52 KDPRFVDLLTEREEEGDELVLHG 74 (233)
T ss_pred cChHHHHHHHHHHhcCCEEEEec
Confidence 57789999999999999998853
No 41
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=32.31 E-value=2.4e+02 Score=27.72 Aligned_cols=42 Identities=24% Similarity=0.279 Sum_probs=32.3
Q ss_pred cchHHHHHHHHhCCCeEEEe--ccCCCChhHHhhcCeEEEechh
Q 008270 132 RDFSNALHQLRMRRYNILLA--QPHKASAPLVAAAKSVWLWTSL 173 (571)
Q Consensus 132 rDFS~aL~~LR~RGYNILLA--qP~~AS~~L~aaAd~vWlWeSL 173 (571)
..|+..|..|+..|-+|.++ .+..-++.+...|+..|....|
T Consensus 83 e~fA~~l~~~~~~G~~i~f~IGG~~Gl~~~~~~~a~~~~sls~l 126 (155)
T COG1576 83 EEFADFLERLRDDGRDISFLIGGADGLSEAVKARADQVLSLSKL 126 (155)
T ss_pred HHHHHHHHHHHhcCCeEEEEEeCcccCCHHHHHHHhhheecccc
Confidence 37999999999988766443 3666788899988888777554
No 42
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=31.85 E-value=4.4e+02 Score=24.75 Aligned_cols=50 Identities=14% Similarity=0.058 Sum_probs=35.9
Q ss_pred CCCceEEEEeCC---cchHHHHHHHHhCCCeEEEeccCCCChhHHhhcCeEEEe
Q 008270 120 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (571)
Q Consensus 120 PpPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~~AS~~L~aaAd~vWlW 170 (571)
.+.+-+++||.- ++-..++..++++|-.|+.+.....+ +|...|+..+..
T Consensus 100 ~~~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s-~La~~aD~~l~~ 152 (177)
T cd05006 100 QPGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGG-KLLELADIEIHV 152 (177)
T ss_pred CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCC-chhhhCCEEEEe
Confidence 344667777742 57788899999999999988754443 477778776554
No 43
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=31.42 E-value=4.8e+02 Score=26.15 Aligned_cols=100 Identities=11% Similarity=0.193 Sum_probs=48.8
Q ss_pred hhHHHHHHHHHHhcCccCc-----e------EEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCccchhhHHHH
Q 008270 48 HTIAQNISSALVKMNYCGP-----V------SISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILV 110 (571)
Q Consensus 48 ~~Va~NIr~AL~klGY~Gp-----V------TIrAY-GD~s~-----ip~~vl~aLsSSGISLihVPaG~KnAADkkMLv 110 (571)
......|..+++++||.-. + +|-+. .++.. +-..+.+++...|..+..+.... +. .-..
T Consensus 35 ~~tr~~V~~~a~elgY~p~~~a~~l~~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~~-~~---~~~~ 110 (342)
T PRK10014 35 TATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQGGK-DG---EQLA 110 (342)
T ss_pred HHHHHHHHHHHHHhCCCcCHHHHhhccCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeCCC-CH---HHHH
Confidence 3467788899999999531 0 12111 22221 12234455666676665543321 11 1112
Q ss_pred HHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEec
Q 008270 111 DMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (571)
Q Consensus 111 DML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq 152 (571)
+++..... ...+-|++...+......+..|+..+..|+++.
T Consensus 111 ~~~~~l~~-~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~ 151 (342)
T PRK10014 111 QRFSTLLN-QGVDGVVIAGAAGSSDDLREMAEEKGIPVVFAS 151 (342)
T ss_pred HHHHHHHh-CCCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEe
Confidence 22222222 124555555444334456677777777776664
No 44
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=30.83 E-value=5.3e+02 Score=25.74 Aligned_cols=99 Identities=9% Similarity=0.118 Sum_probs=51.0
Q ss_pred hHHHHHHHHHHhcCccCc-----------eEEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCccchhhHHHHH
Q 008270 49 TIAQNISSALVKMNYCGP-----------VSISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILVD 111 (571)
Q Consensus 49 ~Va~NIr~AL~klGY~Gp-----------VTIrAY-GD~s~-----ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvD 111 (571)
+....|..+++++||.-. -+|-.. .++.. +-..+.+++...|..+..+...........++..
T Consensus 32 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~~~~~~~~ 111 (327)
T TIGR02417 32 ETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDDNPDQEKVVIEN 111 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHH
Confidence 466778888989998531 022111 23222 1233555667778887765432211111122222
Q ss_pred HHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEec
Q 008270 112 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (571)
Q Consensus 112 ML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq 152 (571)
+ ..+ ..+-|+++..+......+..|+..+..|+++.
T Consensus 112 l----~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~ 147 (327)
T TIGR02417 112 L----LAR-QVDALIVASCMPPEDAYYQKLQNEGLPVVALD 147 (327)
T ss_pred H----HHc-CCCEEEEeCCCCCChHHHHHHHhcCCCEEEEc
Confidence 2 222 23446665544323455677777788887775
No 45
>PF06073 DUF934: Bacterial protein of unknown function (DUF934); InterPro: IPR008318 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.33 E-value=1.1e+02 Score=28.30 Aligned_cols=52 Identities=21% Similarity=0.258 Sum_probs=35.4
Q ss_pred CCCCCChhhHHHHHHHHHH-hcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCC
Q 008270 41 VPKNCDPHTIAQNISSALV-KMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAG 99 (571)
Q Consensus 41 VP~G~da~~Va~NIr~AL~-klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG 99 (571)
+|.=.|++ .-.+-+.|+ ++||.| .|+|.||.- .+-+.-|..+|+.-..++.+
T Consensus 27 FP~F~DGR--gfS~ArlLR~r~gy~G--elRA~Gdvl---~DQl~~l~R~GFdsf~l~~~ 79 (110)
T PF06073_consen 27 FPKFTDGR--GFSQARLLRERYGYTG--ELRAVGDVL---RDQLFYLRRCGFDSFELRED 79 (110)
T ss_pred CCCcCCch--HhHHHHHHHHHcCCCC--cEEEeccch---HHHHHHHHHcCCCEEEeCCC
Confidence 45444543 223445566 889999 689999963 35566788999988887653
No 46
>TIGR01675 plant-AP plant acid phosphatase. This model explicitly excludes the VSPs which lack the nucleophilc aspartate. The possibility exists, however, that some members of this family may, while containing all of the conserved HAD-superfamily catalytic residues, lack activity and have a function related to the function of the VSPs rather than the acid phosphatases.
Probab=30.08 E-value=1.9e+02 Score=29.63 Aligned_cols=70 Identities=14% Similarity=0.120 Sum_probs=39.7
Q ss_pred hHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEe-CCcc------hHHHHHHHHhCCCeEEEecc
Q 008270 81 SVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS-GDRD------FSNALHQLRMRRYNILLAQP 153 (571)
Q Consensus 81 ~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLIS-GDrD------FS~aL~~LR~RGYNILLAqP 153 (571)
++.+.|.+.|+.++.+ .|+...-....+..+....+ +.-..++|=. +|.. -+.....|...||+|++..-
T Consensus 127 ~l~~~l~~~G~~Vf~l-TGR~e~~r~~T~~nL~~~G~--~~~~~LiLR~~~d~~~~~~~yKs~~R~~l~~~GYrIv~~iG 203 (229)
T TIGR01675 127 KLYQKIIELGIKIFLL-SGRWEELRNATLDNLINAGF--TGWKHLILRGLEDSNKTVVTYKSEVRKSLMEEGYRIWGNIG 203 (229)
T ss_pred HHHHHHHHCCCEEEEE-cCCChHHHHHHHHHHHHcCC--CCcCeeeecCCCCCCchHhHHHHHHHHHHHhCCceEEEEEC
Confidence 3667788999999998 44433221222222222221 2225666654 3432 33455578889999998764
No 47
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=29.85 E-value=1.5e+02 Score=28.53 Aligned_cols=44 Identities=20% Similarity=0.347 Sum_probs=28.7
Q ss_pred hcCCceeeccCCCccchhhHHHHHHHHhhhcCCC-CceEEEEeCCcchHHH
Q 008270 88 STGIALNHVPAGVKDASDKKILVDMLFWAVDNPA-PSNYLLISGDRDFSNA 137 (571)
Q Consensus 88 SSGISLihVPaG~KnAADkkMLvDML~WAlDNPp-PANIMLISGDrDFS~a 137 (571)
..||++++.+.|. .||..|. +++. +... +..++|+|+|......
