Query 006692
Match_columns 635
No_of_seqs 139 out of 269
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 13:06:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006692hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01936 NYN: NYN domain; Int 99.8 3.7E-20 7.9E-25 164.1 6.3 133 29-169 1-144 (146)
2 cd06167 LabA_like LabA_like pr 99.6 1.3E-15 2.9E-20 137.4 9.5 135 29-167 2-146 (149)
3 TIGR00288 conserved hypothetic 99.3 1.7E-11 3.7E-16 117.4 13.5 132 27-170 22-155 (160)
4 PF14418 OHA: OST-HTH Associat 99.1 1.2E-11 2.6E-16 105.2 1.2 59 568-627 9-70 (75)
5 COG1432 Uncharacterized conser 97.7 0.0002 4.3E-09 69.5 9.5 147 27-175 5-165 (181)
6 KOG0260 RNA polymerase II, lar 85.0 45 0.00098 42.1 17.8 42 24-65 1205-1254(1605)
7 PF04263 TPK_catalytic: Thiami 81.4 5.7 0.00012 37.0 7.1 76 70-151 39-121 (123)
8 KOG0260 RNA polymerase II, lar 77.5 77 0.0017 40.2 16.3 7 281-287 1448-1454(1605)
9 COG4634 Uncharacterized protei 73.2 16 0.00034 34.5 7.4 72 77-157 8-80 (113)
10 cd05013 SIS_RpiR RpiR-like pro 69.2 66 0.0014 27.9 10.1 94 65-169 14-110 (139)
11 cd05014 SIS_Kpsf KpsF-like pro 62.9 31 0.00067 30.4 7.0 93 66-170 2-98 (128)
12 PRK00124 hypothetical protein; 55.6 35 0.00075 33.5 6.4 81 31-138 2-82 (151)
13 PLN02714 thiamin pyrophosphoki 55.0 60 0.0013 33.2 8.3 82 70-155 57-148 (229)
14 TIGR01378 thi_PPkinase thiamin 52.9 78 0.0017 31.5 8.6 89 60-156 33-128 (203)
15 COG0794 GutQ Predicted sugar p 51.4 73 0.0016 32.7 8.2 107 49-169 27-136 (202)
16 COG1671 Uncharacterized protei 48.0 72 0.0016 31.5 7.3 80 30-138 2-81 (150)
17 cd05005 SIS_PHI Hexulose-6-pho 47.0 1.5E+02 0.0032 28.3 9.2 91 65-171 34-127 (179)
18 PF07283 TrbH: Conjugal transf 44.1 54 0.0012 31.1 5.6 53 104-156 4-60 (121)
19 TIGR03127 RuMP_HxlB 6-phospho 44.0 1.7E+02 0.0036 27.8 9.0 91 64-170 30-123 (179)
20 TIGR00393 kpsF KpsF/GutQ famil 43.5 76 0.0016 31.7 6.9 94 65-170 1-98 (268)
21 PF08497 Radical_SAM_N: Radica 40.8 34 0.00074 37.1 4.2 41 111-154 8-56 (302)
22 cd07995 TPK Thiamine pyrophosp 40.7 1.5E+02 0.0033 29.4 8.4 88 58-153 35-129 (208)
23 PRK14820 NADH dehydrogenase su 39.4 28 0.00061 35.1 3.1 29 449-480 137-165 (180)
24 PRK01045 ispH 4-hydroxy-3-meth 38.5 1E+02 0.0022 33.2 7.3 43 50-95 15-58 (298)
25 PRK11557 putative DNA-binding 38.5 2.1E+02 0.0045 29.1 9.2 94 65-169 129-225 (278)
26 cd08502 PBP2_NikA_DppA_OppA_li 38.1 31 0.00068 37.3 3.5 34 488-521 254-287 (472)
27 PRK11337 DNA-binding transcrip 36.9 2.5E+02 0.0053 28.8 9.5 95 65-170 141-238 (292)
28 PF02590 SPOUT_MTase: Predicte 36.7 2.6E+02 0.0056 27.3 9.1 42 132-173 83-127 (155)
29 PF09314 DUF1972: Domain of un 36.5 3.3E+02 0.0072 27.4 10.1 103 41-151 12-124 (185)
30 PRK05628 coproporphyrinogen II 36.0 3.7E+02 0.008 28.9 11.0 53 45-97 73-125 (375)
31 COG0796 MurI Glutamate racemas 34.9 2E+02 0.0044 30.8 8.7 85 43-153 13-99 (269)
32 PRK14814 NADH dehydrogenase su 34.5 40 0.00087 34.2 3.3 26 449-477 137-162 (186)
33 PF09419 PGP_phosphatase: Mito 33.6 4.2E+02 0.0091 26.4 10.1 113 28-151 40-164 (168)
34 cd05008 SIS_GlmS_GlmD_1 SIS (S 33.5 2.5E+02 0.0055 24.6 7.9 48 121-169 46-96 (126)
35 PRK00414 gmhA phosphoheptose i 33.0 3.3E+02 0.0071 26.9 9.4 49 120-169 110-161 (192)
36 PRK11543 gutQ D-arabinose 5-ph 32.5 2.6E+02 0.0055 29.0 8.9 94 65-170 43-140 (321)
37 KOG2236 Uncharacterized conser 32.4 2.8E+02 0.006 32.1 9.6 19 304-323 416-434 (483)
38 COG1737 RpiR Transcriptional r 32.0 3.4E+02 0.0073 28.3 9.7 90 69-169 133-227 (281)
39 PRK14818 NADH dehydrogenase su 32.0 43 0.00093 33.7 3.1 24 119-142 67-92 (173)
40 PF06073 DUF934: Bacterial pro 31.1 1.1E+02 0.0024 28.7 5.4 40 55-99 39-79 (110)
41 TIGR00216 ispH_lytB (E)-4-hydr 31.0 1.5E+02 0.0033 31.6 7.1 41 50-93 14-56 (280)
42 PRK12360 4-hydroxy-3-methylbut 31.0 1.6E+02 0.0035 31.5 7.3 42 50-94 15-58 (281)
43 cd05006 SIS_GmhA Phosphoheptos 30.5 4.8E+02 0.01 24.8 10.1 49 121-170 101-152 (177)
44 KOG1610 Corticosteroid 11-beta 30.3 77 0.0017 34.7 4.9 45 120-164 26-73 (322)
45 PRK15482 transcriptional regul 29.8 4.3E+02 0.0094 27.1 10.0 95 65-170 136-233 (285)
46 PF02602 HEM4: Uroporphyrinoge 29.5 2.3E+02 0.0051 27.4 7.6 71 68-150 75-145 (231)
47 TIGR02764 spore_ybaN_pdaB poly 29.2 4.4E+02 0.0095 25.3 9.4 100 45-151 74-187 (191)
48 COG1576 Uncharacterized conser 28.8 2.8E+02 0.0061 27.7 7.9 108 66-173 2-126 (155)
49 PRK14816 NADH dehydrogenase su 28.7 45 0.00097 33.8 2.6 25 119-143 78-104 (182)
50 PRK14815 NADH dehydrogenase su 28.6 47 0.001 33.7 2.7 24 119-142 70-95 (183)
51 PRK10014 DNA-binding transcrip 28.0 5.9E+02 0.013 25.8 10.5 100 48-152 35-151 (342)
52 PF10073 DUF2312: Uncharacteri 27.7 18 0.0004 31.8 -0.2 41 462-508 6-48 (74)
53 TIGR01675 plant-AP plant acid 27.5 2.3E+02 0.005 29.5 7.5 70 81-153 127-203 (229)
54 COG3233 Predicted deacetylase 27.4 1.4E+02 0.0029 31.6 5.8 23 130-152 52-74 (233)
55 PRK13883 conjugal transfer pro 27.0 1.3E+02 0.0027 29.8 5.2 53 103-155 31-87 (151)
56 PF07582 AP_endonuc_2_N: AP en 26.8 56 0.0012 27.2 2.4 19 52-70 3-21 (55)
57 PRK13835 conjugal transfer pro 26.8 1.4E+02 0.0031 29.4 5.5 51 100-150 34-87 (145)
58 COG2179 Predicted hydrolase of 26.3 2.8E+02 0.0061 28.2 7.6 117 27-158 26-144 (175)
59 PF02739 5_3_exonuc_N: 5'-3' e 25.7 1.1E+02 0.0023 30.0 4.5 60 84-153 93-152 (169)
60 PRK10294 6-phosphofructokinase 25.2 5.6E+02 0.012 26.2 9.8 43 51-96 41-83 (309)
61 PRK14828 undecaprenyl pyrophos 25.2 1.6E+02 0.0035 31.0 6.0 72 29-101 74-155 (256)
62 PF05991 NYN_YacP: YacP-like N 25.1 1.8E+02 0.0038 28.4 5.9 44 88-137 65-109 (166)
63 PRK07334 threonine dehydratase 24.8 2E+02 0.0043 31.5 6.8 94 45-151 307-402 (403)
64 PRK11302 DNA-binding transcrip 24.2 4.6E+02 0.01 26.5 8.9 94 65-170 129-225 (284)
65 TIGR00441 gmhA phosphoheptose 24.0 4.6E+02 0.01 24.7 8.3 51 120-171 78-131 (154)
66 KOG3154 Uncharacterized conser 23.5 1.1E+02 0.0024 32.4 4.3 66 30-97 44-110 (263)
67 PRK11303 DNA-binding transcrip 23.4 7.2E+02 0.016 25.1 10.1 99 49-152 33-148 (328)
68 PF00496 SBP_bac_5: Bacterial 23.1 59 0.0013 33.3 2.4 31 490-520 210-240 (374)
69 PRK06411 NADH dehydrogenase su 23.0 70 0.0015 32.4 2.8 27 449-478 139-165 (183)
70 cd08491 PBP2_NikA_DppA_OppA_li 22.8 58 0.0013 35.3 2.4 33 488-520 237-269 (473)
71 TIGR02417 fruct_sucro_rep D-fr 22.7 8E+02 0.017 24.8 10.4 100 49-153 32-148 (327)
72 PRK14813 NADH dehydrogenase su 22.7 73 0.0016 32.5 2.9 27 449-478 133-159 (189)
73 cd08519 PBP2_NikA_DppA_OppA_li 22.6 61 0.0013 35.0 2.5 34 487-520 247-280 (469)
74 smart00645 Pept_C1 Papain fami 22.4 1.1E+02 0.0023 29.5 3.8 54 457-510 26-79 (174)
