Query 007795
Match_columns 589
No_of_seqs 140 out of 267
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 15:26:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007795.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007795hhsearch_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 2.4E-20 5.3E-25 164.3 6.2 133 29-169 1-144 (146)
2 cd06167 LabA_like LabA_like pr 99.6 1.2E-15 2.6E-20 136.8 9.4 135 29-167 2-146 (149)
3 TIGR00288 conserved hypothetic 99.4 1.1E-11 2.3E-16 118.0 13.4 135 24-170 19-155 (160)
4 PF14418 OHA: OST-HTH Associat 99.2 7.7E-12 1.7E-16 105.6 1.2 60 522-582 9-71 (75)
5 COG1432 Uncharacterized conser 97.7 0.00015 3.3E-09 69.8 9.3 147 27-175 5-165 (181)
6 PF04263 TPK_catalytic: Thiami 81.1 5.8 0.00013 36.6 7.0 76 70-151 39-121 (123)
7 COG4634 Uncharacterized protei 76.8 12 0.00025 35.1 7.4 72 77-157 8-80 (113)
8 cd05013 SIS_RpiR RpiR-like pro 69.0 73 0.0016 27.4 10.3 94 65-169 14-110 (139)
9 cd05014 SIS_Kpsf KpsF-like pro 65.1 27 0.00059 30.6 7.0 93 66-170 2-98 (128)
10 PLN02714 thiamin pyrophosphoki 57.8 50 0.0011 33.5 8.2 82 70-155 57-148 (229)
11 COG0794 GutQ Predicted sugar p 53.7 66 0.0014 32.8 8.2 107 49-169 27-136 (202)
12 TIGR01378 thi_PPkinase thiamin 53.1 76 0.0016 31.4 8.5 90 59-156 32-128 (203)
13 cd05005 SIS_PHI Hexulose-6-pho 51.0 1.1E+02 0.0024 28.9 8.9 91 65-171 34-127 (179)
14 PRK00124 hypothetical protein; 47.6 54 0.0012 31.9 6.3 81 31-138 2-82 (151)
15 PF08497 Radical_SAM_N: Radica 47.0 24 0.00052 37.8 4.2 41 111-154 8-56 (302)
16 TIGR03127 RuMP_HxlB 6-phospho 45.9 1.5E+02 0.0033 27.9 9.0 91 64-170 30-123 (179)
17 TIGR00393 kpsF KpsF/GutQ famil 44.0 73 0.0016 31.6 6.9 94 65-170 1-98 (268)
18 COG1671 Uncharacterized protei 42.7 97 0.0021 30.4 7.2 80 30-138 2-81 (150)
19 PRK11557 putative DNA-binding 40.0 1.7E+02 0.0037 29.4 8.9 94 65-169 129-225 (278)
20 PRK01045 ispH 4-hydroxy-3-meth 39.9 93 0.002 33.2 7.2 43 50-95 15-58 (298)
21 PRK11337 DNA-binding transcrip 38.6 2E+02 0.0044 29.2 9.2 95 65-170 141-238 (292)
22 PRK11543 gutQ D-arabinose 5-ph 37.2 1.9E+02 0.0042 29.6 8.9 94 65-170 43-140 (321)
23 PF09314 DUF1972: Domain of un 36.6 3.1E+02 0.0067 27.4 9.8 103 41-151 12-124 (185)
24 PF07283 TrbH: Conjugal transf 36.5 89 0.0019 29.4 5.7 53 104-156 4-60 (121)
25 cd08502 PBP2_NikA_DppA_OppA_li 36.3 34 0.00075 36.7 3.5 34 442-475 254-287 (472)
26 KOG1610 Corticosteroid 11-beta 36.2 50 0.0011 35.8 4.6 45 120-164 26-73 (322)
27 PF02590 SPOUT_MTase: Predicte 35.4 2.5E+02 0.0055 27.1 8.8 42 132-173 83-127 (155)
28 PRK00414 gmhA phosphoheptose i 35.1 2.9E+02 0.0063 27.1 9.3 49 120-169 110-161 (192)
29 cd05008 SIS_GlmS_GlmD_1 SIS (S 34.6 2.4E+02 0.0052 24.6 7.9 48 121-169 46-96 (126)
30 PRK05628 coproporphyrinogen II 34.4 3.8E+02 0.0082 28.6 10.8 54 44-97 72-125 (375)
31 cd07995 TPK Thiamine pyrophosp 34.1 2E+02 0.0043 28.3 8.1 88 58-153 35-129 (208)
32 PF07415 Herpes_LMP2: Gammaher 33.3 15 0.00032 40.5 0.1 55 262-332 7-61 (489)
33 PRK12360 4-hydroxy-3-methylbut 32.8 1.4E+02 0.0031 31.6 7.2 42 50-94 15-58 (281)
34 COG0796 MurI Glutamate racemas 32.4 2.3E+02 0.0049 30.2 8.5 85 43-153 13-99 (269)
35 TIGR00216 ispH_lytB (E)-4-hydr 32.4 1.4E+02 0.0031 31.6 7.1 41 50-93 14-56 (280)
36 PRK14820 NADH dehydrogenase su 32.4 43 0.00093 33.5 3.2 29 403-434 137-165 (180)
37 PRK11302 DNA-binding transcrip 31.6 3.6E+02 0.0078 27.0 9.6 94 65-170 129-225 (284)
38 KOG1924 RhoA GTPase effector D 31.5 1.9E+02 0.0041 35.3 8.5 38 420-461 626-665 (1102)
39 COG3233 Predicted deacetylase 31.5 84 0.0018 32.8 5.1 34 119-152 31-74 (233)
40 KOG0260 RNA polymerase II, lar 31.3 1E+03 0.023 30.8 14.6 42 24-65 1205-1254(1605)
41 COG1576 Uncharacterized conser 31.2 2.5E+02 0.0054 27.8 8.0 42 132-173 83-126 (155)
42 PF09419 PGP_phosphatase: Mito 31.2 4.8E+02 0.01 25.7 10.1 113 28-151 40-164 (168)
43 COG1737 RpiR Transcriptional r 31.2 3.4E+02 0.0074 28.0 9.5 90 69-169 133-227 (281)
44 PRK15482 transcriptional regul 30.4 4.1E+02 0.0088 27.1 9.8 95 65-170 136-233 (285)
45 PF07582 AP_endonuc_2_N: AP en 29.7 47 0.001 27.3 2.5 19 52-70 3-21 (55)
46 PF02602 HEM4: Uroporphyrinoge 29.2 2.3E+02 0.0049 27.3 7.5 64 81-150 82-145 (231)
47 PRK10294 6-phosphofructokinase 28.4 4.4E+02 0.0095 26.7 9.7 45 50-97 40-84 (309)
48 cd05006 SIS_GmhA Phosphoheptos 28.2 5.1E+02 0.011 24.4 10.3 49 121-170 101-152 (177)
49 PRK14814 NADH dehydrogenase su 27.8 61 0.0013 32.7 3.3 26 403-431 137-162 (186)
50 PRK13883 conjugal transfer pro 27.7 1.1E+02 0.0024 29.9 5.0 53 103-155 31-87 (151)
51 PF06073 DUF934: Bacterial pro 27.5 1.3E+02 0.0029 27.9 5.3 40 55-99 39-79 (110)
52 PRK10014 DNA-binding transcrip 27.1 6E+02 0.013 25.6 10.3 100 48-152 35-151 (342)
53 COG2247 LytB Putative cell wal 27.0 2.8E+02 0.0062 30.5 8.3 87 65-157 75-164 (337)
54 PRK13835 conjugal transfer pro 26.8 1.4E+02 0.0029 29.3 5.3 51 100-150 34-87 (145)
55 TIGR00441 gmhA phosphoheptose 26.8 4E+02 0.0086 24.9 8.4 51 120-171 78-131 (154)
56 TIGR02764 spore_ybaN_pdaB poly 26.5 5.1E+02 0.011 24.6 9.2 100 45-151 74-187 (191)
57 PRK01254 hypothetical protein; 26.4 73 0.0016 37.9 4.1 41 123-163 40-89 (707)
58 KOG4307 RNA binding protein RB 26.1 7.2E+02 0.016 30.4 11.7 44 273-316 217-260 (944)
59 PRK07334 threonine dehydratase 26.0 1.8E+02 0.0039 31.5 6.8 94 45-151 307-402 (403)
60 PRK10401 DNA-binding transcrip 25.4 3.9E+02 0.0084 27.2 8.7 112 31-148 141-263 (346)
61 PRK14818 NADH dehydrogenase su 25.3 67 0.0015 32.1 3.1 24 119-142 67-92 (173)
62 PF10073 DUF2312: Uncharacteri 25.3 22 0.00047 31.1 -0.2 41 416-462 6-48 (74)
63 COG2179 Predicted hydrolase of 25.1 3E+02 0.0064 27.8 7.4 117 27-158 26-144 (175)
64 PF02739 5_3_exonuc_N: 5'-3' e 24.7 1.1E+02 0.0023 29.7 4.3 62 83-154 92-153 (169)
65 PRK14816 NADH dehydrogenase su 23.4 65 0.0014 32.4 2.6 34 110-143 65-104 (182)
66 KOG3154 Uncharacterized conser 22.9 1.1E+02 0.0024 32.1 4.3 66 30-97 44-110 (263)
67 PRK14828 undecaprenyl pyrophos 22.9 1.8E+02 0.0039 30.4 5.8 71 30-101 75-155 (256)
68 PF01380 SIS: SIS domain SIS d 22.8 2.4E+02 0.0051 24.4 5.7 96 65-170 6-104 (131)
69 PRK14815 NADH dehydrogenase su 22.5 73 0.0016 32.1 2.8 33 110-142 57-95 (183)
70 KOG2972 Uncharacterized conser 22.5 3.1E+02 0.0066 29.4 7.3 27 123-149 204-231 (276)
71 PF00496 SBP_bac_5: Bacterial 22.4 61 0.0013 32.9 2.3 31 444-474 210-240 (374)
72 TIGR01675 plant-AP plant acid 22.3 3.2E+02 0.007 28.2 7.4 71 81-154 127-204 (229)
73 PF05991 NYN_YacP: YacP-like N 22.3 2.2E+02 0.0047 27.5 5.8 44 88-137 65-109 (166)
74 cd08519 PBP2_NikA_DppA_OppA_li 22.1 63 0.0014 34.7 2.4 34 441-474 247-280 (469)
75 cd08491 PBP2_NikA_DppA_OppA_li 21.9 61 0.0013 34.9 2.3 33 442-474 237-269 (473)
76 TIGR02417 fruct_sucro_rep D-fr 21.9 8.1E+02 0.018 24.5 10.4 99 49-152 32-147 (327)
77 PRK11303 DNA-binding transcrip 21.7 7.7E+02 0.017 24.6 9.9 99 49-152 33-148 (328)
78 COG1564 THI80 Thiamine pyropho 21.5 4E+02 0.0087 27.4 7.8 89 58-155 37-132 (212)
79 cd08496 PBP2_NikA_DppA_OppA_li 21.5 70 0.0015 34.1 2.6 87 445-536 243-338 (454)
80 PRK14101 bifunctional glucokin 20.9 5.8E+02 0.013 29.4 9.9 93 65-169 469-564 (638)
81 PRK11382 frlB fructoselysine-6 20.6 8.4E+02 0.018 25.8 10.3 107 52-171 33-144 (340)
82 PF13380 CoA_binding_2: CoA bi 20.4 1.6E+02 0.0034 26.7 4.2 83 79-164 16-98 (116)
83 smart00645 Pept_C1 Papain fami 20.4 1.2E+02 0.0027 28.8 3.8 54 411-464 26-79 (174)
84 COG1105 FruK Fructose-1-phosph 20.3 1.9E+02 0.0042 31.2 5.5 97 51-154 39-168 (310)
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=99.81 E-value=2.4e-20 Score=164.33 Aligned_cols=133 Identities=33% Similarity=0.500 Sum_probs=93.4
Q ss_pred ceEEEEEecCCCCCCC---CChhhhHHHHHHHHHhcCccCce-EEEEEecCCC-CChhHHHHhhhcCCceeeccC-----
Q 007795 29 KTSVWWDIENCQVPKN---CDPHTIAQNISSALVKMNYCGPV-SISAYGDTNR-IPASVQHALSSTGIALNHVPA----- 98 (589)
Q Consensus 29 kTaVFWDIENCPVP~G---~da~~V~~NIrsAL~klGY~GpV-TIrAYGD~s~-ip~~vr~aLsSSGIsLihVPa----- 98 (589)
+|+||||+|||+.+.+ +++..+...|+. .|++ .+++|+++.. ....+.++|...||.+.++|.
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 555555444443 5667 7999999543 235677899999999999986
Q ss_pred CCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEec-cCCCChhHHhhcCeEEE
Q 007795 99 GVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWL 169 (589)
Q Consensus 99 G~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq-P~nAS~~L~~aAd~vWl 169 (589)
+.|+.+|.+|.+||+.|+.+++. +++||||||.||.+++..|+.+|++|.++. +..++..|..+|+.++.