T Consensus 65 ~~gi~Vvft~~~~--tAD~~Ie-~~v~---~~~~~~~~v~VVTSD~~iq~~ 109 (166)
T PF05991_consen 65 YGGIEVVFTKEGE--TADDYIE-RLVR---ELKNRPRQVTVVTSDREIQRA 109 (166)
T ss_pred eCceEEEECCCCC--CHHHHHH-HHHH---HhccCCCeEEEEeCCHHHHHH
Confidence 3799999987643 5776544 3332 3333 6899999999754443
No 48
>PRK10294 6-phosphofructokinase 2; Provisional
Probab=29.68 E-value=4.2e+02 Score=26.71 Aligned_cols=44 Identities=14% Similarity=0.186 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeec
Q 008270 50 IAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHV 96 (571)
Q Consensus 50 Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihV 96 (571)
..-|+-.+|.++|.. ...|.+.|+ ..-..+++.|...||.+.++
T Consensus 40 ~~~NvA~~l~~lG~~-~~~i~~vG~--~~g~~i~~~l~~~gv~~~~~ 83 (309)
T PRK10294 40 GGINVARAIAHLGGS-ATAIFPAGG--ATGEHLVSLLADENVPVATV 83 (309)
T ss_pred cHHHHHHHHHHcCCC-eEEEEEecC--ccHHHHHHHHHHcCCCceEE
Confidence 345677788888763 124556676 45566888999999976665
No 49
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=29.21 E-value=2.3e+02 Score=27.17 Aligned_cols=73 Identities=18% Similarity=0.285 Sum_probs=45.6
Q ss_pred eEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCC
Q 008270 67 VSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRY 146 (571)
Q Consensus 67 VTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGY 146 (571)
+.|-|.|+ ...++|...|+...++|...-++ ..| .+++. ....+..++++.|+..=..+...|+++|+
T Consensus 74 ~~i~avG~------~Ta~~l~~~G~~~~~~~~~~~~s--~~L-~~~l~---~~~~~~~vl~~~g~~~~~~l~~~L~~~g~ 141 (231)
T PF02602_consen 74 IKIFAVGP------KTAEALREYGFQPDFVPSSEGSS--EGL-AELLK---EQLRGKRVLILRGEGGRPDLPEKLREAGI 141 (231)
T ss_dssp SEEEESSH------HHHHHHHHTT-EECEE-TTSSSH--HHH-HGGHH---HCCTTEEEEEEESSSSCHHHHHHHHHTTE
T ss_pred CeEEEEcH------HHHHHHHHcCCCccccCCCCCCH--HHH-HHHHH---hhCCCCeEEEEcCCCccHHHHHHHHHCCC
Confidence 34555555 45678888899988887633332 122 23222 24445889999998766667788999998
Q ss_pred eEEEe
Q 008270 147 NILLA 151 (571)
Q Consensus 147 NILLA 151 (571)
+|.-+
T Consensus 142 ~v~~~ 146 (231)
T PF02602_consen 142 EVTEV 146 (231)
T ss_dssp EEEEE
T ss_pred eEEEE
Confidence 88443
No 50
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=29.14 E-value=1.1e+02 Score=29.80 Aligned_cols=53 Identities=21% Similarity=0.308 Sum_probs=36.5
Q ss_pred chhhHHHHHHHHhhhcC-CCCceEEEEeCC-c-chHHH-HHHHHhCCCeEEEeccCC
Q 008270 103 ASDKKILVDMLFWAVDN-PAPSNYLLISGD-R-DFSNA-LHQLRMRRYNILLAQPHK 155 (571)
Q Consensus 103 AADkkMLvDML~WAlDN-PpPANIMLISGD-r-DFS~a-L~~LR~RGYNILLAqP~~ 155 (571)
.....|-.||....... ||-.|.+.|--| . .|..+ +..||.+||-|+--.+..
T Consensus 31 ~~a~~iA~D~v~qL~~~ypPA~Tt~~l~q~~~D~Fg~aL~~aLR~~GYaV~e~~~~~ 87 (151)
T PRK13883 31 ADQQKLATDAVQQLATLYPPAQTRFELQQPTPDAFGQALVKALRDKGYALLEYNPAG 87 (151)
T ss_pred HHHHHHHHHHHHHHHHhCCCcceEEEEecCCCcHHHHHHHHHHHHcCeEEEecCCcc
Confidence 45677999999876655 444444444443 4 68775 577999999999766543
No 51
>PRK07334 threonine dehydratase; Provisional
Probab=28.87 E-value=1.6e+02 Score=31.77 Aligned_cols=94 Identities=16% Similarity=0.176 Sum_probs=58.6
Q ss_pred CChhhHHHHHHHHHHhcCccCceEEEEEe-cCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCc
Q 008270 45 CDPHTIAQNISSALVKMNYCGPVSISAYG-DTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPS 123 (571)
Q Consensus 45 ~da~~Va~NIr~AL~klGY~GpVTIrAYG-D~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPA 123 (571)
.+...+..-+..+|...||. +.|.+.+ |...+-.++...|...++.|..+-.. ++... ..+....-
T Consensus 307 ~d~~~l~~il~~~l~~~~y~--v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~-~~~~~----------~~~~~~~i 373 (403)
T PRK07334 307 IDTRLLANVLLRGLVRAGRL--ARLRVDIRDRPGALARVTALIGEAGANIIEVSHQ-RLFTD----------LPAKGAEL 373 (403)
T ss_pred CCHHHHHHHHHHHHHhCCCE--EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEE-ecccC----------CCCCeEEE
Confidence 56777777788888888884 4555443 34445577888898899988876321 00000 00011122
Q ss_pred eEEEEeCC-cchHHHHHHHHhCCCeEEEe
Q 008270 124 NYLLISGD-RDFSNALHQLRMRRYNILLA 151 (571)
Q Consensus 124 NIMLISGD-rDFS~aL~~LR~RGYNILLA 151 (571)
+|.|-..| ..+..++.+||..||.|-|+
T Consensus 374 ~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 374 ELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred EEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 33343345 47889999999999998775
No 52
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=28.64 E-value=1.4e+02 Score=31.16 Aligned_cols=67 Identities=18% Similarity=0.281 Sum_probs=41.8
Q ss_pred EEccCCCCCCCCChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhh--------cCCceeec-cCCCc
Q 008270 34 WDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSS--------TGIALNHV-PAGVK 101 (571)
Q Consensus 34 WDIENCPVP~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsS--------SGISLihV-PaG~K 101 (571)
.-+||+.-|.. +-..+..-++..|.++.-.+.|.|+..||.+.+|.++++++.. .|+.|.-+ ..|.+
T Consensus 80 FS~eN~~R~~~-Ev~~Lm~L~~~~l~~~~~~~~irv~~iG~~~~lp~~~~~~~~~~e~~T~~~~~~~Lnia~~Yggr 155 (256)
T PRK14828 80 LSTDNLGRPSE-ELNPLLDIIEDVVRQLAPDGRWRVRHVGSLDLLPAPSANRLKEAEEATVGNDGIKVNVAVGYGGR 155 (256)
T ss_pred EEhhhcCCCHH-HHHHHHHHHHHHHHHHHHhCCeEEEEECChhhCCHHHHHHHHHHHHhhcCCCCcEEEEEecCCCH