75 cd08496 PBP2_NikA_DppA_OppA_li 22.3 67 0.0014 34.5 2.7 87 491-582 243-338 (454)
76 KOG2972 Uncharacterized conser 22.1 3.1E+02 0.0067 29.6 7.3 27 123-149 204-231 (276)
77 TIGR01957 nuoB_fam NADH-quinon 22.0 75 0.0016 31.0 2.7 42 110-151 41-90 (145)
78 PRK10401 DNA-binding transcrip 21.9 5.1E+02 0.011 26.5 8.8 112 31-148 141-263 (346)
79 PRK01254 hypothetical protein; 21.9 1E+02 0.0022 37.1 4.1 41 111-154 31-79 (707)
80 KOG1924 RhoA GTPase effector D 21.3 3.9E+02 0.0084 33.2 8.6 39 466-508 626-666 (1102)
81 PRK14101 bifunctional glucokin 20.1 5.7E+02 0.012 29.7 9.6 93 65-169 469-564 (638)
82 PRK09058 coproporphyrinogen II 20.1 1.1E+03 0.023 26.5 11.3 53 43-96 126-179 (449)
83 cd00995 PBP2_NikA_DppA_OppA_li 20.0 75 0.0016 33.6 2.4 30 491-520 248-277 (466)
84 PF10965 DUF2767: Protein of u 20.0 1.5E+02 0.0033 26.0 3.8 54 457-510 10-66 (69)
No 1
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=99.80 E-value=3.7e-20 Score=164.06 Aligned_cols=133 Identities=33% Similarity=0.500 Sum_probs=93.5
Q ss_pred ceEEEEEecCCCCCCC---CChhhhHHHHHHHHHhcCccCce-EEEEEecCCC-CChhHHHHhhhcCCceeeccC-----
Q 006692 29 KTSVWWDIENCQVPKN---CDPHTIAQNISSALVKMNYCGPV-SISAYGDTNR-IPASVQHALSSTGIALNHVPA----- 98 (635)
Q Consensus 29 kTAVFWDIENCPVPsG---~da~~Va~NIrsAL~klGY~GpV-TIrAYGDls~-ip~~vl~aLsSSGIsLihVPa----- 98 (635)
+|+||||+|||+.+.+ ++...+...|+. .|++ .+++|+++.. ....+.++|...||.+.++|.
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 555555554443 5667 7999999543 235677899999999999986
Q ss_pred CCcchhhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEec-cCCCChhHHhhcCeEEE
Q 006692 99 GVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWL 169 (635)
Q Consensus 99 G~KDAADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAq-P~~AS~~L~aaAd~vWl 169 (635)
+.|+++|.+|.+||+.|+.+++. +++||||||.||.+++..|+.+|++|.++. +..++..|..+|+.++.
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 68899999999999999988766 999999999999999999999999999888 56789999999998764
No 2
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=99.62 E-value=1.3e-15 Score=137.36 Aligned_cols=135 Identities=23% Similarity=0.220 Sum_probs=108.1
Q ss_pred ceEEEEEecCCCCCCCCCh--hhhHHHHHHHHHhcCccCce-EEEEEecCCC--CChhHHHHhhhcCCceeeccC----C
Q 006692 29 KTSVWWDIENCQVPKNCDP--HTIAQNISSALVKMNYCGPV-SISAYGDTNR--IPASVQHALSSTGIALNHVPA----G 99 (635)
Q Consensus 29 kTAVFWDIENCPVPsG~da--~~Va~NIrsAL~klGY~GpV-TIrAYGDls~--ip~~vl~aLsSSGIsLihVPa----G 99 (635)
+++||||.||+..-..... ..-...+...+.. .+.+ ..++|+++.. ......++|...|+.+++++. +
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 6899999999975321111 1112223333333 2444 6899999874 557788999999999999984 6
Q ss_pred CcchhhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEeccC-CCChhHHhhcCeE
Q 006692 100 VKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSV 167 (635)
Q Consensus 100 ~KDAADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAqP~-~AS~~L~aaAd~v 167 (635)
.|+++|.+|.+||+.++.++ .++.+||+|||.||.+++..|+++|++|+++.+. ..|..|..+|+.+
T Consensus 79 ~~~~~D~~l~~d~~~~~~~~-~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d~f 146 (149)
T cd06167 79 GKKGVDVALAIDALELAYKR-RIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSRELRKAADRF 146 (149)
T ss_pred cccCccHHHHHHHHHHhhhc-CCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCCcc
Confidence 78999999999999999988 8899999999999999999999999999999977 7889999998854
No 3
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=99.33 E-value=1.7e-11 Score=117.38 Aligned_cols=132 Identities=16% Similarity=0.161 Sum_probs=105.5
Q ss_pred cCceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceE-EEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhh
Q 006692 27 TAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVS-ISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASD 105 (635)
Q Consensus 27 ~AkTAVFWDIENCPVPsG~da~~Va~NIrsAL~klGY~GpVT-IrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAAD 105 (635)
.-+++||-|.+|.. +..+. .+ ...|...|.+ .|.++ -++||++.. ...+++.|...|++.+.+ |++.|
T Consensus 22 ~~riAvfID~~Nv~-~~~~~-~d-~~~i~~~ls~---~G~i~~~R~Y~~a~a-~~~l~~~l~~~Gf~pv~~----kG~~D 90 (160)
T TIGR00288 22 EKKIGLLVDGPNML-RKEFN-ID-LDEIREILSE---YGDIKIGKVLLNQYA-SDKLIEAVVNQGFEPIIV----AGDVD 90 (160)
T ss_pred CCcEEEEEeCCccC-hhhhc-cC-HHHHHHHHHh---cCCeEEEEEEechhc-cHHHHHHHHHCCceEEEe----cCccc
Confidence 55799999999996 22221 11 3456666655 57665 689999643 346888999999998764 56899
Q ss_pred hHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEec-cCCCChhHHhhcCeEEEe
Q 006692 106 KKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 106 kkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAq-P~~AS~~L~aaAd~vWlW 170 (635)
..|.+|+|..++ .+..+.|+|+|||.||.+++.+||++|..|+++. +..++.+|..+|+.++.-
T Consensus 91 v~laIDame~~~-~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~acd~FI~L 155 (160)
T TIGR00288 91 VRMAVEAMELIY-NPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNSADIAIIL 155 (160)
T ss_pred HHHHHHHHHHhc-cCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHhcCeEEeC
Confidence 999999999986 4788999999999999999999999999999998 556888999999987654
No 4
>PF14418 OHA: OST-HTH Associated domain
Probab=99.13 E-value=1.2e-11 Score=105.18 Aligned_cols=59 Identities=36% Similarity=0.451 Sum_probs=53.9
Q ss_pred hhhhHHHHHHHHhh---hhhhhhhhhHHHHHHHhhccceeeecCCCCceeeEEEEeeecCCCC
Q 006692 568 SQCRYEAALILKNS---CLPELALGEILKILNMVITPKKWIIHHQSGWQPVTITLAEYKSDSG 627 (635)
Q Consensus 568 s~~ry~aa~~lk~~---cl~~~~lg~vlqil~~~i~~kkw~~~h~sgwqp~~i~~~~~~~~~~ 627 (635)
+.|||++|..||+. ||+++.||+|++|++|.|..|||+ +|+++|+|+.++..++++..+
T Consensus 9 ~~gRY~~A~~Lk~~gp~~lr~l~Lg~i~~iVqlai~~k~l~-y~~~~l~P~~~~~~~a~s~~~ 70 (75)
T PF14418_consen 9 SGGRYGMAQFLKKRGPPFLRSLSLGDICHIVQLAISKKKLI-YENSNLKPFCISQKVANSFLG 70 (75)
T ss_pred CCcHHHHHHHHHhcCchhhcCCcHHHHHHHHHHHHhCCeee-eCCCccccHHHHHHHHHhhhc
Confidence 38999999999998 999999999999999999999999 999999999888777766543
No 5
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=97.70 E-value=0.0002 Score=69.53 Aligned_cols=147 Identities=20% Similarity=0.159 Sum_probs=99.6
Q ss_pred cCceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCce-EEEEEe---cCCCCChhHHH--HhhhcCCceeeccC--
Q 006692 27 TAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPV-SISAYG---DTNRIPASVQH--ALSSTGIALNHVPA-- 98 (635)
Q Consensus 27 ~AkTAVFWDIENCPVPsG~da~~Va~NIrsAL~klGY~GpV-TIrAYG---Dls~ip~~vl~--aLsSSGIsLihVPa-- 98 (635)
...+++|-|++|-+.-.. ....+.-.....|++......+ ....|. +...+...... ++.+.|+.++-.+.