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 67899999999999999988766 999999999999999999999999999888 67799999999997764
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=99.62 E-value=1.2e-15 Score=136.83 Aligned_cols=135 Identities=23% Similarity=0.220 Sum_probs=108.2
Q ss_pred ceEEEEEecCCCCCCCCCh--hhhHHHHHHHHHhcCccCce-EEEEEecCCC--CChhHHHHhhhcCCceeeccC----C
Q 007795 29 KTSVWWDIENCQVPKNCDP--HTIAQNISSALVKMNYCGPV-SISAYGDTNR--IPASVQHALSSTGIALNHVPA----G 99 (589)
Q Consensus 29 kTaVFWDIENCPVP~G~da--~~V~~NIrsAL~klGY~GpV-TIrAYGD~s~--ip~~vr~aLsSSGIsLihVPa----G 99 (589)
+++||||.||+..-..... ..-...+...+.. .+.+ ..++|+++.. ......++|...|+.+++++. +
T Consensus 2 r~~ifiD~~Nl~~~~~~~~~~~~d~~~l~~~~~~---~~~~~~~r~y~~~~~~~~~~~~~~~L~~~g~~~~~~~~~~~~~ 78 (149)
T cd06167 2 RVAVFIDGENLYYSLRDLGGKRFDYRKLLEFLRD---GGEIVLARAYGNWTSPERQRGFLDALRRLGFEPIQKPLRTRGS 78 (149)
T ss_pred eEEEEEeHHHHHHHHHHhcCCCcCHHHHHHHHHh---CCeEEEEEEEEecCCchhHHHHHHHHHHCCcEEEEEcceecCC
Confidence 6899999999975421111 1122223333333 2444 6899999874 557788999999999999984 6
Q ss_pred CccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEeccC-CCChhHHhhcCeE
Q 007795 100 VKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSV 167 (589)
Q Consensus 100 ~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~-nAS~~L~~aAd~v 167 (589)
.|+.+|.+|.+||+.++.++ .++.|||+|||.||.+++..|+++|++|+++.+. ..|..|..+|+.+
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 8899999999999999999999999999999976 7899999998844
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=99.35 E-value=1.1e-11 Score=118.02 Aligned_cols=135 Identities=16% Similarity=0.148 Sum_probs=107.1
Q ss_pred hhccCceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceE-EEEEecCCCCChhHHHHhhhcCCceeeccCCCcc
Q 007795 24 QYVTAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVS-ISAYGDTNRIPASVQHALSSTGIALNHVPAGVKD 102 (589)
Q Consensus 24 eya~AkTaVFWDIENCPVP~G~da~~V~~NIrsAL~klGY~GpVT-IrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~Kd 102 (589)
+--.-+++||-|.+|.. +..+. .+ ...|...|.+ .|.++ -++||++.. ...+++.|...|++.+.+ |+
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 33356899999999996 32221 11 3456666665 56665 589999643 356889999999998764 56
Q ss_pred chhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEec-cCCCChhHHhhcCeEEEe
Q 007795 103 ASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 103 AADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq-P~nAS~~L~~aAd~vWlW 170 (589)
+.|..|.+|+|..++ .+..+.|+|+|||.||.+++.+||++|..|+++. +..++.+|..+|+.++.-
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 899999999999986 5789999999999999999999999999999998 556889999999987654
No 4
>PF14418 OHA: OST-HTH Associated domain
Probab=99.16 E-value=7.7e-12 Score=105.61 Aligned_cols=60 Identities=35% Similarity=0.434 Sum_probs=54.6
Q ss_pred hhhhHHHHHHHHhh---hhhhhhhhhHHHHHHHhhccceeeecCCCCceeeEEEEeeecCCCCc
Q 007795 522 SQCRYEAALILKNS---CLPELALGEILKILNMVITPKKWIIHHQSGWQPVTITLAEYKSDSGS 582 (589)
Q Consensus 522 s~~ry~aa~~lk~~---cl~~~~lg~vlqil~~~i~~kkw~~~h~sgwqp~~i~~~~~~~~~~~ 582 (589)
+.|||++|..||+. ||+++.||||++|++|.|..|||+ +|+++|+|+.++..++++..+.
T Consensus 9 ~~gRY~~A~~Lk~~gp~~lr~l~Lg~i~~iVqlai~~k~l~-y~~~~l~P~~~~~~~a~s~~~~ 71 (75)
T PF14418_consen 9 SGGRYGMAQFLKKRGPPFLRSLSLGDICHIVQLAISKKKLI-YENSNLKPFCISQKVANSFLGI 71 (75)
T ss_pred CCcHHHHHHHHHhcCchhhcCCcHHHHHHHHHHHHhCCeee-eCCCccccHHHHHHHHHhhhcc
Confidence 38999999999998 999999999999999999999999 9999999998888777765443
No 5
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=97.73 E-value=0.00015 Score=69.81 Aligned_cols=147 Identities=20% Similarity=0.147 Sum_probs=99.0
Q ss_pred cCceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCce-EEEEEe---cCCCCChhHHH--HhhhcCCceeeccC--
Q 007795 27 TAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPV-SISAYG---DTNRIPASVQH--ALSSTGIALNHVPA-- 98 (589)
Q Consensus 27 ~AkTaVFWDIENCPVP~G~da~~V~~NIrsAL~klGY~GpV-TIrAYG---D~s~ip~~vr~--aLsSSGIsLihVPa-- 98 (589)
...+++|-|++|-+.-.. ....+.-.....|++......+ ....|. +...+..-... .+.+.|+.+.-.+.
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 347899999998654321 1111222234444443333333 233332 23333333333 67777877765543
Q ss_pred -----CCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEecc-CCCChhHHhhcCeEEEecc
Q 007795 99 -----GVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQP-HKASAPLVAAAKSVWLWTS 172 (589)
Q Consensus 99 -----G~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP-~nAS~~L~~aAd~vWlWeS 172 (589)
-.|..-|..|.+||+..+ +++.-.+++|+|||.||.+++..++.+|..|+++.- ...|..|..+|+.+..-.+
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 235567899999999987 577889999999999999999999999999999874 3578899999998877766
Q ss_pred ccc
Q 007795 173 LVA 175 (589)
Q Consensus 173 LLa 175 (589)
+..
T Consensus 163 ~~~ 165 (181)
T COG1432 163 LEE 165 (181)
T ss_pred hhh
Confidence 544
No 6
>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=81.11 E-value=5.8 Score=36.62 Aligned_cols=76 Identities=24% Similarity=0.429 Sum_probs=49.7
Q ss_pred EEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeC--Cc---chHH--HHHHHh
Q 007795 70 SAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISG--DR---DFSN--ALHQLR 142 (589)
Q Consensus 70 rAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISG--Dr---DFS~--aL~~LR 142 (589)
-+.||...+..++++.+.+.|+.+++.| .||..|-...++.+ .. ..+..|+++-+ -| -++. +|.+++
T Consensus 39 ~iiGDfDSi~~~~~~~~~~~~~~~~~~p--~kD~TD~e~Al~~~---~~-~~~~~i~v~Ga~GgR~DH~lanl~~l~~~~ 112 (123)
T PF04263_consen 39 LIIGDFDSISPEVLEFYKSKGVEIIHFP--EKDYTDLEKALEYA---IE-QGPDEIIVLGALGGRFDHTLANLNLLYKYK 112 (123)
T ss_dssp EEEC-SSSS-HHHHHHHHHCTTEEEEE---STTS-HHHHHHHHH---HH-TTTSEEEEES-SSSSHHHHHHHHHHHHHHH
T ss_pred EEEecCCCCChHHHHHHHhhccceeccc--ccccCHHHHHHHHH---HH-CCCCEEEEEecCCCcHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999 68888877766655 33 33445555442 22 2333 344455
Q ss_pred hcCCeEEEe
Q 007795 143 MRRYNILLA 151 (589)
Q Consensus 143 ~RGYNILLA 151 (589)
+++.+|+|+
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 7
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.76 E-value=12 Score=35.06 Aligned_cols=72 Identities=24% Similarity=0.352 Sum_probs=50.6
Q ss_pred CCChhHHHHhhhcCCceeecc-CCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEeccCC
Q 007795 77 RIPASVQHALSSTGIALNHVP-AGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHK 155 (589)
Q Consensus 77 ~ip~~vr~aLsSSGIsLihVP-aG~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~n 155 (589)
++|..+.+-|..+|++-+|+- -|-+|+.|.. ++.+|. -.+.||+|-|.||.. |..+...-..|+.+.-++
T Consensus 8 ~Lp~rlad~l~~~g~e~~h~r~lg~~da~D~E----I~a~A~----~~~~iivTkDsDF~~-la~~~G~Ppki~wLr~gN 78 (113)
T COG4634 8 QLPPRLADWLPMAGIEAVHWRDLGLRDATDIE----IWAYAR----RNNRIIVTKDSDFAD-LALTLGSPPKIVWLRCGN 78 (113)
T ss_pred CCChHHHHHhhhcccceeeecccCcCCCccHH----HHHHHH----hcCcEEEEcCccHHH-HHHHcCCCCeEEEEEecC
Confidence 477888899999999888886 4557776643 333443 368999999999944 444444556787776666
Q ss_pred CC
Q 007795 156 AS 157 (589)
Q Consensus 156 AS 157 (589)
.+
T Consensus 79 vs 80 (113)
T COG4634 79 VS 80 (113)
T ss_pred CC
Confidence 55
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=68.99 E-value=73 Score=27.45 Aligned_cols=94 Identities=15% Similarity=0.110 Sum_probs=56.3
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCc---chHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDR---DFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGDr---DFS~aL~~L 141 (589)
++|-+.+.|....+-..+...|...|.....++... ....++ ..-.+.+-+++||-.. +...++..+
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 566666666654455556667777787665553311 111111 1123456777888543 466778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
+++|-.|+++..... .+|...++..+.
T Consensus 84 ~~~g~~iv~iT~~~~-~~l~~~~d~~i~ 110 (139)
T cd05013 84 KERGAKVIAITDSAN-SPLAKLADIVLL 110 (139)
T ss_pred HHcCCeEEEEcCCCC-ChhHHhcCEEEE
Confidence 999999998875433 456666665544
No 9
>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=65.09 E-value=27 Score=30.57 Aligned_cols=93 Identities=19% Similarity=0.220 Sum_probs=55.0
Q ss_pred ceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcC-CCCcEEEEEeCC---cchHHHHHHH
Q 007795 66 PVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 66 pVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldN-PpPANIMLISGD---rDFS~aL~~L 141 (589)
+|-|.+.|....+-..+...|...|+....+... +.+.+...+ .+-+-+++||-. ++...++..+
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 3444444543333344555666677766665221 111111112 334667777754 5688899999
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
|++|-.|+++..... .+|...|+..+..
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 999999998875433 4577777766665
No 10
>PLN02714 thiamin pyrophosphokinase
Probab=57.84 E-value=50 Score=33.46 Aligned_cols=82 Identities=20% Similarity=0.225 Sum_probs=52.2
Q ss_pred EEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCC-----cEEEEEe--CCc---chHHHHH
Q 007795 70 SAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAP-----SNYLLIS--GDR---DFSNALH 139 (589)
Q Consensus 70 rAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpP-----ANIMLIS--GDr---DFS~aL~ 139 (589)
.+.||...+..+.++.+.+.|+.++..|. .||..|..+.+ .||.++.+. ..|+|+- |.| -|+.+..
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 47899999999999999999999888766 57878876654 445444221 3344432 222 3444433
Q ss_pred HHhhcCCeEEEeccCC
Q 007795 140 QLRMRRYNILLAQPHK 155 (589)
Q Consensus 140 ~LR~RGYNILLAqP~n 155 (589)
.++..+.+|.|+...+
T Consensus 133 L~~~~~~~i~lid~~~ 148 (229)
T PLN02714 133 LYRFPDLRIVLLSDDC 148 (229)
T ss_pred HHhcCCceEEEEcCCc
Confidence 3333566777776444
No 11
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=53.67 E-value=66 Score=32.75 Aligned_cols=107 Identities=18% Similarity=0.187 Sum_probs=71.9
Q ss_pred hhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEE
Q 007795 49 TIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI 128 (589)
Q Consensus 49 ~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLI 128 (589)
.+.+.++..++. .|+|.+...|..-.+-+.+--.|.++|...+.|-.+.-.--|--|+ -+-+-+++|
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 344445544443 7889998889888887778888999999998884211000011111 234678899
Q ss_pred eCCc---chHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 129 SGDR---DFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 129 SGDr---DFS~aL~~LR~RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
|+.. ....++..+|.+|-.|+.+..... +.|...||.+..
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 9874 466778888899999988874433 458888887765
No 12
>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=53.05 E-value=76 Score=31.37 Aligned_cols=90 Identities=18% Similarity=0.303 Sum_probs=57.1
Q ss_pred HhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEE--eCCc---c
Q 007795 59 VKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI--SGDR---D 133 (589)
Q Consensus 59 ~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLI--SGDr---D 133 (589)
.++|+.- -.+.||...++.+.++.+.+.|+.+...|. .||..|..+.+ .||.++. +..|+++ +|.| -
T Consensus 32 ~~~gi~P---d~iiGDfDSi~~~~~~~~~~~~~~~~~~~~-eKD~TD~e~Al---~~~~~~~-~~~i~i~Ga~GgR~DH~ 103 (203)
T TIGR01378 32 LKLGLTP---DLIVGDFDSIDEEELDFYKKAGVKIIVFPP-EKDTTDLELAL---KYALERG-ADEITILGATGGRLDHT 103 (203)
T ss_pred HHCCCCC---CEEEeCcccCCHHHHHHHHHcCCceEEcCC-CCCCCHHHHHH---HHHHHCC-CCEEEEEcCCCCcHHHH
Confidence 3456542 346799999999999999999999888776 48888876654 4555543 3455555 3333 2
Q ss_pred hHHH--HHHHhhcCCeEEEeccCCC
Q 007795 134 FSNA--LHQLRMRRYNILLAQPHKA 156 (589)
Q Consensus 134 FS~a--L~~LR~RGYNILLAqP~nA 156 (589)
++.+ |.+++.++.+|.++...+.