Confidence 45799976631 1122344455555543334568999999999999998887754 35655553 34433
No 53
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=28.61 E-value=51 Score=27.02 Aligned_cols=19 Identities=42% Similarity=0.494 Sum_probs=14.1
Q ss_pred HHHHHHHHhcCccCceEEE
Q 008270 52 QNISSALVKMNYCGPVSIS 70 (571)
Q Consensus 52 ~NIr~AL~klGY~GpVTIr 70 (571)
..|-++|+..||.|.|+|-
T Consensus 3 ~~i~~~L~~~GYdG~~siE 21 (55)
T PF07582_consen 3 KRIFSALREIGYDGWLSIE 21 (55)
T ss_dssp HHHHHHHHHTT--SEEEE-
T ss_pred HHHHHHHHHcCCCceEEEE
Confidence 4688999999999999985
No 54
>PRK13835 conjugal transfer protein TrbH; Provisional
Probab=28.57 E-value=1.3e+02 Score=29.34 Aligned_cols=50 Identities=16% Similarity=0.186 Sum_probs=33.6
Q ss_pred ccchhhHHHHHHHHhhhc-CCCCceEEEEeCC-cchHHH-HHHHHhCCCeEEE
Q 008270 101 KDASDKKILVDMLFWAVD-NPAPSNYLLISGD-RDFSNA-LHQLRMRRYNILL 150 (571)
Q Consensus 101 KnAADkkMLvDML~WAlD-NPpPANIMLISGD-rDFS~a-L~~LR~RGYNILL 150 (571)
...+...|.-||..-... .||-.+-+.+--| ..|..+ +..||.+||.|+=
T Consensus 35 t~~aa~~iA~D~vsqLae~~pPa~tt~~l~q~~d~Fg~aL~~aLr~~GYaVvt 87 (145)
T PRK13835 35 SGPAASAIAGDMVSRLAEQIGPGTTTIKLKKDTSPFGQALEAALKGWGYAVVT 87 (145)
T ss_pred cchHHHHHHHHHHHHHHHhcCCCceEEEEeecCcHHHHHHHHHHHhcCeEEee
Confidence 345677899999875544 4444444444443 568775 5679999999994
No 55
>PF10965 DUF2767: Protein of unknown function (DUF2767); InterPro: IPR024493 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=28.19 E-value=1.1e+02 Score=26.57 Aligned_cols=53 Identities=21% Similarity=0.127 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHHhhhhccccCCCCcccchhhhc---CCCCCCChhHHHHHHHHHHH
Q 008270 458 VQGLIGVILLALNTLKIERVVPSEANITDCIRY---GEPKHRNTDVRKALNCAIEQ 510 (571)
Q Consensus 458 ~qgli~vil~al~~lk~e~~~pte~ni~dcir~---gd~k~~~~dv~kal~~aie~ 510 (571)
.|..-+||=-|.=.|-.+-.-|+-.+|+|-+|- ...-.+.-+..+|+|.||+.
T Consensus 11 Y~EmCRVVGd~Vl~L~~~G~etk~~~Ia~~LrT~l~~~~~kr~~~~~~~me~aI~~ 66 (69)
T PF10965_consen 11 YQEMCRVVGDAVLELADLGHETKRIVIADVLRTELANGRSKRSELQQQAMELAIDL 66 (69)
T ss_pred HHHHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHhccccccCHHHHHHHHHHHHH
Confidence 344444444444445566677899999999997 55667788999999999975
No 56
>PRK01254 hypothetical protein; Provisional
Probab=27.88 E-value=1e+02 Score=36.62 Aligned_cols=41 Identities=24% Similarity=0.550 Sum_probs=29.2
Q ss_pred HHHHhhhcCCCCceEEEEeCCc-----chHHHH--HHHHhCCCeE-EEeccC
Q 008270 111 DMLFWAVDNPAPSNYLLISGDR-----DFSNAL--HQLRMRRYNI-LLAQPH 154 (571)
Q Consensus 111 DML~WAlDNPpPANIMLISGDr-----DFS~aL--~~LR~RGYNI-LLAqP~ 154 (571)
||-...||- .-|+|||||- .|..+| +-|...||.| |++||.
T Consensus 31 em~~~Gwd~---~DiilVtGDAYVDHPsFG~AiigR~Le~~G~rVgIiaQPd 79 (707)
T PRK01254 31 EMDQLGWDS---CDIIIVTGDAYVDHPSFGMAIIGRMLEAQGFRVGIIAQPD 79 (707)
T ss_pred HHHHcCCCc---cCEEEEeCcccccCccchHHHHHHHHHHcCCeEEEEeCCC
Confidence 455555553 4589999993 576654 5577899999 888886
No 57
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=27.55 E-value=5.3e+02 Score=24.37 Aligned_cols=100 Identities=18% Similarity=0.275 Sum_probs=52.8
Q ss_pred CChhhHHHHHHHH---HHhc-CccCceEEEEEecCCCCChhHHHHhhhcCCceeecc--CCC-ccchhhHHHHHHHHhhh
Q 008270 45 CDPHTIAQNISSA---LVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP--AGV-KDASDKKILVDMLFWAV 117 (571)
Q Consensus 45 ~da~~Va~NIr~A---L~kl-GY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVP--aG~-KnAADkkMLvDML~WAl 117 (571)
.+...+...|.++ |++. |..-+.-.--||.. ...+++.|...|+.++.-- ..+ .......|+..+ .
T Consensus 74 ~~~~~~~~ei~~~~~~l~~~~g~~~~~fr~P~G~~---~~~~~~~l~~~G~~~v~w~~~~~D~~~~~~~~i~~~~----~ 146 (191)
T TIGR02764 74 LEDEKIKKDILRAQEIIEKLTGKKPTLFRPPSGAF---NKAVLKAAESLGYTVVHWSVDSRDWKNPGVESIVDRV----V 146 (191)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCCEEECCCcCC---CHHHHHHHHHcCCeEEEecCCCCccCCCCHHHHHHHH----H
Confidence 4455555556553 3332 22211222334554 3567888888999877642 111 111222333333 3
Q ss_pred cCCCCceEEEEe--CCc-----chHHHHHHHHhCCCeEEEe
Q 008270 118 DNPAPSNYLLIS--GDR-----DFSNALHQLRMRRYNILLA 151 (571)
Q Consensus 118 DNPpPANIMLIS--GDr-----DFS~aL~~LR~RGYNILLA 151 (571)
++-.+..|||+= ++. -+..+|..|+.+||.++-+
T Consensus 147 ~~~~~g~Iil~Hd~~~~~~t~~~l~~~i~~l~~~Gy~~vtl 187 (191)
T TIGR02764 147 KNTKPGDIILLHASDSAKQTVKALPTIIKKLKEKGYEFVTI 187 (191)
T ss_pred hcCCCCCEEEEeCCCCcHhHHHHHHHHHHHHHHCCCEEEEH
Confidence 343445566655 222 3566788999999998643
No 58
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=27.00 E-value=4.3e+02 Score=30.36 Aligned_cols=93 Identities=12% Similarity=0.069 Sum_probs=54.7
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (571)
.+|-|.++|....+-..+...|...|+..+... |..+.. ..+..-.+-+-+++||-- .+...++..+
T Consensus 469 ~rI~i~G~G~S~~~A~~~~~~l~~lg~~~~~~~-------d~~~~~---~~~~~l~~~DvvI~iS~sG~t~e~i~~~~~A 538 (638)
T PRK14101 469 RRIEFYGLGNSNIVAQDAHYKFFRFGIPTIAYG-------DLYMQA---ASAALLGKGDVIVAVSKSGRAPELLRVLDVA 538 (638)
T ss_pred CEEEEEEccHHHHHHHHHHHHHhcCCceEEEcC-------CHHHHH---HHHhcCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 345555555443333445556777787665431 111111 111122344667778854 3566778888
Q ss_pred HhCCCeEEEeccCCCChhHHhhcCeEEE
Q 008270 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (571)
Q Consensus 142 R~RGYNILLAqP~~AS~~L~aaAd~vWl 169 (571)
+++|-.|+++.. . ..+|...|+.++.