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 357899999998654221 1122222334444443333333 233332 23333333333 67777877766543
Q ss_pred ----C-CcchhhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEeccC-CCChhHHhhcCeEEEecc
Q 006692 99 ----G-VKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSVWLWTS 172 (635)
Q Consensus 99 ----G-~KDAADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAqP~-~AS~~L~aaAd~vWlWeS 172 (635)
+ .|..-|..|.+||+..+ +++.-.+++|+|||.||.+++..++.+|..|+++.-. ..|..|..+|+.+..-.+
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 2 35567899999999987 5778899999999999999999999999999998743 577889999998877766
Q ss_pred ccc
Q 006692 173 LVA 175 (635)
Q Consensus 173 LLa 175 (635)
+..
T Consensus 163 ~~~ 165 (181)
T COG1432 163 LEE 165 (181)
T ss_pred hhh
Confidence 544
No 6
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=84.99 E-value=45 Score=42.06 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=20.2
Q ss_pred hhccCceEEEEEecC-------CCCCCCCChhhhHHHHHH-HHHhcCccC
Q 006692 24 QYVTAKTSVWWDIEN-------CQVPKNCDPHTIAQNISS-ALVKMNYCG 65 (635)
Q Consensus 24 ryA~AkTAVFWDIEN-------CPVPsG~da~~Va~NIrs-AL~klGY~G 65 (635)
+-.....++||.-+| |.+-..-+-.....+|+. +|.++-..|
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 333455667776555 222222223345556765 455554444
No 7
>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=81.37 E-value=5.7 Score=36.96 Aligned_cols=76 Identities=24% Similarity=0.429 Sum_probs=49.8
Q ss_pred EEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeC--Cc---chHH--HHHHHh
Q 006692 70 SAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISG--DR---DFSN--ALHQLR 142 (635)
Q Consensus 70 rAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISG--Dr---DFS~--aL~~LR 142 (635)
-+.||...+..++++.+.+.|+.+++.| .||..|-.+.++.+ .. ..+..|+++-+ -| -++. +|.+++
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 4689999998899999999999999999 68888887766655 33 33445555443 22 2433 344455
Q ss_pred hcCCeEEEe
Q 006692 143 MRRYNILLA 151 (635)
Q Consensus 143 eRGYNILLA 151 (635)
+++.+|+|+
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 8
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=77.55 E-value=77 Score=40.20 Aligned_cols=7 Identities=43% Similarity=0.999 Sum_probs=2.9
Q ss_pred CCCCCCC
Q 006692 281 SNPNFFP 287 (635)
Q Consensus 281 ~~p~~~~ 287 (635)
++|.|-|
T Consensus 1448 ssp~~s~ 1454 (1605)
T KOG0260|consen 1448 SSPGYSP 1454 (1605)
T ss_pred CCCCCCC
Confidence 3344444
No 9
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.18 E-value=16 Score=34.54 Aligned_cols=72 Identities=25% Similarity=0.359 Sum_probs=49.3
Q ss_pred CCChhHHHHhhhcCCceeecc-CCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEeccCC
Q 006692 77 RIPASVQHALSSTGIALNHVP-AGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHK 155 (635)
Q Consensus 77 ~ip~~vl~aLsSSGIsLihVP-aG~KDAADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAqP~~ 155 (635)
++|..+.+-|..+|++-+|+- -|-+|+.|..| +.+|. -.+.||+|.|.||.. |..+...-..|+.+.-.+
T Consensus 8 ~Lp~rlad~l~~~g~e~~h~r~lg~~da~D~EI----~a~A~----~~~~iivTkDsDF~~-la~~~G~Ppki~wLr~gN 78 (113)
T COG4634 8 QLPPRLADWLPMAGIEAVHWRDLGLRDATDIEI----WAYAR----RNNRIIVTKDSDFAD-LALTLGSPPKIVWLRCGN 78 (113)
T ss_pred CCChHHHHHhhhcccceeeecccCcCCCccHHH----HHHHH----hcCcEEEEcCccHHH-HHHHcCCCCeEEEEEecC
Confidence 377788899999999888885 45577765533 33443 368999999999944 444444445777665555
Q ss_pred CC
Q 006692 156 AS 157 (635)
Q Consensus 156 AS 157 (635)
.+
T Consensus 79 vs 80 (113)
T COG4634 79 VS 80 (113)
T ss_pred CC
Confidence 54
No 10
>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=69.19 E-value=66 Score=27.94 Aligned_cols=94 Identities=15% Similarity=0.110 Sum_probs=55.7
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCCc---chHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDR---DFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGDr---DFS~aL~~L 141 (635)
++|-+.+.|....+-..+...|...|.....++... ....++ ..-.+.+-+++||... +...++..+
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 566666666644444556667777787655553210 011111 1123456677788543 466678888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
+++|-.|+++..... .+|...++..+.
T Consensus 84 ~~~g~~iv~iT~~~~-~~l~~~~d~~i~ 110 (139)
T cd05013 84 KERGAKVIAITDSAN-SPLAKLADIVLL 110 (139)
T ss_pred HHcCCeEEEEcCCCC-ChhHHhcCEEEE
Confidence 999999998876433 456666665544
No 11
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=62.86 E-value=31 Score=30.45 Aligned_cols=93 Identities=19% Similarity=0.220 Sum_probs=54.4
Q ss_pred ceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcC-CCCceEEEEeCC---cchHHHHHHH
Q 006692 66 PVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGD---RDFSNALHQL 141 (635)
Q Consensus 66 pVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDN-PpPANIMLISGD---rDFS~aL~~L 141 (635)
+|-|.+.|....+-..+...|...|+........ +.+.+...+ .+-+-+++||-. ++...++..+
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 3444444433333344555666677766665221 111111112 344667777754 5688899999
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
|++|-.|+++..... .+|...|+..+..
T Consensus 71 ~~~g~~vi~iT~~~~-s~la~~ad~~l~~ 98 (128)
T cd05014 71 KRRGAPIIAITGNPN-STLAKLSDVVLDL 98 (128)
T ss_pred HHCCCeEEEEeCCCC-CchhhhCCEEEEC
Confidence 999999998875443 4577777766665
No 12
>PRK00124 hypothetical protein; Validated
Probab=55.57 E-value=35 Score=33.51 Aligned_cols=81 Identities=20% Similarity=0.231 Sum_probs=49.3
Q ss_pred EEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHH
Q 006692 31 SVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILV 110 (635)
Q Consensus 31 AVFWDIENCPVPsG~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLV 110 (635)
-||-|-+-||| ..-|.++.++.| +.+..+++.++.- .-=++..|+.+.|+.| .|++|..|+.
T Consensus 2 ~I~VDADACPV---------k~~i~r~a~r~~----i~v~~Vas~n~~~----~~~~~~~v~~v~V~~g-~D~AD~~Iv~ 63 (151)
T PRK00124 2 KIYVDADACPV---------KDIIIRVAERHG----IPVTLVASFNHFL----RVPYSPFIRTVYVDAG-FDAADNEIVQ 63 (151)
T ss_pred EEEEECCCCcH---------HHHHHHHHHHHC----CeEEEEEeCCccc----CCCCCCceEEEEeCCC-CChHHHHHHH
Confidence 38999999983 444555555543 3445566554421 0012356888999864 6788877663
Q ss_pred HHHHhhhcCCCCceEEEEeCCcchHHHH
Q 006692 111 DMLFWAVDNPAPSNYLLISGDRDFSNAL 138 (635)
Q Consensus 111 DML~WAlDNPpPANIMLISGDrDFS~aL 138 (635)
.+ -..=++||.|..++..+
T Consensus 64 ~~---------~~gDiVIT~Di~LAa~~ 82 (151)
T PRK00124 64 LA---------EKGDIVITQDYGLAALA 82 (151)
T ss_pred hC---------CCCCEEEeCCHHHHHHH
Confidence 32 22357889998776543
No 13
>PLN02714 thiamin pyrophosphokinase
Probab=55.00 E-value=60 Score=33.17 Aligned_cols=82 Identities=20% Similarity=0.227 Sum_probs=52.0
Q ss_pred EEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCC-----ceEEEEe--C---CcchHHHHH
Q 006692 70 SAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAP-----SNYLLIS--G---DRDFSNALH 139 (635)
Q Consensus 70 rAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpP-----ANIMLIS--G---DrDFS~aL~ 139 (635)
.+.||...+..+.++.+.+.|+.++..|. .||..|-.+.+ .||.++.+. ..|+|+- | |--|+.+..