T Consensus 104 lani~~L~~~~~~~~~i~l~d~~~~ 128 (203)
T TIGR01378 104 LANLNLLLEYAKRGIKVRLIDEQNV 128 (203)
T ss_pred HHHHHHHHHHHhcCCeEEEEcCCcE
Confidence 3332 2233345778888765443
No 13
>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=50.97 E-value=1.1e+02 Score=28.92 Aligned_cols=91 Identities=15% Similarity=0.163 Sum_probs=57.5
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~L 141 (589)
.+|-|.+.|....+-..+...|...|+....+... .+..-.+-+-+++||-. ++...++..+
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 55666666654434444556677788877665321 01122345667778854 4667788888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEec
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWlWe 171 (589)
+++|..|+++.... ..+|...|+..+...
T Consensus 99 k~~g~~iI~IT~~~-~s~la~~ad~~l~~~ 127 (179)
T cd05005 99 KKAGAKVVLITSNP-DSPLAKLADVVVVIP 127 (179)
T ss_pred HHCCCeEEEEECCC-CCchHHhCCEEEEeC
Confidence 99999999887443 345777777766543
No 14
>PRK00124 hypothetical protein; Validated
Probab=47.63 E-value=54 Score=31.93 Aligned_cols=81 Identities=19% Similarity=0.217 Sum_probs=48.8
Q ss_pred EEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHH
Q 007795 31 SVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILV 110 (589)
Q Consensus 31 aVFWDIENCPVP~G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlV 110 (589)
-||-|-+-|| |..-|.++-++.|. .+..+++.++.- .-=.+..|+.+.|+.| .|++|..|+.
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---------VKDIIIRVAERHGI----PVTLVASFNHFL----RVPYSPFIRTVYVDAG-FDAADNEIVQ 63 (151)
T ss_pred EEEEECCCCc---------HHHHHHHHHHHHCC----eEEEEEeCCccc----CCCCCCceEEEEeCCC-CChHHHHHHH
Confidence 3899999998 34445555555443 444556544421 0012356888899864 7788876663
Q ss_pred HHhhhhhcCCCCcEEEEEeCCcchHHHH
Q 007795 111 DMLFWAVDNPAPSNYLLISGDRDFSNAL 138 (589)
Q Consensus 111 DML~WAldNPpPANIMLISGDrDFS~aL 138 (589)
.+ . ..=++||.|..++..+
T Consensus 64 ~~--------~-~gDiVIT~Di~LAa~~ 82 (151)
T PRK00124 64 LA--------E-KGDIVITQDYGLAALA 82 (151)
T ss_pred hC--------C-CCCEEEeCCHHHHHHH
Confidence 32 2 2247789987766643
No 15
>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=47.04 E-value=24 Score=37.85 Aligned_cols=41 Identities=29% Similarity=0.573 Sum_probs=28.5
Q ss_pred HHhhhhhcCCCCcEEEEEeCC-----cchHHHH--HHHhhcCCeE-EEeccC
Q 007795 111 DMLFWAVDNPAPSNYLLISGD-----RDFSNAL--HQLRMRRYNI-LLAQPH 154 (589)
Q Consensus 111 DML~WAldNPpPANIMLISGD-----rDFS~aL--~~LR~RGYNI-LLAqP~ 154 (589)
||....++. --|+||||| ..|..+| +-|..+||+| |++||.
T Consensus 8 em~~rGWd~---lDvilVtGDAYVDHPsFG~AiIgR~Le~~GyrVgIiaQPd 56 (302)
T PF08497_consen 8 EMKARGWDE---LDVILVTGDAYVDHPSFGAAIIGRVLEAHGYRVGIIAQPD 56 (302)
T ss_pred HHHHcCCcc---ccEEEEeCcccccCcchhHHHHHHHHHHcCCeEEEEeCCC
Confidence 444444443 359999999 3576654 4577799999 778886
No 16
>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=45.86 E-value=1.5e+02 Score=27.86 Aligned_cols=91 Identities=11% Similarity=0.064 Sum_probs=57.3
Q ss_pred cCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHH
Q 007795 64 CGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQ 140 (589)
Q Consensus 64 ~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~ 140 (589)
.++|.|.+.|....+-..+...|...|+........ . ...-.+-+-+++||.. ++...++..
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 456666666654434445666677778766665321 0 0112344667778854 466778888
Q ss_pred HhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 141 LR~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
++++|-.|+++..... .+|...|+.++.-
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 8999999999875433 4577777776654
No 17
>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=44.03 E-value=73 Score=31.59 Aligned_cols=94 Identities=18% Similarity=0.174 Sum_probs=59.3
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcC-CCCcEEEEEeCC---cchHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGD---RDFSNALHQ 140 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldN-PpPANIMLISGD---rDFS~aL~~ 140 (589)
|+|-|.+.|....+-..+...|...|+.+.++.. .++..+...+ .+-+-+++||-. ++...++..
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 5666667775444445566678888888776522 1122222122 344667778854 467778888
Q ss_pred HhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 141 LR~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
++++|..|+.+..... .+|...|+..+.+
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 9999999998875433 3466667776665
No 18
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.72 E-value=97 Score=30.42 Aligned_cols=80 Identities=23% Similarity=0.287 Sum_probs=51.9
Q ss_pred eEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHH
Q 007795 30 TSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKIL 109 (589)
Q Consensus 30 TaVFWDIENCPVP~G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMl 109 (589)
.-||-|-+-|| |...|.++.+++|. +|++ .++....+ ..+..|+.+.|-+ ..|++|..|+
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 44544321 1445677777755 4788887766
Q ss_pred HHHhhhhhcCCCCcEEEEEeCCcchHHHH
Q 007795 110 VDMLFWAVDNPAPSNYLLISGDRDFSNAL 138 (589)
Q Consensus 110 VDML~WAldNPpPANIMLISGDrDFS~aL 138 (589)
.. .-..=++||.|.-++..|
T Consensus 62 ~~---------a~~gDlVVT~Di~LA~~l 81 (150)
T COG1671 62 NL---------AEKGDLVVTADIPLASLL 81 (150)
T ss_pred Hh---------CCCCCEEEECchHHHHHH
Confidence 32 233447789998887755
No 19
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=39.98 E-value=1.7e+02 Score=29.42 Aligned_cols=94 Identities=15% Similarity=0.119 Sum_probs=56.3
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~L 141 (589)
.+|.|.+.|....+-..+...|...|+...... |..++...+. .-.+.+-+++||-. ++...++..+
T Consensus 129 ~~I~i~G~G~s~~~A~~~~~~l~~~g~~~~~~~-------d~~~~~~~~~---~~~~~Dv~I~iS~sg~~~~~~~~~~~a 198 (278)
T PRK11557 129 RRIILTGIGASGLVAQNFAWKLMKIGINAVAER-------DMHALLATVQ---ALSPDDLLLAISYSGERRELNLAADEA 198 (278)
T ss_pred CeEEEEecChhHHHHHHHHHHHhhCCCeEEEcC-------ChHHHHHHHH---hCCCCCEEEEEcCCCCCHHHHHHHHHH
Confidence 455666666443444556667888887665531 2222222111 22455667777754 3456778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
+++|..|+++.... ..+|...|+.++.
T Consensus 199 k~~ga~iI~IT~~~-~s~la~~ad~~l~ 225 (278)
T PRK11557 199 LRVGAKVLAITGFT-PNALQQRASHCLY 225 (278)
T ss_pred HHcCCCEEEEcCCC-CCchHHhCCEEEE
Confidence 99999999997543 3456667776654
No 20
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=39.92 E-value=93 Score=33.23 Aligned_cols=43 Identities=16% Similarity=0.190 Sum_probs=28.8
Q ss_pred hHHHHHHHHHhc-CccCceEEEEEecCCCCChhHHHHhhhcCCceee
Q 007795 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNH 95 (589)
Q Consensus 50 V~~NIrsAL~kl-GY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLih 95 (589)
|...|+.+.+.+ ...++ |..||++=+. ..+.+.|...||..++
T Consensus 15 V~rAi~~a~~~~~~~~~~--iytlG~iIHN-~~vv~~L~~~GV~~v~ 58 (298)
T PRK01045 15 VDRAIEIVERALEKYGAP--IYVRHEIVHN-RYVVERLEKKGAIFVE 58 (298)
T ss_pred HHHHHHHHHHHHHhcCCC--eEEEecCccC-HHHHHHHHHCCCEEec
Confidence 556666665432 22233 5778998665 4688899999998775
No 21
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=38.65 E-value=2e+02 Score=29.23 Aligned_cols=95 Identities=18% Similarity=0.167 Sum_probs=57.2
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~L 141 (589)
.+|-|.++|....+-..+...|...|+....++ |..++.... . .-.+-+-+++||.. ++...++...
T Consensus 141 ~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~-------d~~~~~~~~--~-~~~~~Dl~I~iS~sG~t~~~~~~~~~a 210 (292)
T PRK11337 141 RQRDLYGAGGSAAIARDVQHKFLRIGVRCQAYD-------DAHIMLMSA--A-LLQEGDVVLVVSHSGRTSDVIEAVELA 210 (292)
T ss_pred CeEEEEEecHHHHHHHHHHHHHhhCCCeEEEcC-------CHHHHHHHH--h-cCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 345566666544444445566777887766542 222221111 1 12345667888854 4567778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
+.+|-.|+++.... ..+|...|+.++.-
T Consensus 211 k~~g~~ii~IT~~~-~s~la~~ad~~l~~ 238 (292)
T PRK11337 211 KKNGAKIICITNSY-HSPIAKLADYVICS 238 (292)
T ss_pred HHCCCeEEEEeCCC-CChhHHhCCEEEEc
Confidence 89999999987544 34577777776653
No 22
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=37.22 E-value=1.9e+02 Score=29.63 Aligned_cols=94 Identities=23% Similarity=0.248 Sum_probs=62.0
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhh-hcCCCCcEEEEEeCC---cchHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWA-VDNPAPSNYLLISGD---RDFSNALHQ 140 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WA-ldNPpPANIMLISGD---rDFS~aL~~ 140 (589)
++|-|.+.|....+-..+...|...|+...++.. .+++... ..-.+.+-+++||.. .+...++..
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 4677777775555556677788888987776621 1111111 122455778888865 356778888
Q ss_pred HhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 141 LR~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
++++|-.|+.+..... .+|...|+.++.-
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 8999999999885544 4588888877654
No 23
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=36.62 E-value=3.1e+02 Score=27.40 Aligned_cols=103 Identities=20% Similarity=0.361 Sum_probs=63.2
Q ss_pred CCCCCCh-hhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhh--hhh
Q 007795 41 VPKNCDP-HTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLF--WAV 117 (589)
Q Consensus 41 VP~G~da-~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~--WAl 117 (589)
||+.+-+ +..++++..-|.+.|. .+++||-....+.. .-.=.|+.|+++|...... -..|.-|++. +|+
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 IPARYGGFETFVEELAPRLVSKGI----DVTVYCRSDYYPYK---EFEYNGVRLVYIPAPKNGS-AESIIYDFLSLLHAL 83 (185)
T ss_pred CCcccCcHHHHHHHHHHHHhcCCc----eEEEEEccCCCCCC---CcccCCeEEEEeCCCCCCc-hHHHHHHHHHHHHHH
Confidence 7877775 5778888888876544 56677765433211 1222699999998654432 3467767553 444
Q ss_pred c----CCCCcEEEEEeCCc--c-hHHHHHHHhhcCCeEEEe
Q 007795 118 D----NPAPSNYLLISGDR--D-FSNALHQLRMRRYNILLA 151 (589)
Q Consensus 118 d----NPpPANIMLISGDr--D-FS~aL~~LR~RGYNILLA 151 (589)
. +..-.-+++|-|-. - |...+..|+.+|..|++-
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 21223377777754 2 566777788888777754
No 24
>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=36.45 E-value=89 Score=29.44 Aligned_cols=53 Identities=23% Similarity=0.382 Sum_probs=36.2
Q ss_pred hhhHHHHHHhhhhhcC-CCCcE-EEEEeCC-cchHHH-HHHHhhcCCeEEEeccCCC
Q 007795 104 SDKKILVDMLFWAVDN-PAPSN-YLLISGD-RDFSNA-LHQLRMRRYNILLAQPHKA 156 (589)
Q Consensus 104 ADkkMlVDML~WAldN-PpPAN-IMLISGD-rDFS~a-L~~LR~RGYNILLAqP~nA 156 (589)
.+..|..||....... ||-.| |.|--.| ..|..+ ++.||.+||-|+-..+...