T Consensus 539 k~~Ga~vIaIT~-~-~spLa~~aD~~L~ 564 (638)
T PRK14101 539 MQAGAKVIAITS-S-NTPLAKRATVALE 564 (638)
T ss_pred HHCCCeEEEEcC-C-CChhHhhCCEEEE
Confidence 899999999986 3 4668888886653
No 59
>cd08491 PBP2_NikA_DppA_OppA_like_12 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=26.92 E-value=46 Score=35.68 Aligned_cols=31 Identities=32% Similarity=0.429 Sum_probs=26.8
Q ss_pred cCCCCCCChhHHHHHHHHHHHhHHHHhhcCc
Q 008270 490 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (571)
Q Consensus 490 ~gd~k~~~~dv~kal~~aie~~~v~~~~~g~ 520 (571)
...+...+..|||||..||-.+.|+++.++-
T Consensus 239 ~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 269 (473)
T cd08491 239 AQIPPLDDVRVRKALNLAIDRDGIVGALFGG 269 (473)
T ss_pred CCCCcccCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 3467789999999999999999999987753
No 60
>PF10740 DUF2529: Protein of unknown function (DUF2529); InterPro: IPR019676 This entry represents a protein family conserved in the Bacillales. Their function is not known. ; PDB: 3JX9_A.
Probab=26.56 E-value=1.9e+02 Score=28.90 Aligned_cols=102 Identities=17% Similarity=0.119 Sum_probs=49.4
Q ss_pred HHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeC
Q 008270 51 AQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISG 130 (571)
Q Consensus 51 a~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISG 130 (571)
++.+.+|+- =-|.|-|.+|++..-+ ...+|.+ .+-. +. -+++.-|.-.|. +--+-+.++|+|.
T Consensus 28 ARlLAQA~v---geG~IYi~G~~Em~~v---~~~Al~g--~E~l------~~--~k~l~~~~~~~~-~lt~~DRVllfs~ 90 (172)
T PF10740_consen 28 ARLLAQAIV---GEGTIYIYGFGEMEAV---EAEALYG--AEPL------PS--AKRLSEDLENFD-ELTETDRVLLFSP 90 (172)
T ss_dssp HHHHHHHHH---TT--EEEEE-GGGGGG---HHHHHCS--TT--------TT--EEE--TT---------TT-EEEEEES
T ss_pred HHHHHHHHh---cCCEEEEEecChHHHH---HHHHHcC--CCCC------ch--hhcCcccccccc-cccccceEEEEeC
Confidence 344444443 2477889999998765 2334432 2110 10 111111221111 1124578899886
Q ss_pred C---cchHHHHHHHHhCCCeEEEec-cCCCChhHHhhcCeEEE
Q 008270 131 D---RDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWL 169 (571)
Q Consensus 131 D---rDFS~aL~~LR~RGYNILLAq-P~~AS~~L~aaAd~vWl 169 (571)
. .+-..++.+|...|..+++++ .......|...++.++.
T Consensus 91 ~~~~~e~~~~a~~L~~~gi~~v~Vs~~~~~~~~l~~~~~~~Id 133 (172)
T PF10740_consen 91 FSTDEEAVALAKQLIEQGIPFVGVSPNKPDEEDLEDLADVHID 133 (172)
T ss_dssp -S--HHHHHHHHHHHHHT--EEEEE-SS---TTGGG-SSS-EE
T ss_pred CCCCHHHHHHHHHHHHCCCCEEEEEecCCCCCchhhhhhheee
Confidence 4 467889999999999999999 44566678887776665
No 61
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=26.53 E-value=5.8e+02 Score=25.41 Aligned_cols=99 Identities=11% Similarity=0.054 Sum_probs=51.3
Q ss_pred hHHHHHHHHHHhcCccCc-----------eEEEEEe-cCCC-----CChhHHHHhhhcCCceeeccCCCccchhhHHHHH
Q 008270 49 TIAQNISSALVKMNYCGP-----------VSISAYG-DTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILVD 111 (571)
Q Consensus 49 ~Va~NIr~AL~klGY~Gp-----------VTIrAYG-D~s~-----ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvD 111 (571)
.....|..+++++||.-. -+|-... ++.. +-..+.+++...|+.+..+.... +. + -..+
T Consensus 33 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~-~~-~--~~~~ 108 (328)
T PRK11303 33 KTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDD-QP-D--NEMR 108 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCC-CH-H--HHHH
Confidence 466788899999999531 0222221 2221 12345556677888877653321 11 1 1112
Q ss_pred HHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEec
Q 008270 112 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (571)
Q Consensus 112 ML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq 152 (571)
++.+.... ..+-|++.+.+..-...+..|...+..|+++.
T Consensus 109 ~~~~l~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~v~ 148 (328)
T PRK11303 109 CAEHLLQR-QVDALIVSTSLPPEHPFYQRLQNDGLPIIALD 148 (328)
T ss_pred HHHHHHHc-CCCEEEEcCCCCCChHHHHHHHhcCCCEEEEC
Confidence 33332222 34555655543333455677777788887775
No 62
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=26.47 E-value=49 Score=35.09 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=25.6
Q ss_pred CCCCCCChhHHHHHHHHHHHhHHHHhhcC
Q 008270 491 GEPKHRNTDVRKALNCAIEQHMVIKRSLG 519 (571)
Q Consensus 491 gd~k~~~~dv~kal~~aie~~~v~~~~~g 519 (571)
..+.+.+..|||||..||..+.++++.++
T Consensus 243 ~~~~~~d~~vRkAl~~aidr~~i~~~~~~ 271 (454)
T cd08496 243 TGAPFDDPKVRQAINYAIDRKAFVDALLF 271 (454)
T ss_pred CCCCCCCHHHHHHHHhhcCHHHHHHHHhc
Confidence 34678899999999999999999998876
No 63
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=26.00 E-value=2.2e+02 Score=30.39 Aligned_cols=43 Identities=14% Similarity=0.135 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhc-CccCceEEEEEecCCCCChhHHHHhhhcCCceee
Q 008270 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNH 95 (571)
Q Consensus 50 Va~NIr~AL~kl-GY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLih 95 (571)
|..+|+.+.+.+ ...+ .|..||++=+- ..+.+.|...||..++
T Consensus 15 V~rAi~~a~~~~~~~~~--~iytlG~iIHN-~~vv~~L~~~GV~~v~ 58 (298)
T PRK01045 15 VDRAIEIVERALEKYGA--PIYVRHEIVHN-RYVVERLEKKGAIFVE 58 (298)
T ss_pred HHHHHHHHHHHHHhcCC--CeEEEecCccC-HHHHHHHHHCCCEEec
Confidence 666676665432 2223 35778988664 4688899999998775
No 64
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=25.95 E-value=1e+02 Score=29.71 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=34.0
Q ss_pred HHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeEEEecc
Q 008270 84 HALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQP 153 (571)
Q Consensus 84 ~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP 153 (571)
+.|...||....+|. - -||..|-.-+..+.. . -..++|+|+|+||.-++ ..+.+|.+..+
T Consensus 93 ~~l~~~gi~~~~~~g-~--EADDvIatla~~~~~-~--~~~v~IvS~DkD~~QLv----~~~~~V~~~~~ 152 (169)
T PF02739_consen 93 ELLEALGIPVLEVPG-Y--EADDVIATLAKKASE-E--GFEVIIVSGDKDLLQLV----DENVNVYLLDP 152 (169)
T ss_dssp HHHHHTTSEEEEETT-B---HHHHHHHHHHHHHH-T--TCEEEEE-SSGGGGGGT----CS-TSEEEEET
T ss_pred HHHHHCCCCEecCCC-C--cHHHHHHHHHhhhcc-C--CCEEEEEcCCCCHHHhc----CCCceEEEeec
Confidence 345567888877763 2 145544433333332 2 35789999999987544 33456666655
No 65
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=25.86 E-value=4.7e+02 Score=24.35 Aligned_cols=51 Identities=10% Similarity=0.045 Sum_probs=35.5
Q ss_pred CCCceEEEEeCC---cchHHHHHHHHhCCCeEEEeccCCCChhHHhhcCeEEEec
Q 008270 120 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (571)
Q Consensus 120 PpPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~~AS~~L~aaAd~vWlWe 171 (571)
.+-+-+++||.. .+-..++..++++|-.|+.+.... ..+|...|+.++.-.