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 47899999999999999999999888765 57777776654 445443221 3344432 2 223554433
Q ss_pred HHhhcCCeEEEeccCC
Q 006692 140 QLRMRRYNILLAQPHK 155 (635)
Q Consensus 140 ~LReRGYNILLAqP~~ 155 (635)
.++..+.+|.|+...+
T Consensus 133 L~~~~~~~i~lid~~~ 148 (229)
T PLN02714 133 LYRFPDLRIVLLSDDC 148 (229)
T ss_pred HHhcCCceEEEEcCCc
Confidence 3344566777775443
No 14
>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=52.89 E-value=78 Score=31.55 Aligned_cols=89 Identities=18% Similarity=0.300 Sum_probs=56.4
Q ss_pred hcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEE--eCCc---ch
Q 006692 60 KMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI--SGDR---DF 134 (635)
Q Consensus 60 klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLI--SGDr---DF 134 (635)
++|+.- -.+.||...+..+.++.+.+.|+.++..|. .||..|-.+.+ .||.++. +..|+++ +|.| -+
T Consensus 33 ~~gi~P---d~iiGDfDSi~~~~~~~~~~~~~~~~~~~~-eKD~TD~e~Al---~~~~~~~-~~~i~i~Ga~GgR~DH~l 104 (203)
T TIGR01378 33 KLGLTP---DLIVGDFDSIDEEELDFYKKAGVKIIVFPP-EKDTTDLELAL---KYALERG-ADEITILGATGGRLDHTL 104 (203)
T ss_pred HCCCCC---CEEEeCcccCCHHHHHHHHHcCCceEEcCC-CCCCCHHHHHH---HHHHHCC-CCEEEEEcCCCCcHHHHH
Confidence 455532 346799999999999999999999888776 48888876654 4555543 3455554 3333 24
Q ss_pred HHH--HHHHhhcCCeEEEeccCCC
Q 006692 135 SNA--LHQLRMRRYNILLAQPHKA 156 (635)
Q Consensus 135 S~a--L~~LReRGYNILLAqP~~A 156 (635)
+.+ |.+++.++.+|.++...+.
T Consensus 105 ani~~L~~~~~~~~~i~l~d~~~~ 128 (203)
T TIGR01378 105 ANLNLLLEYAKRGIKVRLIDEQNV 128 (203)
T ss_pred HHHHHHHHHHhcCCeEEEEcCCcE
Confidence 433 2333345778888765443
No 15
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=51.43 E-value=73 Score=32.69 Aligned_cols=107 Identities=18% Similarity=0.187 Sum_probs=72.2
Q ss_pred hhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEE
Q 006692 49 TIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLI 128 (635)
Q Consensus 49 ~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLI 128 (635)
.+.+.++..++. .|+|.+...|..-.+-+.+-..|.+.|...+.|-.+.-.--|--|+ .+-+-+++|
T Consensus 27 ~~~~a~~~i~~~---~gkv~V~G~GkSG~Igkk~Aa~L~s~G~~a~fv~p~ea~hgdlg~i----------~~~Dvviai 93 (202)
T COG0794 27 DFVRAVELILEC---KGKVFVTGVGKSGLIGKKFAARLASTGTPAFFVGPAEALHGDLGMI----------TPGDVVIAI 93 (202)
T ss_pred HHHHHHHHHHhc---CCcEEEEcCChhHHHHHHHHHHHHccCCceEEecCchhccCCccCC----------CCCCEEEEE
Confidence 444555555543 6889998888888887788888999999998884211000011111 235778999
Q ss_pred eCCc---chHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 129 SGDR---DFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 129 SGDr---DFS~aL~~LReRGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
|+.. ....++..+|.+|-.|+.+..... +.|...||.+..
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 467778888999999998875333 347788877765
No 16
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.05 E-value=72 Score=31.54 Aligned_cols=80 Identities=23% Similarity=0.287 Sum_probs=52.5
Q ss_pred eEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHH
Q 006692 30 TSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKIL 109 (635)
Q Consensus 30 TAVFWDIENCPVPsG~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkML 109 (635)
.-||-|-+.|| |..-|.++.+++|. +|++ .++....+ ..+..|+.+.|-+ ..|++|..|+
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 34557777777665 3444 44544331 1456777788855 4788888776
Q ss_pred HHHHHhhhcCCCCceEEEEeCCcchHHHH
Q 006692 110 VDMLFWAVDNPAPSNYLLISGDRDFSNAL 138 (635)
Q Consensus 110 VDML~WAlDNPpPANIMLISGDrDFS~aL 138 (635)
.. .-..=++||.|.-++..|
T Consensus 62 ~~---------a~~gDlVVT~Di~LA~~l 81 (150)
T COG1671 62 NL---------AEKGDLVVTADIPLASLL 81 (150)
T ss_pred Hh---------CCCCCEEEECchHHHHHH
Confidence 32 233447889998887755
No 17
>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=46.97 E-value=1.5e+02 Score=28.31 Aligned_cols=91 Identities=15% Similarity=0.160 Sum_probs=56.9
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (635)
.+|-|.+.|....+-..+...|...|+....+... .+..-.+-+-+++||-. ++...++..+
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 55666666654333344556677788876665221 01112345667778854 4567788888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEec
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWlWe 171 (635)
+++|..|+++..... .+|...|+..+...
T Consensus 99 k~~g~~iI~IT~~~~-s~la~~ad~~l~~~ 127 (179)
T cd05005 99 KKAGAKVVLITSNPD-SPLAKLADVVVVIP 127 (179)
T ss_pred HHCCCeEEEEECCCC-CchHHhCCEEEEeC
Confidence 999999998875433 45777777766543
No 18
>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=44.11 E-value=54 Score=31.12 Aligned_cols=53 Identities=23% Similarity=0.360 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHhhhcCCCC-ce-EEEEeCC-cchHHH-HHHHhhcCCeEEEeccCCC
Q 006692 104 SDKKILVDMLFWAVDNPAP-SN-YLLISGD-RDFSNA-LHQLRMRRYNILLAQPHKA 156 (635)
Q Consensus 104 ADkkMLVDML~WAlDNPpP-AN-IMLISGD-rDFS~a-L~~LReRGYNILLAqP~~A 156 (635)
.+..|..||.......-+| .| |.|--.| ..|..+ +..||.+||-|+-..+...
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 4567889999877665443 33 5552344 358764 5779999999998876554
No 19
>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=43.96 E-value=1.7e+02 Score=27.83 Aligned_cols=91 Identities=11% Similarity=0.064 Sum_probs=56.9
Q ss_pred cCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHH
Q 006692 64 CGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQ 140 (635)
Q Consensus 64 ~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~ 140 (635)
.++|.|.+.|....+-..+...|...|+........ . ...-.+-+-+++||.. ++...++..
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 456666666654434344556677778766665221 0 0112345667778854 456778888
Q ss_pred HhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 141 LReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
++++|-.|+++..... .+|...|+.++.-
T Consensus 95 ak~~g~~ii~IT~~~~-s~la~~ad~~l~~ 123 (179)
T TIGR03127 95 AKEIGATVAAITTNPE-STLGKLADVVVEI 123 (179)
T ss_pred HHHCCCeEEEEECCCC-CchHHhCCEEEEe
Confidence 9999999999875444 4577777776654
No 20
>TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.
Probab=43.51 E-value=76 Score=31.72 Aligned_cols=94 Identities=18% Similarity=0.174 Sum_probs=59.0
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcC-CCCceEEEEeCC---cchHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDN-PAPSNYLLISGD---RDFSNALHQ 140 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDN-PpPANIMLISGD---rDFS~aL~~ 140 (635)
|+|-|.+.|....+-..+...|...|+.+.++.. .++..+...+ .+-+-+++||-. ++-..++..