T Consensus 4 ~~~~iA~D~v~qL~~~ypPA~Tt~~L~q~~~d~Fg~aL~~~LR~~GYaV~e~~~~~~ 60 (121)
T PF07283_consen 4 DAQAIAGDMVSQLAEQYPPAKTTFELKQKDPDPFGQALENALRAKGYAVIEDDPPDN 60 (121)
T ss_pred HHHHHHHHHHHHHHHhcCCCccEEEEEcCCCChHHHHHHHHHHhcCcEEEecCCccc
Confidence 4567889999876654 43333 5553344 358765 5779999999998876653
No 25
>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=36.31 E-value=34 Score=36.74 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=28.3
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCCc
Q 007795 442 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGAL 475 (589)
Q Consensus 442 irygd~~~~~~dvkkal~~ai~~~~v~~~~~g~~ 475 (589)
+....+-+.+.+|||||..||-++.++++.+|..
T Consensus 254 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g~ 287 (472)
T cd08502 254 FNHLQPPFDNPKIRRAVLAALDQEDLLAAAVGDP 287 (472)
T ss_pred EcCCCCCCcCHHHHHHHHHhcCHHHHHHHHhCCC
Confidence 3344667889999999999999999999987654
No 26
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=36.19 E-value=50 Score=35.79 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=34.5
Q ss_pred CCCcEEEEEeC-CcchHHHHHH-HhhcCCeEEEeccCC-CChhHHhhc
Q 007795 120 PAPSNYLLISG-DRDFSNALHQ-LRMRRYNILLAQPHK-ASAPLVAAA 164 (589)
Q Consensus 120 PpPANIMLISG-DrDFS~aL~~-LR~RGYNILLAqP~n-AS~~L~~aA 164 (589)
+.+...||||| |..|...|.+ |-.+||+|+..+... ..+.|...+
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 56788999998 8899988754 889999999998543 335566544
No 27
>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=35.44 E-value=2.5e+02 Score=27.14 Aligned_cols=42 Identities=12% Similarity=0.166 Sum_probs=28.4
Q ss_pred cchHHHHHHHhhcCC-eEEE-ec-cCCCChhHHhhcCeEEEeccc
Q 007795 132 RDFSNALHQLRMRRY-NILL-AQ-PHKASAPLVAAAKSVWLWTSL 173 (589)
Q Consensus 132 rDFS~aL~~LR~RGY-NILL-Aq-P~nAS~~L~~aAd~vWlWeSL 173 (589)
.+|+..|..+...|. +|.+ +. +...+..+...|+..|....|
T Consensus 83 ~~fA~~l~~~~~~g~~~i~F~IGG~~G~~~~~~~~a~~~lSLS~m 127 (155)
T PF02590_consen 83 EEFAKKLERWMNQGKSDIVFIIGGADGLSEEVRKRADEKLSLSKM 127 (155)
T ss_dssp HHHHHHHHHHHHTTS-EEEEEE-BTTB--HHHHHH-SEEEES-SS
T ss_pred HHHHHHHHHHHhcCCceEEEEEecCCCCCHHHHhhcCceEEEecC
Confidence 379999999999887 7744 44 566788899888877766544
No 28
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=35.08 E-value=2.9e+02 Score=27.07 Aligned_cols=49 Identities=12% Similarity=0.093 Sum_probs=35.1
Q ss_pred CCCcEEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 120 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 120 PpPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
.+.+-+++||.. ++...++..++.+|-.|+.+..... .+|...++.++.
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 455677888865 4567788888999999998875433 457777776654
No 29
>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=34.63 E-value=2.4e+02 Score=24.56 Aligned_cols=48 Identities=17% Similarity=0.099 Sum_probs=34.0
Q ss_pred CCcEEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 121 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 121 pPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
+.+-+++||-. ++-..++..++++|..|+.+... ...+|...++..+.
T Consensus 46 ~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~-~~s~la~~ad~~l~ 96 (126)
T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNV-VGSTLAREADYVLY 96 (126)
T ss_pred CCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECC-CCChHHHhCCEEEE
Confidence 44567778754 35667788889999999988754 33567777776654
No 30
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=34.37 E-value=3.8e+02 Score=28.59 Aligned_cols=54 Identities=7% Similarity=0.086 Sum_probs=34.6
Q ss_pred CCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 007795 44 NCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (589)
Q Consensus 44 G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVP 97 (589)
-+++..+..-|+..-+..+....+.|+..++-..+..+.++.|...|+.-+++.
T Consensus 72 ~l~~~~l~~ll~~i~~~~~~~~~~e~t~e~~p~~i~~e~l~~l~~~G~~rvslG 125 (375)
T PRK05628 72 LLGAEGLARVLDAVRDTFGLAPGAEVTTEANPESTSPEFFAALRAAGFTRVSLG 125 (375)
T ss_pred cCCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCCCCHHHHHHHHHcCCCEEEEe
Confidence 344444444333322223444445677788877788899999999998877774
No 31
>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=34.12 E-value=2e+02 Score=28.29 Aligned_cols=88 Identities=23% Similarity=0.345 Sum_probs=56.0
Q ss_pred HHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEe--CCc---
Q 007795 58 LVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS--GDR--- 132 (589)
Q Consensus 58 L~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLIS--GDr--- 132 (589)
|.++|+.- --+.||...+..+.++.+.+.|+.+.+.|. .||..|-.+.+. +|.+... ..|+++- |.|
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 44556543 235799999989999999999999999998 688888766544 4444422 4555544 322
Q ss_pred chHHH--HHHHhhcCCeEEEecc
Q 007795 133 DFSNA--LHQLRMRRYNILLAQP 153 (589)
Q Consensus 133 DFS~a--L~~LR~RGYNILLAqP 153 (589)
-++.+ |.+++..+.++.++..
T Consensus 107 ~lani~~l~~~~~~~~~~~l~d~ 129 (208)
T cd07995 107 TLANLNLLLKYAKDGIKIVLIDE 129 (208)
T ss_pred HHHHHHHHHHHHhcCCeEEEEcC
Confidence 23332 2233335777877764
No 32
>PF07415 Herpes_LMP2: Gammaherpesvirus latent membrane protein (LMP2) protein; InterPro: IPR010881 This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) is a human gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear [].; GO: 0019042 latent virus infection, 0033644 host cell membrane; PDB: 2JO9_B 1UXW_C.
Probab=33.27 E-value=15 Score=40.51 Aligned_cols=55 Identities=25% Similarity=0.449 Sum_probs=0.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCcCCCCCCCC
Q 007795 262 HLLRPNNFPMQPNFPQDNFLPHNSQNHGFRPIPPSSNGPRFPPAPPANLPDIGKLNMSEYPNYAQNCPNFH 332 (589)
Q Consensus 262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~f~~~~~~~~pd~~~~~~s~~p~~~~~~~~~~ 332 (589)
+|+|+. ++.++-++++- +-..++-+|...|-.-.++-|++.| +||.+-||||...
T Consensus 7 ~pl~~~--~p~~~~~~dg~------e~~~~~~~ps~~~~~~~~~~~p~~~--------d~~~~~~~pp~y~ 61 (489)
T PF07415_consen 7 QPLGAG--PPSPHGGPDGY------EGSNNSQYPSSFGSSWNSPGPPNYE--------DYPSNSHNPPPYD 61 (489)
T ss_dssp ---------------------------------------------------------------------S-
T ss_pred eeCCCC--CCCCCCCCCCC------CCCCCCCCCcccCCCCCCCCCCCcc--------cCCCCCCCCCCCC
Confidence 677764 34444444442 2222344566666555554445666 5888888888874
No 33
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=32.75 E-value=1.4e+02 Score=31.60 Aligned_cols=42 Identities=17% Similarity=0.177 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhc-Cc-cCceEEEEEecCCCCChhHHHHhhhcCCcee
Q 007795 50 IAQNISSALVKM-NY-CGPVSISAYGDTNRIPASVQHALSSTGIALN 94 (589)
Q Consensus 50 V~~NIrsAL~kl-GY-~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLi 94 (589)
|...|+.+.+.+ .+ .++ |..||+.=+. ..+.+.|...||.++
T Consensus 15 V~rAi~~a~~~~~~~~~~~--vy~lG~iVHN-~~Vv~~L~~~Gv~~v 58 (281)
T PRK12360 15 VKRAIDTAYDEIEKNDGKK--IYTLGPLIHN-NQVVSDLEEKGVKTI 58 (281)
T ss_pred HHHHHHHHHHHHHhcCCCC--eEEecCCcCC-HHHHHHHHHCcCEEE
Confidence 566666664422 22 244 5789998665 468889999999888
No 34
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=32.43 E-value=2.3e+02 Score=30.16 Aligned_cols=85 Identities=20% Similarity=0.280 Sum_probs=58.5
Q ss_pred CCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccch-hhHHHHHHhhhhhcCCC
Q 007795 43 KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDAS-DKKILVDMLFWAVDNPA 121 (589)
Q Consensus 43 ~G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAA-DkkMlVDML~WAldNPp 121 (589)
+|+-+-.|...|++.|=. -.+..|||.-++| .|.|... -+....+++.|..++-
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 678888899988877733 3566779976654 4433311 1334566777776665
Q ss_pred CcEEEEEeCCcchHHHHHHHhhc-CCeEEEecc
Q 007795 122 PSNYLLISGDRDFSNALHQLRMR-RYNILLAQP 153 (589)
Q Consensus 122 PANIMLISGDrDFS~aL~~LR~R-GYNILLAqP 153 (589)
..+++|.-..-.+.+|..||++ ...|+.+.|
T Consensus 68 -ik~lVIACNTASa~al~~LR~~~~iPVvGviP 99 (269)
T COG0796 68 -IKALVIACNTASAVALEDLREKFDIPVVGVIP 99 (269)
T ss_pred -CCEEEEecchHHHHHHHHHHHhCCCCEEEecc
Confidence 6788888888888889999875 677776664
No 35
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=32.43 E-value=1.4e+02 Score=31.63 Aligned_cols=41 Identities=15% Similarity=0.174 Sum_probs=26.0
Q ss_pred hHHHHHHHHHhc-CccCceEEEEEecCCCCChhHHHHhhhcCC-ce
Q 007795 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGI-AL 93 (589)
Q Consensus 50 V~~NIrsAL~kl-GY~GpVTIrAYGD~s~ip~~vr~aLsSSGI-sL 93 (589)
|...|+.+.+.+ .+.+ .|..||+.=+. ..+.+.|...|| .+
T Consensus 14 V~rAi~~a~~~~~~~~~--~iy~lG~iIHN-~~Vv~~L~~~Gv~~~ 56 (280)
T TIGR00216 14 VKRAIQMAEEALKESGK--PVYTLGPIVHN-PQVVERLRERGVFFF 56 (280)
T ss_pred HHHHHHHHHHHHhhcCC--CeEEecCCccC-HHHHHHHHHCCCEEe
Confidence 556666554433 2233 35778987665 467888999996 44
No 36
>PRK14820 NADH dehydrogenase subunit B; Provisional
Probab=32.40 E-value=43 Score=33.54 Aligned_cols=29 Identities=14% Similarity=0.103 Sum_probs=21.9
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhccccCCC
Q 007795 403 QGRLTPSEYVQGLIGVILLALNTLKIERVVPS 434 (589)
Q Consensus 403 ~~~~~~s~~~q~li~~il~al~~lk~ek~~pt 434 (589)
+|||+ .++.+++.|+++++.++.|.+-+.
T Consensus 137 PGCPP---~Pe~il~~l~~l~~~i~~~~~~~~ 165 (180)
T PRK14820 137 PGCPP---RPEQIIDGVMRVQELVKNESLRRR 165 (180)
T ss_pred cCCCC---CHHHHHHHHHHHHHHHhhcccccc
Confidence 78887 455678888888888888876543
No 37
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=31.56 E-value=3.6e+02 Score=27.04 Aligned_cols=94 Identities=12% Similarity=0.151 Sum_probs=54.3
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~L 141 (589)
.+|.|.+.|-...+-..+...|...|+...... |..+. . +. +..-.+-+.+++||-- .+...++...
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 345555555333332334445666787666531 11111 1 11 1122345678888854 3566778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
+++|-.|+++.. . ..+|...|+.++.-
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 45688888877664
No 38
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=31.51 E-value=1.9e+02 Score=35.33 Aligned_cols=38 Identities=26% Similarity=0.449 Sum_probs=21.1
Q ss_pred HHHHhhhhccccCCCCccccch--hhcCCCCCCCchHHHHHHHH
Q 007795 420 LLALNTLKIERVVPSEANITDC--IRYGEPKHRNTDVRKALNCA 461 (589)
Q Consensus 420 l~al~~lk~ek~~pte~ni~dc--irygd~~~~~~dvkkal~~a 461 (589)
+.-+|-.| |.|++=. -+| ++.-+-|+.|-|.=--|+.-
T Consensus 626 Mrr~nW~k---I~p~d~s-~~cFWvkv~Edk~en~dlfakL~~~ 665 (1102)
T KOG1924|consen 626 MRRFNWSK---IVPRDLS-ENCFWVKVNEDKLENDDLFAKLALK 665 (1102)
T ss_pred cccCCccc---cCccccC-ccceeeecchhhccchHHHHHHHHH
Confidence 34455555 6676521 245 45567788887764444433
No 39
>COG3233 Predicted deacetylase [General function prediction only]
Probab=31.48 E-value=84 Score=32.80 Aligned_cols=34 Identities=24% Similarity=0.294 Sum_probs=26.1
Q ss_pred CCCCcEEEEE----------eCCcchHHHHHHHhhcCCeEEEec
Q 007795 119 NPAPSNYLLI----------SGDRDFSNALHQLRMRRYNILLAQ 152 (589)
Q Consensus 119 NPpPANIMLI----------SGDrDFS~aL~~LR~RGYNILLAq 152 (589)
++.+.+++|| +.|..|+..|++++++||.++|=.