T Consensus 78 ~~~D~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~-~s~l~~~ad~~l~~~ 131 (154)
T TIGR00441 78 QKGDVLLGISTSGNSKNVLKAIEAAKDKGMKTITLAGKD-GGKMAGLADIELRVP 131 (154)
T ss_pred CCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCC-CCchhhhCCEEEEeC
Confidence 445678888865 356677888899999999887533 345667777666543
No 66
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=25.67 E-value=6.9e+02 Score=26.52 Aligned_cols=53 Identities=6% Similarity=0.120 Sum_probs=32.0
Q ss_pred CChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 008270 45 CDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (571)
Q Consensus 45 ~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVP 97 (571)
+++..+..-++.+-+..+..+.+.|+..++-..+..+.++.|...|+.-+.+.
T Consensus 65 l~~~~l~~ll~~i~~~~~~~~~~eit~e~~p~~l~~e~l~~l~~~G~~rvsiG 117 (377)
T PRK08599 65 LSAEQLERLLTAIHRNLPLSGLEEFTFEANPGDLTKEKLQVLKDSGVNRISLG 117 (377)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCCCCHHHHHHHHHcCCCEEEEe
Confidence 44444444343333333443334566666766777888899999998777664
No 67
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=25.65 E-value=7.3e+02 Score=27.38 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=32.8
Q ss_pred CCCChhhHHHHHHHHHHh-cCccCceEEEEEecCCCCChhHHHHhhhcCCceeec
Q 008270 43 KNCDPHTIAQNISSALVK-MNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHV 96 (571)
Q Consensus 43 ~G~da~~Va~NIr~AL~k-lGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihV 96 (571)
..+++..+..-+ .+|++ +.......|+..++-..+..+.++.|...||.-+.+
T Consensus 126 s~L~~~~l~~ll-~~i~~~~~l~~~~eitiE~~p~~~t~e~l~~l~~aGvnRiSi 179 (449)
T PRK09058 126 TALSAEDLARLI-TALREYLPLAPDCEITLEGRINGFDDEKADAALDAGANRFSI 179 (449)
T ss_pred ccCCHHHHHHHH-HHHHHhCCCCCCCEEEEEeCcCcCCHHHHHHHHHcCCCEEEe
Confidence 344554444433 33333 233333567888887778888888888888876665
No 68
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=25.41 E-value=6.7e+02 Score=26.45 Aligned_cols=107 Identities=13% Similarity=0.112 Sum_probs=59.4
Q ss_pred HHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhh-cCCceeeccCCCccchhhHHHHHHHHhhhcCCCC-ceEEEEe
Q 008270 52 QNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSS-TGIALNHVPAGVKDASDKKILVDMLFWAVDNPAP-SNYLLIS 129 (571)
Q Consensus 52 ~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsS-SGISLihVPaG~KnAADkkMLvDML~WAlDNPpP-ANIMLIS 129 (571)
..|...|.+.+. -+|.|.+.|.....-...+..|.. .++.+..... .++..+...+..+ +-++.||
T Consensus 33 ~~~~~~l~~~~~-~~I~~~g~GsS~~aa~~~~~~~~k~~~i~v~~~~~-----------~~~~~~~~~~~~~~~lvI~iS 100 (340)
T PRK11382 33 HAIVEEMVKRDI-DRIYFVACGSPLNAAQTAKHLADRFSDLQVYAISG-----------WEFCDNTPYRLDDRCAVIGVS 100 (340)
T ss_pred HHHHHHHHhCCC-CEEEEEEechHHHHHHHHHHHHHHHcCCCeEEecc-----------HHHHhcCCcCCCCCCEEEEEc
Confidence 345555554333 256777777765433333322322 2433222111 1222332223334 4466676
Q ss_pred --CC-cchHHHHHHHHhCCCeEEEeccCCCChhHHhhcCeEEEec
Q 008270 130 --GD-RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (571)
Q Consensus 130 --GD-rDFS~aL~~LR~RGYNILLAqP~~AS~~L~aaAd~vWlWe 171 (571)
|. .|-..++..++.+|..||.+.... .++|...|+.++...
T Consensus 101 ~SGeT~e~i~al~~ak~~Ga~~I~IT~~~-~S~L~~~ad~~l~~~ 144 (340)
T PRK11382 101 DYGKTEEVIKALELGRACGALTAAFTKRA-DSPITSAAEFSIDYQ 144 (340)
T ss_pred CCCCCHHHHHHHHHHHHcCCeEEEEECCC-CChHHHhCCEEEEeC
Confidence 33 578889999999999888887543 346888888887765
No 69
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.08 E-value=4.5e+02 Score=30.11 Aligned_cols=19 Identities=32% Similarity=0.459 Sum_probs=10.4
Q ss_pred ccccCCCCCCCCCCCCCCCC
Q 008270 304 FRNQHLLRPNNFPMQPNFPQ 323 (571)
Q Consensus 304 ~~~~~~~rp~~~~~~~~~~~ 323 (571)
+||..|.-|. |+|+++|.+
T Consensus 416 ~qNyppp~p~-f~m~~~hP~ 434 (483)
T KOG2236|consen 416 QQNYPPPSPS-FPMFQPHPP 434 (483)
T ss_pred cCCCCCCCCC-CCccCCCCC
Confidence 4455555555 667755443
No 70
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=24.73 E-value=4.4e+02 Score=26.64 Aligned_cols=112 Identities=16% Similarity=0.077 Sum_probs=56.0
Q ss_pred EEEEEcc--CCCCC-CCCChhhHHHHHHHHHHhcCccCceEEEEEecCCC-C----ChhHHHHhhhcCCceee--ccCCC
Q 008270 31 SVWWDIE--NCQVP-KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNR-I----PASVQHALSSTGIALNH--VPAGV 100 (571)
Q Consensus 31 aVFWDIE--NCPVP-~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~-i----p~~vl~aLsSSGISLih--VPaG~ 100 (571)
.||+|-. ++.++ -+.|-+.....+...|.++|++ .|-+-. +.... . -..++++|...|+.+.. +-.+.
T Consensus 141 vV~i~~~~~~~~~~~V~~D~~~~~~~a~~~L~~~G~~-~I~~i~-~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~ 218 (346)
T PRK10401 141 MVLINRVVPGYAHRCVCLDNVSGARMATRMLLNNGHQ-RIGYLS-SSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGT 218 (346)
T ss_pred EEEEecccCCCCCCEEEECcHHHHHHHHHHHHHCCCC-eEEEEe-CCCcCcchHHHHHHHHHHHHHcCCCCChhheecCC
Confidence 5888843 33332 1334444455555666677764 343211 22211 1 13366788888876432 11111
Q ss_pred ccc-hhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeE
Q 008270 101 KDA-SDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNI 148 (571)
Q Consensus 101 KnA-ADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNI 148 (571)
-+. .....+.. |...++.| +-++..+|.--..++..|+++|+.|
T Consensus 219 ~~~~~~~~~~~~---~l~~~~~~-~ai~~~nd~~A~g~~~al~~~G~~v 263 (346)
T PRK10401 219 PDMQGGEAAMVE---LLGRNLQL-TAVFAYNDNMAAGALTALKDNGIAI 263 (346)
T ss_pred CChHHHHHHHHH---HHcCCCCC-cEEEECCcHHHHHHHHHHHHcCCCC
Confidence 110 11122222 32233434 4556667776678899999999864
No 71
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=24.54 E-value=91 Score=29.62 Aligned_cols=54 Identities=15% Similarity=0.087 Sum_probs=40.9
Q ss_pred hhhHHHHHHHHHHhhhhccccCCCCcccchhhhcCCCCCCChhHHHHHHHHHHH
Q 008270 457 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGEPKHRNTDVRKALNCAIEQ 510 (571)
Q Consensus 457 ~~qgli~vil~al~~lk~e~~~pte~ni~dcir~gd~k~~~~dv~kal~~aie~ 510 (571)
+.-..+++|=.++.....+.+.-+|+.|.||.+.++-.=..-+..+||+-++|+
T Consensus 26 wAfa~~~~ie~~~~i~~~~~~~lS~q~l~~C~~~~~~gC~GG~~~~a~~~~~~~ 79 (174)
T smart00645 26 WAFSATGALEGRYCIKTGKLVSLSEQQLVDCSTGGNNGCNGGLPDNAFEYIKKN 79 (174)
T ss_pred HHHHHHHHHHHHHHHhcCCccccCHHHHhhhcCCCCCCCCCcCHHHHHHHHHHc
Confidence 555677777666666666789999999999998744333467788999988887
No 72
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=24.37 E-value=65 Score=32.61 Aligned_cols=30 Identities=30% Similarity=0.584 Sum_probs=24.8
Q ss_pred CCCCCCChhHHHHHHHHHHHhHHHHhhcCc
Q 008270 491 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (571)
Q Consensus 491 gd~k~~~~dv~kal~~aie~~~v~~~~~g~ 520 (571)
..+=..+.+|||||..||..+++++..++-
T Consensus 211 ~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 240 (374)
T PF00496_consen 211 NNPPFSDKAVRQALAYAIDREAIVKNIFGG 240 (374)
T ss_dssp TSTTTTSHHHHHHHHHHS-HHHHHHHTTTT
T ss_pred cccccchhhhHHHHHhhhhHHHHHHHHHhh
Confidence 356678899999999999999999998643
No 73
>cd01174 ribokinase Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides and histidine, and for entry into the pentose phosphate pathway. Ribokinase is dimeric in solution.