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 5666666674434445566678888888776522 1122222222 344667778754 467778888
Q ss_pred HhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 141 LReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
++++|..|+.+..... .+|...|+..+.+
T Consensus 70 a~~~g~~ii~iT~~~~-s~l~~~~d~~l~~ 98 (268)
T TIGR00393 70 LKRLSHKIIAFTGSPN-SSLARAADYVLDI 98 (268)
T ss_pred HHHcCCcEEEEECCCC-CcccccCCEEEEc
Confidence 9999999998876443 3466667776665
No 21
>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=40.77 E-value=34 Score=37.05 Aligned_cols=41 Identities=29% Similarity=0.573 Sum_probs=28.7
Q ss_pred HHHHhhhcCCCCceEEEEeCC-----cchHHHH--HHHhhcCCeE-EEeccC
Q 006692 111 DMLFWAVDNPAPSNYLLISGD-----RDFSNAL--HQLRMRRYNI-LLAQPH 154 (635)
Q Consensus 111 DML~WAlDNPpPANIMLISGD-----rDFS~aL--~~LReRGYNI-LLAqP~ 154 (635)
||....++. --|+||||| ..|..+| +-|..+||.| |++||.
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 455544443 459999999 3576643 4577799999 778885
No 22
>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=40.65 E-value=1.5e+02 Score=29.38 Aligned_cols=88 Identities=23% Similarity=0.345 Sum_probs=55.8
Q ss_pred HHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEe--CCc---
Q 006692 58 LVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS--GDR--- 132 (635)
Q Consensus 58 L~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLIS--GDr--- 132 (635)
|.++|+.- --+.||...+..+.++.+.+.|+.+++.|. .||..|-.+.+. +|.+... ..|+++- |.|
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 44555542 236799999989999999999999999988 677777766544 4444322 4555544 332
Q ss_pred chHHH--HHHHhhcCCeEEEecc
Q 006692 133 DFSNA--LHQLRMRRYNILLAQP 153 (635)
Q Consensus 133 DFS~a--L~~LReRGYNILLAqP 153 (635)
-++.+ |.+++..+.+|.++..
T Consensus 107 ~lani~~l~~~~~~~~~~~l~d~ 129 (208)
T cd07995 107 TLANLNLLLKYAKDGIKIVLIDE 129 (208)
T ss_pred HHHHHHHHHHHHhcCCeEEEEcC
Confidence 23433 2233335777877754
No 23
>PRK14820 NADH dehydrogenase subunit B; Provisional
Probab=39.43 E-value=28 Score=35.12 Aligned_cols=29 Identities=14% Similarity=0.114 Sum_probs=21.8
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhccccCCC
Q 006692 449 QGRLTPSEYVQGLIGVILLALNTLKIERVVPS 480 (635)
Q Consensus 449 ~g~~~~s~~~q~li~~il~al~~lk~eki~pt 480 (635)
+|||+. ++.+++.|+.+++.++.|++-+.
T Consensus 137 PGCPP~---Pe~il~~l~~l~~~i~~~~~~~~ 165 (180)
T PRK14820 137 PGCPPR---PEQIIDGVMRVQELVKNESLRRR 165 (180)
T ss_pred cCCCCC---HHHHHHHHHHHHHHHhhcccccc
Confidence 788884 55677888888888888876553
No 24
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=38.50 E-value=1e+02 Score=33.24 Aligned_cols=43 Identities=16% Similarity=0.190 Sum_probs=28.7
Q ss_pred hHHHHHHHHHhc-CccCceEEEEEecCCCCChhHHHHhhhcCCceee
Q 006692 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNH 95 (635)
Q Consensus 50 Va~NIrsAL~kl-GY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLih 95 (635)
|..+|+.+.+.+ ...++ |..||++=+. ..+.+.|...||..++
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 556666654432 22233 5778998665 4688899999998776
No 25
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=38.46 E-value=2.1e+02 Score=29.06 Aligned_cols=94 Identities=15% Similarity=0.118 Sum_probs=55.8
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (635)
.+|.|.+.|....+-..+...|...|+...... |..++...+. .-.+.+-+++||-. ++...++..+
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 455666666443344456666778887765431 1222222211 22455667777754 3456678888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
+++|..|+++..... .+|...|+.++.
T Consensus 199 k~~ga~iI~IT~~~~-s~la~~ad~~l~ 225 (278)
T PRK11557 199 LRVGAKVLAITGFTP-NALQQRASHCLY 225 (278)
T ss_pred HHcCCCEEEEcCCCC-CchHHhCCEEEE
Confidence 999999999985443 446667776654
No 26
>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=38.10 E-value=31 Score=37.32 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=28.3
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCCc
Q 006692 488 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGAL 521 (635)
Q Consensus 488 irygd~~~~~~dvkkale~ai~~~~vv~~~~g~~ 521 (635)
+....+-+.+.+|||||..||-+++|+++.+|..
T Consensus 254 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g~ 287 (472)
T cd08502 254 FNHLQPPFDNPKIRRAVLAALDQEDLLAAAVGDP 287 (472)
T ss_pred EcCCCCCCcCHHHHHHHHHhcCHHHHHHHHhCCC
Confidence 3345667889999999999999999999987654
No 27
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=36.88 E-value=2.5e+02 Score=28.84 Aligned_cols=95 Identities=17% Similarity=0.148 Sum_probs=56.7
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (635)
.+|-|.++|....+-..+...|...|+....++ |..++..... .-.+-+-+++||.. ++...++..+
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-------DAHIMLMSAA---LLQEGDVVLVVSHSGRTSDVIEAVELA 210 (292)
T ss_pred CeEEEEEecHHHHHHHHHHHHHhhCCCeEEEcC-------CHHHHHHHHh---cCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 345566666544343445566777787766542 1222211111 12345667888854 4567778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
+.+|-.|+++..... .+|...|+.++.-
T Consensus 211 k~~g~~ii~IT~~~~-s~la~~ad~~l~~ 238 (292)
T PRK11337 211 KKNGAKIICITNSYH-SPIAKLADYVICS 238 (292)
T ss_pred HHCCCeEEEEeCCCC-ChhHHhCCEEEEc
Confidence 999999999875443 4577777776653
No 28
>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=36.67 E-value=2.6e+02 Score=27.34 Aligned_cols=42 Identities=12% Similarity=0.173 Sum_probs=28.1
Q ss_pred cchHHHHHHHhhcCC-eEE-Eec-cCCCChhHHhhcCeEEEeccc
Q 006692 132 RDFSNALHQLRMRRY-NIL-LAQ-PHKASAPLVAAAKSVWLWTSL 173 (635)
Q Consensus 132 rDFS~aL~~LReRGY-NIL-LAq-P~~AS~~L~aaAd~vWlWeSL 173 (635)
.+|+..|..+...|. +|. ++. +...+..+...|+..|....|
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 764 444 555778899888877766544
No 29
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=36.47 E-value=3.3e+02 Score=27.43 Aligned_cols=103 Identities=20% Similarity=0.361 Sum_probs=62.5
Q ss_pred CCCCCCh-hhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHH--hhh
Q 006692 41 VPKNCDP-HTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLF--WAV 117 (635)
Q Consensus 41 VPsG~da-~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~--WAl 117 (635)
||+.+.+ +..++++..-|.+.|. ..++||-....+.. .-.=.|++|+++|...... -..|+-|++. +|+
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 6877765 5678888887876443 56677664433211 1222699999998654442 3467766553 444
Q ss_pred c----CCCCceEEEEeCCc--c-hHHHHHHHhhcCCeEEEe
Q 006692 118 D----NPAPSNYLLISGDR--D-FSNALHQLRMRRYNILLA 151 (635)
Q Consensus 118 D----NPpPANIMLISGDr--D-FS~aL~~LReRGYNILLA 151 (635)
. +.--.-+++|-|-. - |...+..|+.+|..|++-
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 21122377777654 3 566777888888777754
No 30
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=36.01 E-value=3.7e+02 Score=28.91 Aligned_cols=53 Identities=8% Similarity=0.106 Sum_probs=34.0
Q ss_pred CChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 006692 45 CDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (635)
Q Consensus 45 ~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVP 97 (635)
+++..+..-|+.+-+..+....+.|+..++-..+..+.++.|...|+.-+++.