T Consensus 31 ~~~~~t~lLViPn~~~~~~l~~d~rf~~~l~~r~e~Gdel~lHG 74 (233)
T COG3233 31 GAQNSTVLLVIPNHANDYPLSKDPRFVDLLTEREEEGDELVLHG 74 (233)
T ss_pred CCCCceEEEEeeccCCCCCcccChHHHHHHHHHHhcCCEEEEec
Confidence 3556666443 356789999999999999998853
No 40
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=31.33 E-value=1e+03 Score=30.83 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=20.3
Q ss_pred hhccCceEEEEEecC-------CCCCCCCChhhhHHHHHH-HHHhcCccC
Q 007795 24 QYVTAKTSVWWDIEN-------CQVPKNCDPHTIAQNISS-ALVKMNYCG 65 (589)
Q Consensus 24 eya~AkTaVFWDIEN-------CPVP~G~da~~V~~NIrs-AL~klGY~G 65 (589)
+-.....++||.-+| |.+-..-+-.....+|+. +|.++-..|
T Consensus 1205 ~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l~G 1254 (1605)
T KOG0260|consen 1205 RGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTLRG 1254 (1605)
T ss_pred hhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhcccCC
Confidence 333456667776554 233222233445566765 455544444
No 41
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=31.24 E-value=2.5e+02 Score=27.78 Aligned_cols=42 Identities=24% Similarity=0.279 Sum_probs=32.4
Q ss_pred cchHHHHHHHhhcCCeEEEe--ccCCCChhHHhhcCeEEEeccc
Q 007795 132 RDFSNALHQLRMRRYNILLA--QPHKASAPLVAAAKSVWLWTSL 173 (589)
Q Consensus 132 rDFS~aL~~LR~RGYNILLA--qP~nAS~~L~~aAd~vWlWeSL 173 (589)
..|+..|..|+..|-+|.++ .+..-++.+...|+..|.+..|
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 36999999999988766443 3667788899988888776554
No 42
>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=31.19 E-value=4.8e+02 Score=25.72 Aligned_cols=113 Identities=23% Similarity=0.291 Sum_probs=59.0
Q ss_pred CceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcC---ccCceEEEEEecC----CCC-ChhHHHHhhhcCCce-eeccC
Q 007795 28 AKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMN---YCGPVSISAYGDT----NRI-PASVQHALSSTGIAL-NHVPA 98 (589)
Q Consensus 28 AkTaVFWDIENCPVP~G~da~~V~~NIrsAL~klG---Y~GpVTIrAYGD~----s~i-p~~vr~aLsSSGIsL-ihVPa 98 (589)
.--+|..|.+||=++.+-+ .+.+.+...++++- ....|.| +-+. .+. ..++...-...||.+ .|- +
T Consensus 40 Gik~li~DkDNTL~~~~~~--~i~~~~~~~~~~l~~~~~~~~v~I--vSNsaGs~~d~~~~~a~~~~~~lgIpvl~h~-~ 114 (168)
T PF09419_consen 40 GIKALIFDKDNTLTPPYED--EIPPEYAEWLNELKKQFGKDRVLI--VSNSAGSSDDPDGERAEALEKALGIPVLRHR-A 114 (168)
T ss_pred CceEEEEcCCCCCCCCCcC--cCCHHHHHHHHHHHHHCCCCeEEE--EECCCCcccCccHHHHHHHHHhhCCcEEEeC-C
Confidence 3468899999998764433 23444444433332 2112433 3332 111 122333334568874 453 1
Q ss_pred CCccchhhHHHHHHhhhhhcC---CCCcEEEEEeCCcchHHHHHHHhhcCCeEEEe
Q 007795 99 GVKDASDKKILVDMLFWAVDN---PAPSNYLLISGDRDFSNALHQLRMRRYNILLA 151 (589)
Q Consensus 99 G~KdAADkkMlVDML~WAldN---PpPANIMLISGDrDFS~aL~~LR~RGYNILLA 151 (589)
.|-... .+++.|-..+ -.|..++ +-||+=|...|---++.-|.|++-
T Consensus 115 -kKP~~~----~~i~~~~~~~~~~~~p~eia-vIGDrl~TDVl~gN~~G~~tilv~ 164 (168)
T PF09419_consen 115 -KKPGCF----REILKYFKCQKVVTSPSEIA-VIGDRLFTDVLMGNRMGSYTILVT 164 (168)
T ss_pred -CCCccH----HHHHHHHhhccCCCCchhEE-EEcchHHHHHHHhhccCceEEEEe
Confidence 233222 2344443333 1344444 459999999998888777888764
No 43
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=31.19 E-value=3.4e+02 Score=27.99 Aligned_cols=90 Identities=18% Similarity=0.197 Sum_probs=57.3
Q ss_pred EEEEe--cCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHHhh
Q 007795 69 ISAYG--DTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQLRM 143 (589)
Q Consensus 69 IrAYG--D~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~LR~ 143 (589)
|..|| -..-+-.++...|..-|+.+..+. |..++. | .+....+-+-+++||-. ++...++...++
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 44444 333355667778889999888873 334444 2 22233455667777744 356777888899
Q ss_pred cCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 144 RRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 144 RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
+|..||.+..... .+|...|+.++.
T Consensus 203 ~ga~vIaiT~~~~-spla~~Ad~~L~ 227 (281)
T COG1737 203 RGAKVIAITDSAD-SPLAKLADIVLL 227 (281)
T ss_pred CCCcEEEEcCCCC-CchhhhhceEEe
Confidence 9999999874433 457777765544
No 44
>PRK15482 transcriptional regulator MurR; Provisional
Probab=30.39 E-value=4.1e+02 Score=27.07 Aligned_cols=95 Identities=12% Similarity=0.097 Sum_probs=57.7
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~L 141 (589)
.+|-|.+.|....+-..+...|...|..+.... |..+...+ +..-.+-+-+++||-. ++...++..+
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 456666666544444455666777787665542 12222111 2122344778888865 3566778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
+++|-.|+++..... .+|...|+..+.-
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 899999998874433 4577777766654
No 45
>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=29.73 E-value=47 Score=27.33 Aligned_cols=19 Identities=42% Similarity=0.494 Sum_probs=14.2
Q ss_pred HHHHHHHHhcCccCceEEE
Q 007795 52 QNISSALVKMNYCGPVSIS 70 (589)
Q Consensus 52 ~NIrsAL~klGY~GpVTIr 70 (589)
..|-++|+..||.|+|+|-
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 46
>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=29.25 E-value=2.3e+02 Score=27.26 Aligned_cols=64 Identities=16% Similarity=0.264 Sum_probs=41.7
Q ss_pred hHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEE
Q 007795 81 SVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILL 150 (589)
Q Consensus 81 ~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILL 150 (589)
...++|...|+...++|...-++ ..| .+++. ....+..++++.|+..=..+...|+++|++|.-
T Consensus 82 ~Ta~~l~~~G~~~~~~~~~~~~s--~~L-~~~l~---~~~~~~~vl~~~g~~~~~~l~~~L~~~g~~v~~ 145 (231)
T PF02602_consen 82 KTAEALREYGFQPDFVPSSEGSS--EGL-AELLK---EQLRGKRVLILRGEGGRPDLPEKLREAGIEVTE 145 (231)
T ss_dssp HHHHHHHHTT-EECEE-TTSSSH--HHH-HGGHH---HCCTTEEEEEEESSSSCHHHHHHHHHTTEEEEE
T ss_pred HHHHHHHHcCCCccccCCCCCCH--HHH-HHHHH---hhCCCCeEEEEcCCCccHHHHHHHHHCCCeEEE
Confidence 45678888999988888633332 122 23222 244458899999987666677888999988854
No 47
>PRK10294 6-phosphofructokinase 2; Provisional
Probab=28.45 E-value=4.4e+02 Score=26.74 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=31.3
Q ss_pred hHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 007795 50 IAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (589)
Q Consensus 50 V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVP 97 (589)
..-|+-.+|.++|.. ...+.+.|| ..-..+++.|...||.+.++.
T Consensus 40 ~~~NvA~~l~~lG~~-~~~i~~vG~--~~g~~i~~~l~~~gv~~~~~~ 84 (309)
T PRK10294 40 GGINVARAIAHLGGS-ATAIFPAGG--ATGEHLVSLLADENVPVATVE 84 (309)
T ss_pred cHHHHHHHHHHcCCC-eEEEEEecC--ccHHHHHHHHHHcCCCceEEE
Confidence 345677788888764 124556676 455668889999999876653
No 48
>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=28.17 E-value=5.1e+02 Score=24.40 Aligned_cols=49 Identities=14% Similarity=0.062 Sum_probs=35.4
Q ss_pred CCcEEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 121 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 121 pPANIMLISGD---rDFS~aL~~LR~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
+.+-+++||.- ++-..++..++++|-.|+.+..... .+|...|+..+..
T Consensus 101 ~~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~-s~La~~aD~~l~~ 152 (177)
T cd05006 101 PGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDG-GKLLELADIEIHV 152 (177)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCC-CchhhhCCEEEEe
Confidence 44667777743 4678888999999999998875443 3477778776554
No 49
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=27.78 E-value=61 Score=32.68 Aligned_cols=26 Identities=12% Similarity=0.216 Sum_probs=18.8
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhcccc
Q 007795 403 QGRLTPSEYVQGLIGVILLALNTLKIERV 431 (589)
Q Consensus 403 ~~~~~~s~~~q~li~~il~al~~lk~ek~ 431 (589)
+|||+. ++.+++.|+..+..+|.|.+
T Consensus 137 PGCPP~---Pe~il~~l~~L~~~i~~~~~ 162 (186)
T PRK14814 137 PGCPPR---PEAILDALVKLQTKLKTQGL 162 (186)
T ss_pred cCCCCC---HHHHHHHHHHHHHHHhcccc
Confidence 789884 45577777777788876655
No 50
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=27.68 E-value=1.1e+02 Score=29.88 Aligned_cols=53 Identities=21% Similarity=0.308 Sum_probs=36.5
Q ss_pred chhhHHHHHHhhhhhcC-CCCcEEEEEeCC-c-chHHH-HHHHhhcCCeEEEeccCC
Q 007795 103 ASDKKILVDMLFWAVDN-PAPSNYLLISGD-R-DFSNA-LHQLRMRRYNILLAQPHK 155 (589)
Q Consensus 103 AADkkMlVDML~WAldN-PpPANIMLISGD-r-DFS~a-L~~LR~RGYNILLAqP~n 155 (589)
.....|..||....... ||-.|.+.|--| . .|..+ ++.||.+||-|+--.+..
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 45678999999876555 444444444443 4 58775 577999999999766543
No 51
>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=27.52 E-value=1.3e+02 Score=27.89 Aligned_cols=40 Identities=20% Similarity=0.268 Sum_probs=30.6
Q ss_pred HHHHH-hcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCC
Q 007795 55 SSALV-KMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAG 99 (589)
Q Consensus 55 rsAL~-klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG 99 (589)
-+.|+ ++||.| .|+|.||.- .+-+.-|..+|+.-..++.+
T Consensus 39 ArlLR~r~gy~G--elRA~Gdvl---~DQl~~l~R~GFdsf~l~~~ 79 (110)
T PF06073_consen 39 ARLLRERYGYTG--ELRAVGDVL---RDQLFYLRRCGFDSFELRED 79 (110)
T ss_pred HHHHHHHcCCCC--cEEEeccch---HHHHHHHHHcCCCEEEeCCC
Confidence 34566 789999 689999963 35566788999988888664
No 52
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=27.11 E-value=6e+02 Score=25.60 Aligned_cols=100 Identities=10% Similarity=0.167 Sum_probs=48.8
Q ss_pred hhhHHHHHHHHHhcCccCce-----------EEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCccchhhHHHH
Q 007795 48 HTIAQNISSALVKMNYCGPV-----------SISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILV 110 (589)
Q Consensus 48 ~~V~~NIrsAL~klGY~GpV-----------TIrAY-GD~s~-----ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlV 110 (589)
......|..+++++||.-.. +|-.. .++.. +-..+.+++...|..+..+..... . .-..
T Consensus 35 ~~tr~~V~~~a~elgY~p~~~a~~l~~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~~~-~---~~~~ 110 (342)
T PRK10014 35 TATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQGGKD-G---EQLA 110 (342)
T ss_pred HHHHHHHHHHHHHhCCCcCHHHHhhccCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeCCCC-H---HHHH
Confidence 34567788889999985410 12111 22221 123344566667766655443211 1 1112
Q ss_pred HHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEec
Q 007795 111 DMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (589)
Q Consensus 111 DML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq 152 (589)
+.+..... -..+-|++...+......+..|+..+..|+++.