Probab=23.29 E-value=5.4e+02 Score=25.26 Aligned_cols=44 Identities=25% Similarity=0.329 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhcCccCceE-EEEEecCCCCChhHHHHhhhcCCceeec
Q 008270 50 IAQNISSALVKMNYCGPVS-ISAYGDTNRIPASVQHALSSTGIALNHV 96 (571)
Q Consensus 50 Va~NIr~AL~klGY~GpVT-IrAYGD~s~ip~~vl~aLsSSGISLihV 96 (571)
..-|+-..|.++|. ++. +.+.|+.. ....+++.|...||.+.++
T Consensus 38 ~~~NvA~~l~~lG~--~~~~~~~vG~D~-~g~~i~~~l~~~gi~~~~~ 82 (292)
T cd01174 38 KGANQAVAAARLGA--RVAMIGAVGDDA-FGDELLENLREEGIDVSYV 82 (292)
T ss_pred cHHHHHHHHHHcCC--ceEEEEEEcCCc-cHHHHHHHHHHcCCCceEE
Confidence 45688888999875 453 56667543 3356888999999988776
No 74
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=23.18 E-value=75 Score=33.79 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=24.7
Q ss_pred CCCCCChhHHHHHHHHHHHhHHHHhhcC
Q 008270 492 EPKHRNTDVRKALNCAIEQHMVIKRSLG 519 (571)
Q Consensus 492 d~k~~~~dv~kal~~aie~~~v~~~~~g 519 (571)
.+-..+.+|||||..||-.+.|++..++
T Consensus 261 ~~~~~d~~vR~Ai~~aidr~~i~~~~~~ 288 (484)
T cd08492 261 RPPFDDVRVRQALQLAIDREAIVETVFF 288 (484)
T ss_pred CCCCCCHHHHHHHHHhhhHHHHHHHHhc
Confidence 4667899999999999999999998775
No 75
>cd08519 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=23.11 E-value=59 Score=34.76 Aligned_cols=33 Identities=24% Similarity=0.424 Sum_probs=26.8
Q ss_pred hhcCCCCCCChhHHHHHHHHHHHhHHHHhhcCc
Q 008270 488 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (571)
Q Consensus 488 ir~gd~k~~~~dv~kal~~aie~~~v~~~~~g~ 520 (571)
+..-.+-..+..|||||..||-.+.|+++.++-
T Consensus 248 ~N~~~~~~~d~~vRkAl~~aiDr~~i~~~~~~g 280 (469)
T cd08519 248 FNVNQPPLDNLAVRQALAYLIDRDLIVNRVYYG 280 (469)
T ss_pred EeCCCCCCCCHHHHHHHHHHcCHHHHHHHHHhc
Confidence 344456677899999999999999999987643
No 76
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=22.80 E-value=63 Score=33.70 Aligned_cols=30 Identities=30% Similarity=0.573 Sum_probs=25.8
Q ss_pred CCCCCCChhHHHHHHHHHHHhHHHHhhcCc
Q 008270 491 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (571)
Q Consensus 491 gd~k~~~~dv~kal~~aie~~~v~~~~~g~ 520 (571)
..+-..+.+|||||..||..+.+++..+|.
T Consensus 248 ~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 277 (466)
T cd00995 248 NKPPFDDKRVRQAISYAIDREEIIDAVLGG 277 (466)
T ss_pred CCCCCCCHHHHHHHHHhcCHHHHHHHHHhC
Confidence 345678999999999999999999988753
No 77
>PRK09997 hydroxypyruvate isomerase; Provisional
Probab=22.55 E-value=6.7e+02 Score=24.84 Aligned_cols=76 Identities=13% Similarity=0.107 Sum_probs=42.4
Q ss_pred HHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCcee--eccCCCcc-------------chhhHHHHHHHH
Q 008270 50 IAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALN--HVPAGVKD-------------ASDKKILVDMLF 114 (571)
Q Consensus 50 Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLi--hVPaG~Kn-------------AADkkMLvDML~ 114 (571)
+...|+ .+.++||.| |.|..+.+ .-..++++.|.+.|+++. ++|.+.-. .....-+.+++.
T Consensus 17 l~~~l~-~~a~~Gf~~-VEl~~~~~--~~~~~~~~~l~~~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 92 (258)
T PRK09997 17 FLARFE-KAAQCGFRG-VEFMFPYD--YDIEELKQVLASNKLEHTLHNLPAGDWAAGERGIACIPGREEEFRDGVAAAIR 92 (258)
T ss_pred HHHHHH-HHHHhCCCE-EEEcCCCC--CCHHHHHHHHHHcCCcEEEEcCCCCccccCcCccccCCCcHHHHHHHHHHHHH
Confidence 333344 445679977 66643222 235678889999999986 45543211 111233567777
Q ss_pred hhhcCCCCceEEEEeC
Q 008270 115 WAVDNPAPSNYLLISG 130 (571)
Q Consensus 115 WAlDNPpPANIMLISG 130 (571)
+|..-..+ .|++.+|
T Consensus 93 ~a~~lga~-~i~~~~g 107 (258)
T PRK09997 93 YARALGNK-KINCLVG 107 (258)
T ss_pred HHHHhCCC-EEEECCC
Confidence 77555444 4555554
No 78
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=22.42 E-value=66 Score=34.13 Aligned_cols=29 Identities=21% Similarity=0.461 Sum_probs=25.2
Q ss_pred CCCCCChhHHHHHHHHHHHhHHHHhhcCc
Q 008270 492 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (571)
Q Consensus 492 d~k~~~~dv~kal~~aie~~~v~~~~~g~ 520 (571)
.+...+.+|||||..||..+.++++.++.
T Consensus 257 ~~~~~d~~vR~Al~~aidr~~i~~~~~~g 285 (480)
T cd08517 257 NPPLKDVRVRQAIAHAIDRQFIVDTVFFG 285 (480)
T ss_pred CCccCCHHHHHHHHHhcCHHHHHHHHHcC
Confidence 45678899999999999999999987764
No 79
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=22.39 E-value=7.8e+02 Score=26.36 Aligned_cols=54 Identities=9% Similarity=0.054 Sum_probs=33.3
Q ss_pred CCCCChhhHHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 008270 42 PKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (571)
Q Consensus 42 P~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVP 97 (571)
|.-+++..+.. |-.+|++. +.....|+..++-..+..+.++.|.+.|+.-+++.