T Consensus 73 l~~~~l~~ll~~i~~~~~~~~~~e~t~e~~p~~i~~e~l~~l~~~G~~rvslG 125 (375)
T PRK05628 73 LGAEGLARVLDAVRDTFGLAPGAEVTTEANPESTSPEFFAALRAAGFTRVSLG 125 (375)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCCCCHHHHHHHHHcCCCEEEEe
Confidence 44444444333322223443345677778877788899999999999877764
No 31
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=34.91 E-value=2e+02 Score=30.76 Aligned_cols=85 Identities=20% Similarity=0.280 Sum_probs=59.7
Q ss_pred CCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchh-hhHHHHHHHHhhhcCCC
Q 006692 43 KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDAS-DKKILVDMLFWAVDNPA 121 (635)
Q Consensus 43 sG~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAA-DkkMLVDML~WAlDNPp 121 (635)
+|+.+-.|...|++.|=. -.|..|||.-++| .|.|... -+....+++.|..++-
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 688888999999887733 3566779987654 4433211 1334566777776665
Q ss_pred CceEEEEeCCcchHHHHHHHhhc-CCeEEEecc
Q 006692 122 PSNYLLISGDRDFSNALHQLRMR-RYNILLAQP 153 (635)
Q Consensus 122 PANIMLISGDrDFS~aL~~LReR-GYNILLAqP 153 (635)
..++||....-.+.+|..||++ ...|+.+.|
T Consensus 68 -ik~lVIACNTASa~al~~LR~~~~iPVvGviP 99 (269)
T COG0796 68 -IKALVIACNTASAVALEDLREKFDIPVVGVIP 99 (269)
T ss_pred -CCEEEEecchHHHHHHHHHHHhCCCCEEEecc
Confidence 7788888888888889999875 677776664
No 32
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=34.48 E-value=40 Score=34.24 Aligned_cols=26 Identities=12% Similarity=0.216 Sum_probs=18.9
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhcccc
Q 006692 449 QGRLTPSEYVQGLIGVILLALNTLKIERV 477 (635)
Q Consensus 449 ~g~~~~s~~~q~li~~il~al~~lk~eki 477 (635)
+|||+. ++.+++.|+..+..+|.|.+
T Consensus 137 PGCPP~---Pe~il~~l~~L~~~i~~~~~ 162 (186)
T PRK14814 137 PGCPPR---PEAILDALVKLQTKLKTQGL 162 (186)
T ss_pred cCCCCC---HHHHHHHHHHHHHHHhcccc
Confidence 899985 44567777777788876655
No 33
>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=33.60 E-value=4.2e+02 Score=26.37 Aligned_cols=113 Identities=24% Similarity=0.317 Sum_probs=58.9
Q ss_pred CceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCcc-C--ceEEEEEecC----CCC-ChhHHHHhhhcCCce-eeccC
Q 006692 28 AKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYC-G--PVSISAYGDT----NRI-PASVQHALSSTGIAL-NHVPA 98 (635)
Q Consensus 28 AkTAVFWDIENCPVPsG~da~~Va~NIrsAL~klGY~-G--pVTIrAYGDl----s~i-p~~vl~aLsSSGIsL-ihVPa 98 (635)
.--+|.-|.+||=++.+-+ .+.+.+...++++--. | .|.| +-+. .+. ..++...-...||.+ .|. +
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 3467889999998764433 2334444433333211 2 2433 3332 111 122333334568884 453 1
Q ss_pred CCcchhhhHHHHHHHHhhhcC---CCCceEEEEeCCcchHHHHHHHhhcCCeEEEe
Q 006692 99 GVKDASDKKILVDMLFWAVDN---PAPSNYLLISGDRDFSNALHQLRMRRYNILLA 151 (635)
Q Consensus 99 G~KDAADkkMLVDML~WAlDN---PpPANIMLISGDrDFS~aL~~LReRGYNILLA 151 (635)
.|-... .+++.|...+ -.|..+ ++-||+=|...|---++.-|.|++-
T Consensus 115 -kKP~~~----~~i~~~~~~~~~~~~p~ei-avIGDrl~TDVl~gN~~G~~tilv~ 164 (168)
T PF09419_consen 115 -KKPGCF----REILKYFKCQKVVTSPSEI-AVIGDRLFTDVLMGNRMGSYTILVT 164 (168)
T ss_pred -CCCccH----HHHHHHHhhccCCCCchhE-EEEcchHHHHHHHhhccCceEEEEe
Confidence 233222 2344443333 124444 4459999999998888777888764
No 34
>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=33.47 E-value=2.5e+02 Score=24.60 Aligned_cols=48 Identities=17% Similarity=0.086 Sum_probs=33.9
Q ss_pred CCceEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 121 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 121 pPANIMLISGD---rDFS~aL~~LReRGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
+.+-+++||-. ++-..++..++++|..|+.+.... ..+|...|+..+.
T Consensus 46 ~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~~-~s~la~~ad~~l~ 96 (126)
T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVV-GSTLAREADYVLY 96 (126)
T ss_pred CCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECCC-CChHHHhCCEEEE
Confidence 44567777754 356677888899999999887543 3467777776654
No 35
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=32.98 E-value=3.3e+02 Score=26.91 Aligned_cols=49 Identities=12% Similarity=0.093 Sum_probs=35.2
Q ss_pred CCCceEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 120 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 120 PpPANIMLISGD---rDFS~aL~~LReRGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
.+.+-+++||.. ++...++..++.+|-.|+.+..... .+|...++.++.
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 36
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=32.54 E-value=2.6e+02 Score=29.00 Aligned_cols=94 Identities=23% Similarity=0.248 Sum_probs=61.7
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhh-hcCCCCceEEEEeCC---cchHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWA-VDNPAPSNYLLISGD---RDFSNALHQ 140 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WA-lDNPpPANIMLISGD---rDFS~aL~~ 140 (635)
++|-|.+.|....+-..+...|...|+...++.. .+++... ..-.+.+-+++||.. .+...++..
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 4677777775555555667778888887776521 1122111 122455778888865 356778888
Q ss_pred HhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 141 LRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 141 LReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
++++|-.|+.+..... .+|...|+.++.-
T Consensus 112 ak~~g~~vI~iT~~~~-s~la~~ad~~l~~ 140 (321)
T PRK11543 112 LEDKSIALLAMTGKPT-SPLGLAAKAVLDI 140 (321)
T ss_pred HHHcCCeEEEEECCCC-ChhHHhCCEEEEc
Confidence 8999999999886444 4588888877654
No 37
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.36 E-value=2.8e+02 Score=32.11 Aligned_cols=19 Identities=32% Similarity=0.459 Sum_probs=10.6
Q ss_pred ccccCCCCCCCCCCCCCCCC
Q 006692 304 FRNQHLLRPNNFPMQPNFPQ 323 (635)
Q Consensus 304 ~~~~~~~rp~~~~~~~~~~~ 323 (635)
+||+.|.-|. |+|++||.+
T Consensus 416 ~qNyppp~p~-f~m~~~hP~ 434 (483)
T KOG2236|consen 416 QQNYPPPSPS-FPMFQPHPP 434 (483)
T ss_pred cCCCCCCCCC-CCccCCCCC
Confidence 4455555555 667755543
No 38
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=31.99 E-value=3.4e+02 Score=28.29 Aligned_cols=90 Identities=18% Similarity=0.197 Sum_probs=57.2
Q ss_pred EEEEe--cCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHHhh
Q 006692 69 ISAYG--DTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQLRM 143 (635)
Q Consensus 69 IrAYG--Dls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~LRe 143 (635)
|..|| -..-+-.++...|...|+.+..+. |..++. | .+....+-+-+++||-. ++...++...++
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 44454 333355667778889999888873 334444 2 22233455667777754 356677888899
Q ss_pred cCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 144 RRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 144 RGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
+|..||.+..... .+|...|+.++.
T Consensus 203 ~ga~vIaiT~~~~-spla~~Ad~~L~ 227 (281)
T COG1737 203 RGAKVIAITDSAD-SPLAKLADIVLL 227 (281)
T ss_pred CCCcEEEEcCCCC-CchhhhhceEEe
Confidence 9999999875433 457777765544
No 39
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=31.98 E-value=43 Score=33.73 Aligned_cols=24 Identities=13% Similarity=0.476 Sum_probs=15.2
Q ss_pred CCCCceEEEEeCC--cchHHHHHHHh
Q 006692 119 NPAPSNYLLISGD--RDFSNALHQLR 142 (635)
Q Consensus 119 NPpPANIMLISGD--rDFS~aL~~LR 142 (635)
+|.-+.+|||+|. ......|.++-
T Consensus 67 SPRhADvLlVtG~vT~km~~~l~~~y 92 (173)
T PRK14818 67 SPRQADFMIVAGTLTYKMAERARLLY 92 (173)
T ss_pred CcccccEEEEeCcCccccHHHHHHHH
Confidence 4556778888885 34555555554
No 40
>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=31.14 E-value=1.1e+02 Score=28.71 Aligned_cols=40 Identities=20% Similarity=0.268 Sum_probs=30.7
Q ss_pred HHHHH-hcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCC
Q 006692 55 SSALV-KMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAG 99 (635)
Q Consensus 55 rsAL~-klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG 99 (635)
-+.|+ ++||.| .|+|.||.- .+-+.-|..+|+.-..++.+
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 44555 889999 689999963 35567788999998888664
No 41
>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=31.03 E-value=1.5e+02 Score=31.63 Aligned_cols=41 Identities=15% Similarity=0.174 Sum_probs=26.0
Q ss_pred hHHHHHHHHHhc-CccCceEEEEEecCCCCChhHHHHhhhcCC-ce
Q 006692 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGI-AL 93 (635)
Q Consensus 50 Va~NIrsAL~kl-GY~GpVTIrAYGDls~ip~~vl~aLsSSGI-sL 93 (635)
|..+|+.+.+.+ .+.+ .|..||+.=+. ..+.+.|...|| .+
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 35778988665 467888999996 44
No 42
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=30.98 E-value=1.6e+02 Score=31.51 Aligned_cols=42 Identities=17% Similarity=0.177 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhc-Cc-cCceEEEEEecCCCCChhHHHHhhhcCCcee
Q 006692 50 IAQNISSALVKM-NY-CGPVSISAYGDTNRIPASVQHALSSTGIALN 94 (635)
Q Consensus 50 Va~NIrsAL~kl-GY-~GpVTIrAYGDls~ip~~vl~aLsSSGIsLi 94 (635)
|..+|+.+.+.+ .+ .++ |..||++=+. ..+.+.|...||.++
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 12 244 5789998665 467889999999888
No 43
>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=30.51 E-value=4.8e+02 Score=24.81 Aligned_cols=49 Identities=14% Similarity=0.061 Sum_probs=35.4
Q ss_pred CCceEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 121 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 121 pPANIMLISGD---rDFS~aL~~LReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
+.+-+++||.- ++-..++..++++|-.|+.+.....+ +|...|+..+..