T Consensus 111 ~~~~~l~~-~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~ 151 (342)
T PRK10014 111 QRFSTLLN-QGVDGVVIAGAAGSSDDLREMAEEKGIPVVFAS 151 (342)
T ss_pred HHHHHHHh-CCCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEe
Confidence 22222221 224555655544444456667777777776664
No 53
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=27.03 E-value=2.8e+02 Score=30.47 Aligned_cols=87 Identities=20% Similarity=0.271 Sum_probs=53.7
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHH---hhhhhcCCCCcEEEEEeCCcchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDM---LFWAVDNPAPSNYLLISGDRDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDM---L~WAldNPpPANIMLISGDrDFS~aL~~L 141 (589)
+|=-+-..|.-.-++.+.-.+|.+-||++.-.-...+.-...++...| +-||+.| .+++|++| .||...|..|
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 343444578888899999999999999988864322222223444444 4456666 67888887 7777544444
Q ss_pred hhcCCeEEEeccCCCC
Q 007795 142 RMRRYNILLAQPHKAS 157 (589)
Q Consensus 142 R~RGYNILLAqP~nAS 157 (589)
-.+ +|+.+.-.+.+
T Consensus 151 ~k~--~~~p~~~~n~~ 164 (337)
T COG2247 151 MKE--GIVPVILKNTS 164 (337)
T ss_pred Hhc--CcceeEecccc
Confidence 323 66555534443
No 54
>PRK13835 conjugal transfer protein TrbH; Provisional
Probab=26.83 E-value=1.4e+02 Score=29.28 Aligned_cols=51 Identities=18% Similarity=0.238 Sum_probs=34.3
Q ss_pred CccchhhHHHHHHhhhhhc-CCCCcEEEEEeCC-cchHHHH-HHHhhcCCeEEE
Q 007795 100 VKDASDKKILVDMLFWAVD-NPAPSNYLLISGD-RDFSNAL-HQLRMRRYNILL 150 (589)
Q Consensus 100 ~KdAADkkMlVDML~WAld-NPpPANIMLISGD-rDFS~aL-~~LR~RGYNILL 150 (589)
....+...|.-||..-... .||-.|-+.+--| ..|..+| ..||.+||.|+=
T Consensus 34 ~t~~aa~~iA~D~vsqLae~~pPa~tt~~l~q~~d~Fg~aL~~aLr~~GYaVvt 87 (145)
T PRK13835 34 LSGPAASAIAGDMVSRLAEQIGPGTTTIKLKKDTSPFGQALEAALKGWGYAVVT 87 (145)
T ss_pred hcchHHHHHHHHHHHHHHHhcCCCceEEEEeecCcHHHHHHHHHHHhcCeEEee
Confidence 3345677899999975544 4544444444444 4687754 679999999994
No 55
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=26.76 E-value=4e+02 Score=24.92 Aligned_cols=51 Identities=10% Similarity=0.016 Sum_probs=35.4
Q ss_pred CCCcEEEEEeCCc---chHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEEec
Q 007795 120 PAPSNYLLISGDR---DFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (589)
Q Consensus 120 PpPANIMLISGDr---DFS~aL~~LR~RGYNILLAqP~nAS~~L~~aAd~vWlWe 171 (589)
.+-+-+++||... +-..++..++++|-.|+.+... ...+|...|+.++.-.
T Consensus 78 ~~~D~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~-~~s~l~~~ad~~l~~~ 131 (154)
T TIGR00441 78 QKGDVLLGISTSGNSKNVLKAIEAAKDKGMKTITLAGK-DGGKMAGLADIELRVP 131 (154)
T ss_pred CCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCC-CCCchhhhCCEEEEeC
Confidence 4456788888653 5667788888999999988754 3345777777666543
No 56
>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=26.47 E-value=5.1e+02 Score=24.61 Aligned_cols=100 Identities=18% Similarity=0.265 Sum_probs=53.1
Q ss_pred CChhhhHHHHHHH---HHhc-CccCceEEEEEecCCCCChhHHHHhhhcCCceeecc--CCC-ccchhhHHHHHHhhhhh
Q 007795 45 CDPHTIAQNISSA---LVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP--AGV-KDASDKKILVDMLFWAV 117 (589)
Q Consensus 45 ~da~~V~~NIrsA---L~kl-GY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVP--aG~-KdAADkkMlVDML~WAl 117 (589)
.+...+...|.++ |++. |..-+.-.--||.. ...+++.|...|+.++.-- ..+ .......++. .+.
T Consensus 74 ~~~~~~~~ei~~~~~~l~~~~g~~~~~fr~P~G~~---~~~~~~~l~~~G~~~v~w~~~~~D~~~~~~~~i~~----~~~ 146 (191)
T TIGR02764 74 LEDEKIKKDILRAQEIIEKLTGKKPTLFRPPSGAF---NKAVLKAAESLGYTVVHWSVDSRDWKNPGVESIVD----RVV 146 (191)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCCEEECCCcCC---CHHHHHHHHHcCCeEEEecCCCCccCCCCHHHHHH----HHH
Confidence 4444555555553 3332 32211222335654 3567888999999877642 111 1112223333 333
Q ss_pred cCCCCcEEEEEe--CCc-----chHHHHHHHhhcCCeEEEe
Q 007795 118 DNPAPSNYLLIS--GDR-----DFSNALHQLRMRRYNILLA 151 (589)
Q Consensus 118 dNPpPANIMLIS--GDr-----DFS~aL~~LR~RGYNILLA 151 (589)
.+-.+..|+|.= ++. -+..+|..|+.+||.++-+
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 344455666665 232 3556788899999998643
No 57
>PRK01254 hypothetical protein; Provisional
Probab=26.44 E-value=73 Score=37.87 Aligned_cols=41 Identities=20% Similarity=0.510 Sum_probs=28.1
Q ss_pred cEEEEEeCC-----cchHHHH--HHHhhcCCeE-EEeccCC-CChhHHhh
Q 007795 123 SNYLLISGD-----RDFSNAL--HQLRMRRYNI-LLAQPHK-ASAPLVAA 163 (589)
Q Consensus 123 ANIMLISGD-----rDFS~aL--~~LR~RGYNI-LLAqP~n-AS~~L~~a 163 (589)
.-|+||||| ..|..+| +-|...||+| |++||.= ..+.+...
T Consensus 40 ~DiilVtGDAYVDHPsFG~AiigR~Le~~G~rVgIiaQPdw~~~~df~~l 89 (707)
T PRK01254 40 CDIIIVTGDAYVDHPSFGMAIIGRMLEAQGFRVGIIAQPDWSSKDDFMRL 89 (707)
T ss_pred cCEEEEeCcccccCccchHHHHHHHHHHcCCeEEEEeCCCCCChHHHHHh
Confidence 459999999 3576654 4467799999 7788863 23444443
No 58
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=26.07 E-value=7.2e+02 Score=30.36 Aligned_cols=44 Identities=16% Similarity=0.216 Sum_probs=31.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 007795 273 PNFPQDNFLPHNSQNHGFRPIPPSSNGPRFPPAPPANLPDIGKL 316 (589)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~~f~~~~~~~~pd~~~~ 316 (589)
+++...-..+|......-+++|+-+-=+.|+..++.|-||.+.+
T Consensus 217 ~~~~t~~~~ppV~n~Pp~~sVp~~tpl~q~SG~~~~n~p~vs~~ 260 (944)
T KOG4307|consen 217 ADLSTTRSLPPVNNPPPPHSVPQFTPLKQFSGNKLGNNPDVSSR 260 (944)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCcCcC
Confidence 44555555566666666667778777788877788899999887
No 59
>PRK07334 threonine dehydratase; Provisional
Probab=26.00 E-value=1.8e+02 Score=31.53 Aligned_cols=94 Identities=16% Similarity=0.173 Sum_probs=59.2
Q ss_pred CChhhhHHHHHHHHHhcCccCceEEEEEe-cCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCc
Q 007795 45 CDPHTIAQNISSALVKMNYCGPVSISAYG-DTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPS 123 (589)
Q Consensus 45 ~da~~V~~NIrsAL~klGY~GpVTIrAYG-D~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPA 123 (589)
.+...+..-+..+|...||. +.|...+ |...+-.++...|+..++.+..+-.. ++...+ .+....-
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-RLFTDL----------PAKGAEL 373 (403)
T ss_pred CCHHHHHHHHHHHHHhCCCE--EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEE-ecccCC----------CCCeEEE
Confidence 56777777788899888885 4444443 33445578888999999999887321 100000 0011122
Q ss_pred EEEEEeCC-cchHHHHHHHhhcCCeEEEe
Q 007795 124 NYLLISGD-RDFSNALHQLRMRRYNILLA 151 (589)
Q Consensus 124 NIMLISGD-rDFS~aL~~LR~RGYNILLA 151 (589)
+|.|-..| ..+..++.+||..||.+-++
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 46889999999999998765
No 60
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=25.42 E-value=3.9e+02 Score=27.20 Aligned_cols=112 Identities=16% Similarity=0.077 Sum_probs=56.2
Q ss_pred EEEEEec--CCCCC-CCCChhhhHHHHHHHHHhcCccCceEEEEEecCCC-C----ChhHHHHhhhcCCceee--ccCCC
Q 007795 31 SVWWDIE--NCQVP-KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNR-I----PASVQHALSSTGIALNH--VPAGV 100 (589)
Q Consensus 31 aVFWDIE--NCPVP-~G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~-i----p~~vr~aLsSSGIsLih--VPaG~ 100 (589)
.||+|-. ++.++ -+.|-+..+..+...|.++|++ .|-+-. +.... . -..++++|...|+.+.. +..+.
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 33222 1234444455556667777764 343211 22211 1 13467788888986432 11111
Q ss_pred ccc-hhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeE
Q 007795 101 KDA-SDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNI 148 (589)
Q Consensus 101 KdA-ADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNI 148 (589)
-+. .....+.. |...++.| +-++..+|.-...++..|+++|++|
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 32234444 4566667776778899999998864
No 61
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=25.33 E-value=67 Score=32.13 Aligned_cols=24 Identities=13% Similarity=0.476 Sum_probs=15.8
Q ss_pred CCCCcEEEEEeCC--cchHHHHHHHh
Q 007795 119 NPAPSNYLLISGD--RDFSNALHQLR 142 (589)
Q Consensus 119 NPpPANIMLISGD--rDFS~aL~~LR 142 (589)
+|.-+.+|||+|. +.....|.++-
T Consensus 67 SPRhADvLlVtG~vT~km~~~l~~~y 92 (173)
T PRK14818 67 SPRQADFMIVAGTLTYKMAERARLLY 92 (173)
T ss_pred CcccccEEEEeCcCccccHHHHHHHH
Confidence 4666778888886 35556665554
No 62
>PF10073 DUF2312: Uncharacterized protein conserved in bacteria (DUF2312); InterPro: IPR018753 This entry is represented by Azospirillum phage Cd, Gp10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family of hypothetical bacterial proteins have no known function.
Probab=25.29 E-value=22 Score=31.12 Aligned_cols=41 Identities=29% Similarity=0.435 Sum_probs=30.4
Q ss_pred HHHHHHHHhhhhccccCCCCccccchhh--cCCCCCCCchHHHHHHHHH
Q 007795 416 IGVILLALNTLKIERVVPSEANITDCIR--YGEPKHRNTDVRKALNCAI 462 (589)
Q Consensus 416 i~~il~al~~lk~ek~~pte~ni~dcir--ygd~~~~~~dvkkal~~ai 462 (589)
++.+..=++-|..|| +.|+|+|+ |.+.|..|||+| +|.-.|
T Consensus 6 Lr~~ieRiErLEeEk-----~~i~~dikdVyaEAK~~GfD~K-~lr~ii 48 (74)
T PF10073_consen 6 LRQFIERIERLEEEK-----KAISDDIKDVYAEAKGNGFDTK-ALRQII 48 (74)
T ss_pred HHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHhCCCCHH-HHHHHH
Confidence 444555667777777 67999997 999999999985 444433
No 63
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=25.13 E-value=3e+02 Score=27.82 Aligned_cols=117 Identities=21% Similarity=0.275 Sum_probs=65.2
Q ss_pred cCceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhh
Q 007795 27 TAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDK 106 (589)
Q Consensus 27 ~AkTaVFWDIENCPVP~G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADk 106 (589)
....+|+-|++|-=||= +-.+..+.++.-|..+-..|. .+...-+ .-...+...++.-||..++- ++ |-.+
T Consensus 26 ~Gikgvi~DlDNTLv~w--d~~~~tpe~~~W~~e~k~~gi-~v~vvSN--n~e~RV~~~~~~l~v~fi~~-A~-KP~~-- 96 (175)
T COG2179 26 HGIKGVILDLDNTLVPW--DNPDATPELRAWLAELKEAGI-KVVVVSN--NKESRVARAAEKLGVPFIYR-AK-KPFG-- 96 (175)
T ss_pred cCCcEEEEeccCceecc--cCCCCCHHHHHHHHHHHhcCC-EEEEEeC--CCHHHHHhhhhhcCCceeec-cc-CccH--
Confidence 45678888988888872 222345566665555544442 2222223 33355666777777766663 21 2111
Q ss_pred HHHHHHhhhhhc--CCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEeccCCCCh
Q 007795 107 KILVDMLFWAVD--NPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHKASA 158 (589)
Q Consensus 107 kMlVDML~WAld--NPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~nAS~ 158 (589)
-.+.+|+. +-+|.++++ -||.-|...|.-=| .|+..||+-|-..+.