T Consensus 67 Ps~L~~~~l~~-ll~~i~~~-~~~~~eitiE~nP~~lt~e~l~~lk~~G~nrisiG 120 (353)
T PRK05904 67 PNCLNDQLLDI-LLSTIKPY-VDNNCEFTIECNPELITQSQINLLKKNKVNRISLG 120 (353)
T ss_pred cccCCHHHHHH-HHHHHHHh-cCCCCeEEEEeccCcCCHHHHHHHHHcCCCEEEEe
Confidence 44455544433 33344332 22223577777777778888899999998777764
No 80
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=22.07 E-value=94 Score=31.26 Aligned_cols=26 Identities=15% Similarity=0.234 Sum_probs=17.3
Q ss_pred CCCCCCchhhhHHHHHHHHHHhhhhcccc
Q 008270 449 QGRLTPSEYVQGLIGVILLALNTLKIERV 477 (571)
Q Consensus 449 ~g~~~p~~~~qgli~vil~al~~lk~e~~ 477 (571)
+|||+-.|. +++.|+..+..+|.|.+
T Consensus 137 PGCPP~Pe~---il~~l~~L~~~i~~~~~ 162 (186)
T PRK14814 137 PGCPPRPEA---ILDALVKLQTKLKTQGL 162 (186)
T ss_pred cCCCCCHHH---HHHHHHHHHHHHhcccc
Confidence 788875554 56666667777776654
No 81
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=21.80 E-value=74 Score=34.04 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=24.8
Q ss_pred CCCCCChhHHHHHHHHHHHhHHHHhhcCc
Q 008270 492 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (571)
Q Consensus 492 d~k~~~~dv~kal~~aie~~~v~~~~~g~ 520 (571)
.+-..+.+|||||..||..+.++++.++.
T Consensus 259 ~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 287 (481)
T cd08498 259 KNPLKDPRVRQALSLAIDREAIVDRVMRG 287 (481)
T ss_pred CCCCCCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 45678899999999999999999986653
No 82
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=21.65 E-value=6.6e+02 Score=25.36 Aligned_cols=114 Identities=14% Similarity=0.087 Sum_probs=55.1
Q ss_pred ceEEEEEcc--CCCCC-CCCChhhHHHHHHHHHHhcCccCceEEEEEecCCCC-----ChhHHHHhhhcCCceee--ccC
Q 008270 29 KTSVWWDIE--NCQVP-KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRI-----PASVQHALSSTGIALNH--VPA 98 (571)
Q Consensus 29 kTaVFWDIE--NCPVP-~G~da~~Va~NIr~AL~klGY~GpVTIrAYGD~s~i-----p~~vl~aLsSSGISLih--VPa 98 (571)
+..|++|-. .+.++ -+.|-+.....+...|.++|++ +|-+-. +..... -..++++|...|+.+.. +-.
T Consensus 139 p~vV~i~~~~~~~~~~~V~~Dn~~~~~~a~~~L~~~G~~-~I~~i~-~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~ 216 (343)
T PRK10727 139 PGMVLINRILPGFENRCIALDDRYGAWLATRHLIQQGHT-RIGYLC-SNHSISDAEDRLQGYYDALAESGIPANDRLVTF 216 (343)
T ss_pred CCEEEEecCCCCCCCCEEEECcHHHHHHHHHHHHHCCCc-cEEEEe-CCccccchHHHHHHHHHHHHHCCCCCChhhEEe
Confidence 335778742 33322 1234334444455566666763 443221 222111 13467788888886432 111
Q ss_pred CCcc-chhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHHhCCCeE
Q 008270 99 GVKD-ASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNI 148 (571)
Q Consensus 99 G~Kn-AADkkMLvDML~WAlDNPpPANIMLISGDrDFS~aL~~LR~RGYNI 148 (571)
+.-+ ......+.+++ ..++.| +-++...|.--..++..|+++|+.|
T Consensus 217 ~~~~~~~~~~~~~~~l---~~~~~~-~ai~~~nD~~A~g~~~al~~~G~~v 263 (343)
T PRK10727 217 GEPDESGGEQAMTELL---GRGRNF-TAVACYNDSMAAGAMGVLNDNGIDV 263 (343)
T ss_pred CCCChhHHHHHHHHHH---hCCCCC-CEEEEcCcHHHHHHHHHHHHcCCCC
Confidence 1111 11112233333 234444 4555566665667889999999854
No 83
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.52 E-value=3.2e+02 Score=29.11 Aligned_cols=27 Identities=15% Similarity=0.455 Sum_probs=24.7
Q ss_pred ce-EEEEeCCcchHHHHHHHHhCCCeEE
Q 008270 123 SN-YLLISGDRDFSNALHQLRMRRYNIL 149 (571)
Q Consensus 123 AN-IMLISGDrDFS~aL~~LR~RGYNIL 149 (571)
.+ |-+|+...++..+.+.||.+||+|.
T Consensus 204 r~~fkiv~e~ssl~qV~~~Lr~~G~~i~ 231 (276)
T KOG2972|consen 204 REEFKIVTEPSSLNQVAHKLRSKGFEIK 231 (276)
T ss_pred cceeEEEeccchHHHHHHHhhcCCceee
Confidence 44 8899999999999999999999996
No 84
>PF10096 DUF2334: Uncharacterized protein conserved in bacteria (DUF2334); InterPro: IPR018763 This group of proteins has no known function.
Probab=21.39 E-value=2.1e+02 Score=29.03 Aligned_cols=24 Identities=25% Similarity=0.301 Sum_probs=20.9
Q ss_pred CcchHHHHHHHHhCCCeEEEeccC
Q 008270 131 DRDFSNALHQLRMRRYNILLAQPH 154 (571)
Q Consensus 131 DrDFS~aL~~LR~RGYNILLAqP~ 154 (571)
+.+|...|+.++.||+.|+|=...
T Consensus 54 ~~~f~~~L~~~~~~Gg~I~lHGYt 77 (243)
T PF10096_consen 54 NPEFVEYLRYLQARGGEIVLHGYT 77 (243)
T ss_pred hHHHHHHHHHHHhcCCEEEEEecc
Confidence 568999999999999999997653
No 85
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=21.37 E-value=4.2e+02 Score=27.11 Aligned_cols=89 Identities=19% Similarity=0.317 Sum_probs=55.9
Q ss_pred HHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcCCCCceEEEE--eCCc---
Q 008270 58 LVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI--SGDR--- 132 (571)
Q Consensus 58 L~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDNPpPANIMLI--SGDr--- 132 (571)
|.++|+. =--++||...+.++.++.+....+. +-.|. .||..|-.+.++ ||.... ++.|+++ .|.|
T Consensus 37 l~~~gl~---P~~~vGDfDSv~~e~~~~~~~~~~~-~~f~~-eKd~TD~elAl~---~a~e~g-~d~i~i~Ga~GGR~DH 107 (212)
T COG1564 37 LLELGLV---PDLAVGDFDSVSEELLAYYKEKTVT-IKFPA-EKDSTDLELALD---EALERG-ADEIVILGALGGRLDH 107 (212)
T ss_pred HHHcCCC---ccEEEecccccCHHHHHHHhhcCcc-eecCh-hhccchHHHHHH---HHHHcC-CCEEEEEecCCChHHH
Confidence 3445543 3357899999999999999988887 54554 477777766554 554443 3666666 5554
Q ss_pred chHH--HHHHHHhCCCeEEEeccCC
Q 008270 133 DFSN--ALHQLRMRRYNILLAQPHK 155 (571)
Q Consensus 133 DFS~--aL~~LR~RGYNILLAqP~~ 155 (571)
-|.. ++.++-.++..|.+....+
T Consensus 108 ~l~nl~ll~~~~~~~~~i~l~~~~n 132 (212)
T COG1564 108 ALANLFLLLRPAKSGFKITLISGQN 132 (212)
T ss_pred HHHHHHHHHhhhhccceEEEecCCc
Confidence 1222 3344444677777775544
No 86
>TIGR01231 lacC tagatose-6-phosphate kinase. This enzyme is part of the tagatose-6-phosphate pathway of lactose degradation.