T Consensus 101 ~~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s-~La~~aD~~l~~ 152 (177)
T cd05006 101 PGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGG-KLLELADIEIHV 152 (177)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCC-chhhhCCEEEEe
Confidence 44667777743 46778889999999999988754443 477778776554
No 44
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=30.34 E-value=77 Score=34.72 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=34.5
Q ss_pred CCCceEEEEeC-CcchHHHHHH-HhhcCCeEEEeccCC-CChhHHhhc
Q 006692 120 PAPSNYLLISG-DRDFSNALHQ-LRMRRYNILLAQPHK-ASAPLVAAA 164 (635)
Q Consensus 120 PpPANIMLISG-DrDFS~aL~~-LReRGYNILLAqP~~-AS~~L~aaA 164 (635)
+.....||||| |..|...|.+ |-++||+|+..|... ..+.|...+
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 46788999998 8899987755 889999999999543 335566544
No 45
>PRK15482 transcriptional regulator MurR; Provisional
Probab=29.83 E-value=4.3e+02 Score=27.09 Aligned_cols=95 Identities=12% Similarity=0.097 Sum_probs=57.4
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (635)
.+|-|.+.|....+-..+...|...|..+.... |..+...+ +..-.+-+-+++||-. ++...++..+
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 456666666544444445566777787665542 11222111 1122345778888865 3566778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
+++|-.|+++..... .+|...|+..+.-
T Consensus 206 ~~~g~~iI~IT~~~~-s~la~~ad~~l~~ 233 (285)
T PRK15482 206 RKQGATVIAITSLAD-SPLRRLAHFTLDT 233 (285)
T ss_pred HHCCCEEEEEeCCCC-CchHHhCCEEEEc
Confidence 899999998875443 4577777766654
No 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=29.46 E-value=2.3e+02 Score=27.41 Aligned_cols=71 Identities=18% Similarity=0.286 Sum_probs=45.1
Q ss_pred EEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCe
Q 006692 68 SISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYN 147 (635)
Q Consensus 68 TIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYN 147 (635)
.+-|.|+ ...++|...|+....+|...-++ ..| .+++ .....+..++++.|+..=..+...|+++|++
T Consensus 75 ~i~avG~------~Ta~~l~~~G~~~~~~~~~~~~s--~~L-~~~l---~~~~~~~~vl~~~g~~~~~~l~~~L~~~g~~ 142 (231)
T PF02602_consen 75 KIFAVGP------KTAEALREYGFQPDFVPSSEGSS--EGL-AELL---KEQLRGKRVLILRGEGGRPDLPEKLREAGIE 142 (231)
T ss_dssp EEEESSH------HHHHHHHHTT-EECEE-TTSSSH--HHH-HGGH---HHCCTTEEEEEEESSSSCHHHHHHHHHTTEE
T ss_pred eEEEEcH------HHHHHHHHcCCCccccCCCCCCH--HHH-HHHH---HhhCCCCeEEEEcCCCccHHHHHHHHHCCCe
Confidence 4455555 45678888999988888633332 122 2222 2244458899999987766677889999988
Q ss_pred EEE
Q 006692 148 ILL 150 (635)
Q Consensus 148 ILL 150 (635)
|.-
T Consensus 143 v~~ 145 (231)
T PF02602_consen 143 VTE 145 (231)
T ss_dssp EEE
T ss_pred EEE
Confidence 854
No 47
>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=29.18 E-value=4.4e+02 Score=25.26 Aligned_cols=100 Identities=18% Similarity=0.275 Sum_probs=52.9
Q ss_pred CChhhhHHHHHHH---HHhc-CccCceEEEEEecCCCCChhHHHHhhhcCCceeecc--CCC-cchhhhHHHHHHHHhhh
Q 006692 45 CDPHTIAQNISSA---LVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP--AGV-KDASDKKILVDMLFWAV 117 (635)
Q Consensus 45 ~da~~Va~NIrsA---L~kl-GY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVP--aG~-KDAADkkMLVDML~WAl 117 (635)
.+...+...|.++ |++. |..-+.-.--||.. ...+++.|...|+.++.-- ..+ .......|+..+ .
T Consensus 74 ~~~~~~~~ei~~~~~~l~~~~g~~~~~fr~P~G~~---~~~~~~~l~~~G~~~v~w~~~~~D~~~~~~~~i~~~~----~ 146 (191)
T TIGR02764 74 LEDEKIKKDILRAQEIIEKLTGKKPTLFRPPSGAF---NKAVLKAAESLGYTVVHWSVDSRDWKNPGVESIVDRV----V 146 (191)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCCEEECCCcCC---CHHHHHHHHHcCCeEEEecCCCCccCCCCHHHHHHHH----H
Confidence 4444555555553 3332 22211222334654 3567888999999887642 111 111222333333 3
Q ss_pred cCCCCceEEEEe--CCc-----chHHHHHHHhhcCCeEEEe
Q 006692 118 DNPAPSNYLLIS--GDR-----DFSNALHQLRMRRYNILLA 151 (635)
Q Consensus 118 DNPpPANIMLIS--GDr-----DFS~aL~~LReRGYNILLA 151 (635)
++-.+..|||.= ++. -+..+|..|+.+||.++-+
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 344455566655 222 3556788899999998643
No 48
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=28.78 E-value=2.8e+02 Score=27.69 Aligned_cols=108 Identities=16% Similarity=0.189 Sum_probs=57.9
Q ss_pred ceEEEEEecC-CCCChhHHHHhh-----hcCCceeeccCCCc-chhhhHHHHHHHHhhh-cCCCCceEEEEeC-------
Q 006692 66 PVSISAYGDT-NRIPASVQHALS-----STGIALNHVPAGVK-DASDKKILVDMLFWAV-DNPAPSNYLLISG------- 130 (635)
Q Consensus 66 pVTIrAYGDl-s~ip~~vl~aLs-----SSGIsLihVPaG~K-DAADkkMLVDML~WAl-DNPpPANIMLISG------- 130 (635)
.|+|-++|.. .+...+-..+.. -++++++.++.... +.++...+..--.-++ ..-++.++++.-+
T Consensus 2 ki~iiaVGk~~~~~~~~g~~eY~KR~~~~~~leliei~~~~~~~~~~~~~~~~~E~~~il~~i~~~~~vi~Ld~~Gk~~s 81 (155)
T COG1576 2 KINIIAVGKKKPKYVKDGIAEYLKRFPRYLKLELIEIPEEKRGKNASAELIKKKEGEAILAAIPKGSYVVLLDIRGKALS 81 (155)
T ss_pred eEEEEEeeccchHHHHHHHHHHHHHhccccCceEEecCCccCccccCHHHHHHHHHHHHHHhcCCCCeEEEEecCCCcCC
Confidence 3567777843 222222222211 26788888875422 2222222222111111 1223333333332
Q ss_pred CcchHHHHHHHhhcCCeEEEe--ccCCCChhHHhhcCeEEEeccc
Q 006692 131 DRDFSNALHQLRMRRYNILLA--QPHKASAPLVAAAKSVWLWTSL 173 (635)
Q Consensus 131 DrDFS~aL~~LReRGYNILLA--qP~~AS~~L~aaAd~vWlWeSL 173 (635)
...|+..|..|+..|-+|.++ .+..-++.+...|+..|.+..|
T Consensus 82 Se~fA~~l~~~~~~G~~i~f~IGG~~Gl~~~~~~~a~~~~sls~l 126 (155)
T COG1576 82 SEEFADFLERLRDDGRDISFLIGGADGLSEAVKARADQVLSLSKL 126 (155)
T ss_pred hHHHHHHHHHHHhcCCeEEEEEeCcccCCHHHHHHHhhheecccc
Confidence 136999999999988666443 3666788899888888776554
No 49
>PRK14816 NADH dehydrogenase subunit B; Provisional
Probab=28.72 E-value=45 Score=33.82 Aligned_cols=25 Identities=16% Similarity=0.421 Sum_probs=15.0
Q ss_pred CCCCceEEEEeCCc--chHHHHHHHhh
Q 006692 119 NPAPSNYLLISGDR--DFSNALHQLRM 143 (635)
Q Consensus 119 NPpPANIMLISGDr--DFS~aL~~LRe 143 (635)
.|.-+.++||+|-- .....|.++.+
T Consensus 78 sPRhADvllVtG~VT~~m~~~l~~~~e 104 (182)
T PRK14816 78 SPRQADMIMVCGTITNKMAPVLKRLYD 104 (182)
T ss_pred CCCcceEEEEecCCcchhHHHHHHHHH
Confidence 35557788888863 44455555543
No 50
>PRK14815 NADH dehydrogenase subunit B; Provisional
Probab=28.61 E-value=47 Score=33.69 Aligned_cols=24 Identities=13% Similarity=0.443 Sum_probs=15.2
Q ss_pred CCCCceEEEEeCCc--chHHHHHHHh
Q 006692 119 NPAPSNYLLISGDR--DFSNALHQLR 142 (635)
Q Consensus 119 NPpPANIMLISGDr--DFS~aL~~LR 142 (635)
.|..+.++||+|.. .....|.++.