T Consensus 97 ----~~fr~Al~~m~l~~~~vvm-VGDqL~TDVlggnr-~G~~tIlV~Pl~~~d 144 (175)
T COG2179 97 ----RAFRRALKEMNLPPEEVVM-VGDQLFTDVLGGNR-AGMRTILVEPLVAPD 144 (175)
T ss_pred ----HHHHHHHHHcCCChhHEEE-Ecchhhhhhhcccc-cCcEEEEEEEecccc
Confidence 12333432 334444333 38998888765433 588888888765543
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=24.70 E-value=1.1e+02 Score=29.74 Aligned_cols=62 Identities=23% Similarity=0.316 Sum_probs=35.9
Q ss_pred HHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEeccC
Q 007795 83 QHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH 154 (589)
Q Consensus 83 r~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~ 154 (589)
++.|...||....+|. - -||..|-.-+..+.. . -..++|+|+|+||.-++ ..+.+|.+..+.
T Consensus 92 ~~~l~~~gi~~~~~~g-~--EADDvIatla~~~~~-~--~~~v~IvS~DkD~~QLv----~~~~~V~~~~~~ 153 (169)
T PF02739_consen 92 KELLEALGIPVLEVPG-Y--EADDVIATLAKKASE-E--GFEVIIVSGDKDLLQLV----DENVNVYLLDPG 153 (169)
T ss_dssp HHHHHHTTSEEEEETT-B---HHHHHHHHHHHHHH-T--TCEEEEE-SSGGGGGGT----CS-TSEEEEETT
T ss_pred HHHHHHCCCCEecCCC-C--cHHHHHHHHHhhhcc-C--CCEEEEEcCCCCHHHhc----CCCceEEEeecC
Confidence 3445567988888763 2 245544443333332 2 35799999999987654 334567666653
No 65
>PRK14816 NADH dehydrogenase subunit B; Provisional
Probab=23.42 E-value=65 Score=32.42 Aligned_cols=34 Identities=18% Similarity=0.383 Sum_probs=19.5
Q ss_pred HHHhhhhh----cCCCCcEEEEEeCCc--chHHHHHHHhh
Q 007795 110 VDMLFWAV----DNPAPSNYLLISGDR--DFSNALHQLRM 143 (589)
Q Consensus 110 VDML~WAl----dNPpPANIMLISGDr--DFS~aL~~LR~ 143 (589)
.|+-.|.. ..|.-+.++||+|-. .....|.++.+
T Consensus 65 yD~eRfGi~~~~~sPRhADvllVtG~VT~~m~~~l~~~~e 104 (182)
T PRK14816 65 YDMARFGFEVARASPRQADMIMVCGTITNKMAPVLKRLYD 104 (182)
T ss_pred ccHHHhCccccCCCCCcceEEEEecCCcchhHHHHHHHHH
Confidence 34555543 345667788888863 44455555543
No 66
>KOG3154 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.93 E-value=1.1e+02 Score=32.05 Aligned_cols=66 Identities=21% Similarity=0.443 Sum_probs=46.6
Q ss_pred eEEEEEecCCCCCCCCChhhhHH-HHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 007795 30 TSVWWDIENCQVPKNCDPHTIAQ-NISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (589)
Q Consensus 30 TaVFWDIENCPVP~G~da~~V~~-NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVP 97 (589)
.-..||++-|- |.-+++..+.. +..+.|+...-.|=|.++-.|+.. ++...++-+...|+.+++|.
T Consensus 44 ~lamwdf~hCd-pkrCsGkKL~rlglv~~lr~g~kF~GvVlSP~gk~~-vsp~D~d~v~~~G~avvdCS 110 (263)
T KOG3154|consen 44 RLAMWDFGHCD-PKRCSGKKLARLGLVRNLRVGQKFGGVVLSPVGKQC-VSPADRDVVERSGAAVVDCS 110 (263)
T ss_pred hhhhhcccCCC-ccccchHHHHhhhhHHHhhccCccCceEECCCCCcc-cCHHHHHHHHhcCceEEecc
Confidence 34579999996 78898876654 455666654334457777777754 44556777888999999873
No 67
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.90 E-value=1.8e+02 Score=30.41 Aligned_cols=71 Identities=17% Similarity=0.300 Sum_probs=43.9
Q ss_pred eEEE-EEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhh--------cCCceeec-cCC
Q 007795 30 TSVW-WDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSS--------TGIALNHV-PAG 99 (589)
Q Consensus 30 TaVF-WDIENCPVP~G~da~~V~~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsS--------SGIsLihV-PaG 99 (589)
+.|| .-+||+.-|.. +-..+..-++..|.++.-.+.|.|+..||.+.+|.++++++.. .|+.|.-+ ..|
T Consensus 75 lTvYaFS~eN~~R~~~-Ev~~Lm~L~~~~l~~~~~~~~irv~~iG~~~~lp~~~~~~~~~~e~~T~~~~~~~Lnia~~Yg 153 (256)
T PRK14828 75 VTLYLLSTDNLGRPSE-ELNPLLDIIEDVVRQLAPDGRWRVRHVGSLDLLPAPSANRLKEAEEATVGNDGIKVNVAVGYG 153 (256)
T ss_pred EEEEEEEhhhcCCCHH-HHHHHHHHHHHHHHHHHHhCCeEEEEECChhhCCHHHHHHHHHHHHhhcCCCCcEEEEEecCC
Confidence 4443 45799976641 1223444455555544334578999999999999998887753 45555543 344
Q ss_pred Cc
Q 007795 100 VK 101 (589)
Q Consensus 100 ~K 101 (589)
.+
T Consensus 154 gr 155 (256)
T PRK14828 154 GR 155 (256)
T ss_pred CH
Confidence 43
No 68
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=22.76 E-value=2.4e+02 Score=24.39 Aligned_cols=96 Identities=16% Similarity=0.154 Sum_probs=54.3
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCC---cchHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGD---rDFS~aL~~L 141 (589)
.+|.|.++|....+-......|...|.....+... . .+..+.+ ....+-+-+++||-. ++....+..+
T Consensus 6 ~~i~i~G~G~s~~~A~~~~~~l~~~~~~~~~~~~~----~--~~~~~~~---~~~~~~d~vi~is~sg~~~~~~~~~~~a 76 (131)
T PF01380_consen 6 KRIYIYGSGSSYGVAQYAALKLQKLGRIVVISYEA----G--EFFHGPL---ENLDPDDLVIIISYSGETRELIELLRFA 76 (131)
T ss_dssp SEEEEEESTHHHHHHHHHHHHHHHHHSSEEEEEEH----H--HHHTTGG---GGCSTTEEEEEEESSSTTHHHHHHHHHH
T ss_pred CEEEEEEcchHHHHHHHHHHHHHHhcCcceeccch----H--HHhhhhc---ccccccceeEeeeccccchhhhhhhHHH
Confidence 35666666665555445555565556555444211 0 0111111 112233557777754 4567788888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWlW 170 (589)
+++|-.|+++.-.. ..++...++.++.-
T Consensus 77 k~~g~~vi~iT~~~-~~~l~~~ad~~l~~ 104 (131)
T PF01380_consen 77 KERGAPVILITSNS-ESPLARLADIVLYI 104 (131)
T ss_dssp HHTTSEEEEEESST-TSHHHHHSSEEEEE
T ss_pred HhcCCeEEEEeCCC-CCchhhhCCEEEEe
Confidence 99999998887443 35577777766553
No 69
>PRK14815 NADH dehydrogenase subunit B; Provisional
Probab=22.51 E-value=73 Score=32.11 Aligned_cols=33 Identities=12% Similarity=0.335 Sum_probs=20.2
Q ss_pred HHHhhhhh----cCCCCcEEEEEeCCcc--hHHHHHHHh
Q 007795 110 VDMLFWAV----DNPAPSNYLLISGDRD--FSNALHQLR 142 (589)
Q Consensus 110 VDML~WAl----dNPpPANIMLISGDrD--FS~aL~~LR 142 (589)
.|+-.|.+ ..|..+.++||+|..- ....|.++.
T Consensus 57 yDieRfGi~~~~~SPR~ADillVtG~VT~~m~~~l~r~y 95 (183)
T PRK14815 57 FDISRFGAEVMRFSPRQADVMIVAGTVTYKMALAVRRIY 95 (183)
T ss_pred ccHHHhCcccCCCCCccccEEEEeCcCchhhHHHHHHHH
Confidence 34555542 3567788888888643 346666654
No 70
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.47 E-value=3.1e+02 Score=29.37 Aligned_cols=27 Identities=15% Similarity=0.455 Sum_probs=24.6
Q ss_pred cE-EEEEeCCcchHHHHHHHhhcCCeEE
Q 007795 123 SN-YLLISGDRDFSNALHQLRMRRYNIL 149 (589)
Q Consensus 123 AN-IMLISGDrDFS~aL~~LR~RGYNIL 149 (589)
.+ |-+|+...++.-+.+.||.+||+|.
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 8899999999999999999999997
No 71
>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=22.38 E-value=61 Score=32.95 Aligned_cols=31 Identities=29% Similarity=0.545 Sum_probs=25.3
Q ss_pred cCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007795 444 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 474 (589)
Q Consensus 444 ygd~~~~~~dvkkal~~ai~~~~v~~~~~g~ 474 (589)
...+=+.+.+|||||..||.++++++..++.
T Consensus 210 ~~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 240 (374)
T PF00496_consen 210 TNNPPFSDKAVRQALAYAIDREAIVKNIFGG 240 (374)
T ss_dssp TTSTTTTSHHHHHHHHHHS-HHHHHHHTTTT
T ss_pred ccccccchhhhHHHHHhhhhHHHHHHHHHhh
Confidence 3456678899999999999999999998654
No 72
>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=22.27 E-value=3.2e+02 Score=28.20 Aligned_cols=71 Identities=14% Similarity=0.106 Sum_probs=39.6
Q ss_pred hHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEe-CCcc------hHHHHHHHhhcCCeEEEecc
Q 007795 81 SVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS-GDRD------FSNALHQLRMRRYNILLAQP 153 (589)
Q Consensus 81 ~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLIS-GDrD------FS~aL~~LR~RGYNILLAqP 153 (589)
++.+.|.+.|+.++.+ .|+...-.......+.... -+.-..++|=. +|.. -+.....|...||+|++..-
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-SGRWEELRNATLDNLINAG--FTGWKHLILRGLEDSNKTVVTYKSEVRKSLMEEGYRIWGNIG 203 (229)
T ss_pred HHHHHHHHCCCEEEEE-cCCChHHHHHHHHHHHHcC--CCCcCeeeecCCCCCCchHhHHHHHHHHHHHhCCceEEEEEC
Confidence 3667788999999998 4443322111222222222 22235666654 4432 23444577788999998763
Q ss_pred C
Q 007795 154 H 154 (589)
Q Consensus 154 ~ 154 (589)
.
T Consensus 204 D 204 (229)
T TIGR01675 204 D 204 (229)
T ss_pred C
Confidence 3
No 73
>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=22.25 E-value=2.2e+02 Score=27.53 Aligned_cols=44 Identities=20% Similarity=0.347 Sum_probs=28.9
Q ss_pred hcCCceeeccCCCccchhhHHHHHHhhhhhcCCC-CcEEEEEeCCcchHHH
Q 007795 88 STGIALNHVPAGVKDASDKKILVDMLFWAVDNPA-PSNYLLISGDRDFSNA 137 (589)
Q Consensus 88 SSGIsLihVPaG~KdAADkkMlVDML~WAldNPp-PANIMLISGDrDFS~a 137 (589)
..||++++.+.|. .||..|. +++. +... +..+.|+|+|......
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 3799999987653 5776443 3332 3333 6899999999755443
No 74
>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=22.06 E-value=63 Score=34.70 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=27.5
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007795 441 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 474 (589)
Q Consensus 441 cirygd~~~~~~dvkkal~~ai~~~~v~~~~~g~ 474 (589)
++..-.+-+....|||||..||-++.++++.++.
T Consensus 247 ~~N~~~~~~~d~~vRkAl~~aiDr~~i~~~~~~g 280 (469)
T cd08519 247 VFNVNQPPLDNLAVRQALAYLIDRDLIVNRVYYG 280 (469)
T ss_pred EEeCCCCCCCCHHHHHHHHHHcCHHHHHHHHHhc
Confidence 3444556778899999999999999999987543
No 75
>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=21.91 E-value=61 Score=34.88 Aligned_cols=33 Identities=33% Similarity=0.440 Sum_probs=27.6
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007795 442 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 474 (589)
Q Consensus 442 irygd~~~~~~dvkkal~~ai~~~~v~~~~~g~ 474 (589)
+....+.+.+..|||||..||-++.++++.++.
T Consensus 237 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 269 (473)
T cd08491 237 IDAQIPPLDDVRVRKALNLAIDRDGIVGALFGG 269 (473)
T ss_pred ecCCCCcccCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 344567788999999999999999999987653
No 76
>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=21.90 E-value=8.1e+02 Score=24.53 Aligned_cols=99 Identities=9% Similarity=0.135 Sum_probs=51.6
Q ss_pred hhHHHHHHHHHhcCccCce-----------EEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCccchhhHHHHH
Q 007795 49 TIAQNISSALVKMNYCGPV-----------SISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILVD 111 (589)
Q Consensus 49 ~V~~NIrsAL~klGY~GpV-----------TIrAY-GD~s~-----ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVD 111 (589)
.....|.++.+++||.-.. +|-.. .++.. +-..+.+++...|..+..+...........++..