Probab=21.27 E-value=6.8e+02 Score=25.25 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhcCccCce-EEEEEecCCCCChhHHHHhhhcCCceeec
Q 008270 50 IAQNISSALVKMNYCGPV-SISAYGDTNRIPASVQHALSSTGIALNHV 96 (571)
Q Consensus 50 Va~NIr~AL~klGY~GpV-TIrAYGD~s~ip~~vl~aLsSSGISLihV 96 (571)
-.-|+-.+|.++|.. + .+.++|+ ..-..+++.|...||...++
T Consensus 37 ~~~NvA~~la~LG~~--v~~i~~vG~--~~G~~i~~~l~~~GV~~~~~ 80 (309)
T TIGR01231 37 KGLNVTRVLAQVGDP--VLASGFLGG--KLGEFIEKELDHSDIKHAFY 80 (309)
T ss_pred cHHHHHHHHHHcCCC--eEEEEEecC--hhHHHHHHHHHHcCCceeEE
Confidence 346788889998864 4 4677786 35667889999999987665
No 87
>PRK09989 hypothetical protein; Provisional
Probab=21.20 E-value=6.5e+02 Score=24.90 Aligned_cols=37 Identities=19% Similarity=0.125 Sum_probs=26.7
Q ss_pred HHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceee
Q 008270 56 SALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNH 95 (571)
Q Consensus 56 ~AL~klGY~GpVTIrAYGD~s~ip~~vl~aLsSSGISLih 95 (571)
.+++++||.| |.|..+.+. ...++++.|.+.|+++.-
T Consensus 22 ~~~~~~Gfd~-VEl~~~~~~--~~~~~~~~l~~~Gl~v~~ 58 (258)
T PRK09989 22 AAARKAGFDA-VEFLFPYDY--STLQIQKQLEQNHLTLAL 58 (258)
T ss_pred HHHHHcCCCE-EEECCcccC--CHHHHHHHHHHcCCcEEE
Confidence 3556789987 777655443 246788999999988774
No 88
>PRK14820 NADH dehydrogenase subunit B; Provisional
Probab=21.08 E-value=93 Score=31.13 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=18.0
Q ss_pred CCCCCCchhhhHHHHHHHHHHhhhhccccCC
Q 008270 449 QGRLTPSEYVQGLIGVILLALNTLKIERVVP 479 (571)
Q Consensus 449 ~g~~~p~~~~qgli~vil~al~~lk~e~~~p 479 (571)
+|||+-.| -++++|+.++..++.|++-+
T Consensus 137 PGCPP~Pe---~il~~l~~l~~~i~~~~~~~ 164 (180)
T PRK14820 137 PGCPPRPE---QIIDGVMRVQELVKNESLRR 164 (180)
T ss_pred cCCCCCHH---HHHHHHHHHHHHHhhccccc
Confidence 67776443 36666777777777766544
No 89
>cd06578 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease.
Probab=20.74 E-value=4.3e+02 Score=24.86 Aligned_cols=64 Identities=22% Similarity=0.194 Sum_probs=42.5
Q ss_pred hHHHHhhhcCCceeeccCCCccchhhHHHHHHHHhhhcC-CCCceEEEEeCCcchHHHHHHHHhCCCeEEEe
Q 008270 81 SVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGDRDFSNALHQLRMRRYNILLA 151 (571)
Q Consensus 81 ~vl~aLsSSGISLihVPaG~KnAADkkMLvDML~WAlDN-PpPANIMLISGDrDFS~aL~~LR~RGYNILLA 151 (571)
...++|...|+...++|.. .+ + .+++.+.... .....|+++.|+..=..+...|+++|.+|.-+
T Consensus 87 ~Ta~~l~~~g~~~~~~~~~-~~-~-----~~L~~~i~~~~~~~~~il~~~g~~~~~~l~~~L~~~g~~v~~~ 151 (239)
T cd06578 87 KTAEALREAGLTADFVPEE-GD-S-----EGLLELLELQDGKGKRILRPRGGRAREDLAEALRERGAEVDEV 151 (239)
T ss_pred HHHHHHHHcCCCceeCCCc-cC-H-----HHHHHHHHhcCCCCCEEEEEcCcchhHHHHHHHHHCCCEEEEE
Confidence 3557788899988887532 11 1 2333333333 45678888888876667778888899888554
No 90
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=20.65 E-value=4.8e+02 Score=28.71 Aligned_cols=87 Identities=20% Similarity=0.271 Sum_probs=51.6
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHH---HHhhhcCCCCceEEEEeCCcchHHHHHHH
Q 008270 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDM---LFWAVDNPAPSNYLLISGDRDFSNALHQL 141 (571)
Q Consensus 65 GpVTIrAYGD~s~ip~~vl~aLsSSGISLihVPaG~KnAADkkMLvDM---L~WAlDNPpPANIMLISGDrDFS~aL~~L 141 (571)
+|=-+-..|...-++.+.-.+|.+-||++.-.-...+--...++...| +-||..| .+++|+.| .||...|..|
T Consensus 75 npd~VLIIGGp~AVs~~yE~~Lks~GitV~RigG~nR~ETa~~v~~~~~~~yp~af~n---~kvvvv~G-wDy~~~~~e~ 150 (337)
T COG2247 75 NPDLVLIIGGPIAVSPNYENALKSLGITVKRIGGANRYETAEKVAKFFREDYPNAFKN---VKVVVVYG-WDYADALMEL 150 (337)
T ss_pred CCceEEEECCCCcCChhHHHHHHhCCcEEEEecCcchHHHHHHHHHHHHhhchhhhcC---eEEEEEec-cccHHHHHHH
Confidence 343444578887888899999999999988763322222223344344 3456666 67888887 6677444443
Q ss_pred HhCCCeEEEeccCCCC
Q 008270 142 RMRRYNILLAQPHKAS 157 (571)
Q Consensus 142 R~RGYNILLAqP~~AS 157 (571)
-.+ +|+.+.-.+.+
T Consensus 151 ~k~--~~~p~~~~n~~ 164 (337)
T COG2247 151 MKE--GIVPVILKNTS 164 (337)
T ss_pred Hhc--CcceeEecccc
Confidence 323 55555433443
No 91
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=20.53 E-value=72 Score=34.12 Aligned_cols=30 Identities=27% Similarity=0.299 Sum_probs=25.4
Q ss_pred cCCCCCCChhHHHHHHHHHHHhHHHHhhcC
Q 008270 490 YGEPKHRNTDVRKALNCAIEQHMVIKRSLG 519 (571)
Q Consensus 490 ~gd~k~~~~dv~kal~~aie~~~v~~~~~g 519 (571)
+..+...+..|||||-.||-.+.++++.+|
T Consensus 249 ~~~~~~~d~~vR~Al~~aiDr~~i~~~~~~ 278 (488)
T cd08489 249 TASEPLSDLKVREAINYAIDKEAISKGILY 278 (488)
T ss_pred CCCCccccHHHHHHHHHhcCHHHHHHHHhc
Confidence 334567889999999999999999998775
No 92
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=20.39 E-value=74 Score=33.84 Aligned_cols=32 Identities=25% Similarity=0.359 Sum_probs=26.9
Q ss_pred hhcCCCCCCChhHHHHHHHHHHHhHHHHhhcC
Q 008270 488 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLG 519 (571)
Q Consensus 488 ir~gd~k~~~~dv~kal~~aie~~~v~~~~~g 519 (571)
+-...+...+..|||||..||..+.|++..++
T Consensus 259 ~N~~~~~~~d~~vR~Al~~aidr~~i~~~~~~ 290 (476)
T cd08512 259 LNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLK 290 (476)
T ss_pred eeCCCCCCCCHHHHHHHHHhcCHHHHHHHHhc
Confidence 33445678899999999999999999998875
No 93
>cd08493 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their li
Probab=20.23 E-value=76 Score=33.89 Aligned_cols=28 Identities=21% Similarity=0.434 Sum_probs=24.6
Q ss_pred CCCCCChhHHHHHHHHHHHhHHHHhhcC
Q 008270 492 EPKHRNTDVRKALNCAIEQHMVIKRSLG 519 (571)
Q Consensus 492 d~k~~~~dv~kal~~aie~~~v~~~~~g 519 (571)
.+...+..|||||..||..+.+++..+|
T Consensus 264 ~~~~~d~~vR~Al~~aidr~~i~~~~~~ 291 (482)
T cd08493 264 KPPFDDPKVRQAIAHAINKEAIVDAVYQ 291 (482)
T ss_pred CCccCCHHHHHHHHHhcCHHHHHHHHhc
Confidence 3567899999999999999999998775
Done!