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 4667788889999985310 22111 23221 2234555677788887766543211111122222
Q ss_pred HhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEec
Q 007795 112 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (589)
Q Consensus 112 ML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq 152 (589)
+ ..+ ..+-+++...+......+..|+..+..|+++.
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 24556665544323455677777788887775
No 77
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=21.65 E-value=7.7e+02 Score=24.65 Aligned_cols=99 Identities=10% Similarity=0.079 Sum_probs=50.2
Q ss_pred hhHHHHHHHHHhcCccCc----------e-EEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCccchhhHHHHH
Q 007795 49 TIAQNISSALVKMNYCGP----------V-SISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILVD 111 (589)
Q Consensus 49 ~V~~NIrsAL~klGY~Gp----------V-TIrAY-GD~s~-----ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVD 111 (589)
.....|..+.+++||.-. - +|-.. -++.. +-..+.+++...|+.+..+......... .+
T Consensus 33 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~~~~~~----~~ 108 (328)
T PRK11303 33 KTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDDQPDNE----MR 108 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHH----HH
Confidence 456778888889998531 0 22222 12221 1234555677788887765432111111 12
Q ss_pred HhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEec
Q 007795 112 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (589)
Q Consensus 112 ML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAq 152 (589)
++.+... ...+-|++.+.+..-...+..|...+..|+++.
T Consensus 109 ~~~~l~~-~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~v~ 148 (328)
T PRK11303 109 CAEHLLQ-RQVDALIVSTSLPPEHPFYQRLQNDGLPIIALD 148 (328)
T ss_pred HHHHHHH-cCCCEEEEcCCCCCChHHHHHHHhcCCCEEEEC
Confidence 2222222 234556665543333445667777777777765
No 78
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=21.49 E-value=4e+02 Score=27.36 Aligned_cols=89 Identities=20% Similarity=0.336 Sum_probs=56.4
Q ss_pred HHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEE--eCCc-c-
Q 007795 58 LVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI--SGDR-D- 133 (589)
Q Consensus 58 L~klGY~GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLI--SGDr-D- 133 (589)
|.++|+. =--++||...++++.++.+...++. +-.|. .||..|-.+.++ ||.... ++.|+++ .|.| |
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 4455553 3357899999999999999988887 55554 478788766544 554433 3666666 4554 1
Q ss_pred -hHH--HHHHHhhcCCeEEEeccCC
Q 007795 134 -FSN--ALHQLRMRRYNILLAQPHK 155 (589)
Q Consensus 134 -FS~--aL~~LR~RGYNILLAqP~n 155 (589)
|.. ++.++-.++.+|.+.-..+
T Consensus 108 ~l~nl~ll~~~~~~~~~i~l~~~~n 132 (212)
T COG1564 108 ALANLFLLLRPAKSGFKITLISGQN 132 (212)
T ss_pred HHHHHHHHHhhhhccceEEEecCCc
Confidence 222 3444445677777775544
No 79
>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=21.47 E-value=70 Score=34.10 Aligned_cols=87 Identities=22% Similarity=0.232 Sum_probs=48.3
Q ss_pred CCCCCCCchHHHHHHHHHHhhHHHHhhcCCcc----eeecCCCcceeeeccCCCCCCCcHHHHHHHHHHHcCcc---chh
Q 007795 445 GEPKHRNTDVRKALNCAIEQHMVIKRSLGALP----LYVPKNEKLWNCENLYGNPNQYPKEVWDRIQKFLTSSS---GRS 517 (589)
Q Consensus 445 gd~~~~~~dvkkal~~ai~~~~v~~~~~g~~~----l~~~k~e~lwkcvn~~~~~~~~pk~~~d~i~~fl~s~~---g~s 517 (589)
..+.+.+..|||||..||..+.++++.++..- -++.... .|-..++.. .|+ --.++-++.|.-+. |-.
T Consensus 243 ~~~~~~d~~vRkAl~~aidr~~i~~~~~~g~~~~~~~~~~~~~-~~~~~~~~~---~~~-~d~~~A~~lL~~aG~~~g~~ 317 (454)
T cd08496 243 TGAPFDDPKVRQAINYAIDRKAFVDALLFGLGEPASQPFPPGS-WAYDPSLEN---TYP-YDPEKAKELLAEAGYPNGFS 317 (454)
T ss_pred CCCCCCCHHHHHHHHhhcCHHHHHHHHhcCCCccccCCCCCCC-ccccccccc---cCC-CCHHHHHHHHHHcCCCCCce
Confidence 34568899999999999999999998865321 1222211 111111111 121 13456667776542 322
Q ss_pred h-h-hhhhhhHHHHHHHHhhh
Q 007795 518 A-I-MASQCRYEAALILKNSC 536 (589)
Q Consensus 518 ~-i-~~s~~ry~aa~~lk~~c 536 (589)
. | ..+.-+-+.|.+|+..+
T Consensus 318 l~i~~~~~~~~~~a~~i~~~l 338 (454)
T cd08496 318 LTIPTGAQNADTLAEIVQQQL 338 (454)
T ss_pred EEEEecCCchhHHHHHHHHHH
Confidence 1 1 12234567788888876
No 80
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=20.95 E-value=5.8e+02 Score=29.43 Aligned_cols=93 Identities=12% Similarity=0.069 Sum_probs=54.8
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCc---chHHHHHHH
Q 007795 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDR---DFSNALHQL 141 (589)
Q Consensus 65 GpVTIrAYGD~s~ip~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGDr---DFS~aL~~L 141 (589)
.+|.|.++|....+-..+...|...|+..+... |..+.. ..+..-.+-+-+++||-.+ +...++..+
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 345555555443343445556777787665431 111111 1111223446677788543 466777888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEE
Q 007795 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (589)
Q Consensus 142 R~RGYNILLAqP~nAS~~L~~aAd~vWl 169 (589)
+++|-.|+++.. . ..+|...|+.++.
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 81
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=20.56 E-value=8.4e+02 Score=25.85 Aligned_cols=107 Identities=14% Similarity=0.105 Sum_probs=59.1
Q ss_pred HHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhh-cCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcE-EEEEe
Q 007795 52 QNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSS-TGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSN-YLLIS 129 (589)
Q Consensus 52 ~NIrsAL~klGY~GpVTIrAYGD~s~ip~~vr~aLsS-SGIsLihVPaG~KdAADkkMlVDML~WAldNPpPAN-IMLIS 129 (589)
..|...|.+.+.. +|.|.+.|.....-...+..|.. .++.+..... .++..+...+..+.. ++.||
T Consensus 33 ~~~~~~l~~~~~~-~I~~~g~GsS~~aa~~~~~~~~k~~~i~v~~~~~-----------~~~~~~~~~~~~~~~lvI~iS 100 (340)
T PRK11382 33 HAIVEEMVKRDID-RIYFVACGSPLNAAQTAKHLADRFSDLQVYAISG-----------WEFCDNTPYRLDDRCAVIGVS 100 (340)
T ss_pred HHHHHHHHhCCCC-EEEEEEechHHHHHHHHHHHHHHHcCCCeEEecc-----------HHHHhcCCcCCCCCCEEEEEc
Confidence 3345555543332 56777777755433333333322 2433222211 122222222333444 66676
Q ss_pred --CC-cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEEec
Q 007795 130 --GD-RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (589)
Q Consensus 130 --GD-rDFS~aL~~LR~RGYNILLAqP~nAS~~L~~aAd~vWlWe 171 (589)
|. .|-..++..++.+|..|+.+... ..++|...|+..+...
T Consensus 101 ~SGeT~e~i~al~~ak~~Ga~~I~IT~~-~~S~L~~~ad~~l~~~ 144 (340)
T PRK11382 101 DYGKTEEVIKALELGRACGALTAAFTKR-ADSPITSAAEFSIDYQ 144 (340)
T ss_pred CCCCCHHHHHHHHHHHHcCCeEEEEECC-CCChHHHhCCEEEEeC
Confidence 33 57888999999999999888644 3456888888887765
No 82
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=20.38 E-value=1.6e+02 Score=26.66 Aligned_cols=83 Identities=13% Similarity=0.041 Sum_probs=39.5
Q ss_pred ChhHHHHhhhcCCceeeccCCCccchhhHHHHHHhhhhhcCCCCcEEEEEeCCcchHHHHHHHhhcCCeEEEeccCCCCh
Q 007795 79 PASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHKASA 158 (589)
Q Consensus 79 p~~vr~aLsSSGIsLihVPaG~KdAADkkMlVDML~WAldNPpPANIMLISGDrDFS~aL~~LR~RGYNILLAqP~nAS~ 158 (589)
...+.+.|.+.|..++-|-...++....+..-++-+ .-..++.++|++....-..+|..+...|-+-+++++...++
T Consensus 16 g~~v~~~l~~~G~~v~~Vnp~~~~i~G~~~y~sl~e---~p~~iDlavv~~~~~~~~~~v~~~~~~g~~~v~~~~g~~~~ 92 (116)
T PF13380_consen 16 GYRVLRNLKAAGYEVYPVNPKGGEILGIKCYPSLAE---IPEPIDLAVVCVPPDKVPEIVDEAAALGVKAVWLQPGAESE 92 (116)
T ss_dssp HHHHHHHHHHTT-EEEEESTTCSEETTEE-BSSGGG---CSST-SEEEE-S-HHHHHHHHHHHHHHT-SEEEE-TTS--H
T ss_pred HHHHHHHHHhCCCEEEEECCCceEECcEEeeccccC---CCCCCCEEEEEcCHHHHHHHHHHHHHcCCCEEEEEcchHHH
Confidence 344666666677666655322222222222222221 12244555555555556667788888887777777776555
Q ss_pred hHHhhc
Q 007795 159 PLVAAA 164 (589)
Q Consensus 159 ~L~~aA 164 (589)
.+.+.|
T Consensus 93 ~~~~~a 98 (116)
T PF13380_consen 93 ELIEAA 98 (116)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 555443
No 83
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=20.38 E-value=1.2e+02 Score=28.83 Aligned_cols=54 Identities=15% Similarity=0.087 Sum_probs=41.4
Q ss_pred chhhHHHHHHHHHhhhhccccCCCCccccchhhcCCCCCCCchHHHHHHHHHHh
Q 007795 411 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGEPKHRNTDVRKALNCAIEQ 464 (589)
Q Consensus 411 ~~q~li~~il~al~~lk~ek~~pte~ni~dcirygd~~~~~~dvkkal~~ai~~ 464 (589)
..-..+.+|-.++.+...+.+.-+|+.+.||..+++-.-.+=+..+||+-+.++
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 555667777666666666788999999999998844334577889999988877
No 84
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=20.28 E-value=1.9e+02 Score=31.20 Aligned_cols=97 Identities=15% Similarity=0.283 Sum_probs=57.5
Q ss_pred HHHHHHHHHhcCccCceEEEEE-ecCCCCChhHHHHhhhcCCceeeccC-C----------Cc--------------cch
Q 007795 51 AQNISSALVKMNYCGPVSISAY-GDTNRIPASVQHALSSTGIALNHVPA-G----------VK--------------DAS 104 (589)
Q Consensus 51 ~~NIrsAL~klGY~GpVTIrAY-GD~s~ip~~vr~aLsSSGIsLihVPa-G----------~K--------------dAA 104 (589)
.=|..++|.++|. +++...| |..+. +-+.+.|...||....++- | .+ ...
T Consensus 39 GINVa~vL~~lG~--~~~a~GflGg~tg--~~~~~~l~~~gi~~~fv~v~g~TRinvki~~~~~~~~Tein~~Gp~is~~ 114 (310)
T COG1105 39 GINVARVLKDLGI--PVTALGFLGGFTG--EFFVALLKDEGIPDAFVEVKGDTRINVKILDEEDGEETEINFPGPEISEA 114 (310)
T ss_pred ceeHHHHHHHcCC--CceEEEecCCccH--HHHHHHHHhcCCCceEEEccCCCeeeEEEEecCCCcEEEecCCCCCCCHH
Confidence 3467778888765 3454444 33322 2356677777776665541 1 00 011
Q ss_pred hhHHHHHHhhhhhcCCCCcEEEEEeCC-------cchHHHHHHHhhcCCeEEEeccC
Q 007795 105 DKKILVDMLFWAVDNPAPSNYLLISGD-------RDFSNALHQLRMRRYNILLAQPH 154 (589)
Q Consensus 105 DkkMlVDML~WAldNPpPANIMLISGD-------rDFS~aL~~LR~RGYNILLAqP~ 154 (589)
+...+.+ .....-...-+|+|||. ..|..+++.+|.+|.+|+|-...
T Consensus 115 ~~~~~l~---~~~~~l~~~d~VvlsGSlP~g~~~d~y~~li~~~~~~g~~vilD~Sg 168 (310)
T COG1105 115 ELEQFLE---QLKALLESDDIVVLSGSLPPGVPPDAYAELIRILRQQGAKVILDTSG 168 (310)
T ss_pred HHHHHHH---HHHHhcccCCEEEEeCCCCCCCCHHHHHHHHHHHHhcCCeEEEECCh
Confidence 2222222 22233456778999994 36888999999999999998633
Done!