T Consensus 70 SPR~ADillVtG~VT~~m~~~l~r~y 95 (183)
T PRK14815 70 SPRQADVMIVAGTVTYKMALAVRRIY 95 (183)
T ss_pred CCccccEEEEeCcCchhhHHHHHHHH
Confidence 46667788888864 3345555554
No 51
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=28.01 E-value=5.9e+02 Score=25.83 Aligned_cols=100 Identities=10% Similarity=0.167 Sum_probs=50.0
Q ss_pred hhhHHHHHHHHHhcCccCce-----------EEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCcchhhhHHHH
Q 006692 48 HTIAQNISSALVKMNYCGPV-----------SISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILV 110 (635)
Q Consensus 48 ~~Va~NIrsAL~klGY~GpV-----------TIrAY-GDls~-----ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLV 110 (635)
......|..+++++||.-.. +|-.. .++.. +-..+.+++...|..+..+..... . .-..
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 34567888999999995420 12111 22221 223344566667776665443211 1 1112
Q ss_pred HHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEec
Q 006692 111 DMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (635)
Q Consensus 111 DML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAq 152 (635)
+++..... ...+-|++...+......+..|+..+..|+++.
T Consensus 111 ~~~~~l~~-~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~ 151 (342)
T PRK10014 111 QRFSTLLN-QGVDGVVIAGAAGSSDDLREMAEEKGIPVVFAS 151 (342)
T ss_pred HHHHHHHh-CCCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEe
Confidence 22222222 224556655544444456677777777777664
No 52
>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=27.65 E-value=18 Score=31.84 Aligned_cols=41 Identities=29% Similarity=0.435 Sum_probs=30.9
Q ss_pred HHHHHHHHhhhhccccCCCCccccchhh--cCCCCCCCchHHHHHHHHH
Q 006692 462 IGVILLALNTLKIERVVPSEANITDCIR--YGEPKHRNTDVRKALNCAI 508 (635)
Q Consensus 462 i~~il~al~~lk~eki~pte~ni~dcir--ygd~~~~~~dvkkale~ai 508 (635)
++.++.=++-|..|| +.|+|+|+ |.++|..|||+| +|.-.|
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 455556667788887 67999997 999999999985 444433
No 53
>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=27.49 E-value=2.3e+02 Score=29.49 Aligned_cols=70 Identities=14% Similarity=0.120 Sum_probs=39.9
Q ss_pred hHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEe-CCcc------hHHHHHHHhhcCCeEEEecc
Q 006692 81 SVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLIS-GDRD------FSNALHQLRMRRYNILLAQP 153 (635)
Q Consensus 81 ~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLIS-GDrD------FS~aL~~LReRGYNILLAqP 153 (635)
++.+.|.+.|+.++.+ .|+...-....+..+....+ +.-..++|=. +|.. -+.....|...||+|++..-
T Consensus 127 ~l~~~l~~~G~~Vf~l-TGR~e~~r~~T~~nL~~~G~--~~~~~LiLR~~~d~~~~~~~yKs~~R~~l~~~GYrIv~~iG 203 (229)
T TIGR01675 127 KLYQKIIELGIKIFLL-SGRWEELRNATLDNLINAGF--TGWKHLILRGLEDSNKTVVTYKSEVRKSLMEEGYRIWGNIG 203 (229)
T ss_pred HHHHHHHHCCCEEEEE-cCCChHHHHHHHHHHHHcCC--CCcCeeeecCCCCCCchHhHHHHHHHHHHHhCCceEEEEEC
Confidence 3667888999999998 55543222222222222222 2225666654 3432 23445577788999998764
No 54
>COG3233 Predicted deacetylase [General function prediction only]
Probab=27.39 E-value=1.4e+02 Score=31.61 Aligned_cols=23 Identities=17% Similarity=0.224 Sum_probs=20.3
Q ss_pred CCcchHHHHHHHhhcCCeEEEec
Q 006692 130 GDRDFSNALHQLRMRRYNILLAQ 152 (635)
Q Consensus 130 GDrDFS~aL~~LReRGYNILLAq 152 (635)
+|..|+..|++++++||.++|=.
T Consensus 52 ~d~rf~~~l~~r~e~Gdel~lHG 74 (233)
T COG3233 52 KDPRFVDLLTEREEEGDELVLHG 74 (233)
T ss_pred cChHHHHHHHHHHhcCCEEEEec
Confidence 57789999999999999998853
No 55
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=27.01 E-value=1.3e+02 Score=29.82 Aligned_cols=53 Identities=21% Similarity=0.308 Sum_probs=36.6
Q ss_pred hhhhHHHHHHHHhhhcC-CCCceEEEEeCC-c-chHHH-HHHHhhcCCeEEEeccCC
Q 006692 103 ASDKKILVDMLFWAVDN-PAPSNYLLISGD-R-DFSNA-LHQLRMRRYNILLAQPHK 155 (635)
Q Consensus 103 AADkkMLVDML~WAlDN-PpPANIMLISGD-r-DFS~a-L~~LReRGYNILLAqP~~ 155 (635)
.....|..||....... ||-.|.+.|--| . .|..+ +..||.+||-|+--.+..
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 45678999999877655 444444444443 4 58775 577999999999766543
No 56
>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=26.84 E-value=56 Score=27.17 Aligned_cols=19 Identities=42% Similarity=0.494 Sum_probs=14.2
Q ss_pred HHHHHHHHhcCccCceEEE
Q 006692 52 QNISSALVKMNYCGPVSIS 70 (635)
Q Consensus 52 ~NIrsAL~klGY~GpVTIr 70 (635)
..|-++|+..||.|.|+|-
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 57
>PRK13835 conjugal transfer protein TrbH; Provisional
Probab=26.80 E-value=1.4e+02 Score=29.40 Aligned_cols=51 Identities=16% Similarity=0.194 Sum_probs=34.5
Q ss_pred CcchhhhHHHHHHHHhhhc-CCCCceEEEEeCC-cchHHH-HHHHhhcCCeEEE
Q 006692 100 VKDASDKKILVDMLFWAVD-NPAPSNYLLISGD-RDFSNA-LHQLRMRRYNILL 150 (635)
Q Consensus 100 ~KDAADkkMLVDML~WAlD-NPpPANIMLISGD-rDFS~a-L~~LReRGYNILL 150 (635)
....+...|.-||..-... .||-.+-+.+--| ..|..+ +..||.+||.|+=
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 3445678899999986544 4444444444444 468775 5679999999994
No 58
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=26.30 E-value=2.8e+02 Score=28.22 Aligned_cols=117 Identities=21% Similarity=0.281 Sum_probs=65.6
Q ss_pred cCceEEEEEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhh
Q 006692 27 TAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDK 106 (635)
Q Consensus 27 ~AkTAVFWDIENCPVPsG~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADk 106 (635)
....+|+-|++|-=||= +-.+..+.++.-|..+-..| +.+...-+ .-...+...++.-||..++- ++ |-.
T Consensus 26 ~Gikgvi~DlDNTLv~w--d~~~~tpe~~~W~~e~k~~g-i~v~vvSN--n~e~RV~~~~~~l~v~fi~~-A~-KP~--- 95 (175)
T COG2179 26 HGIKGVILDLDNTLVPW--DNPDATPELRAWLAELKEAG-IKVVVVSN--NKESRVARAAEKLGVPFIYR-AK-KPF--- 95 (175)
T ss_pred cCCcEEEEeccCceecc--cCCCCCHHHHHHHHHHHhcC-CEEEEEeC--CCHHHHHhhhhhcCCceeec-cc-Ccc---
Confidence 45678888888888862 22334556666555554444 22222333 33345666777778776663 21 211
Q ss_pred HHHHHHHHhhhc--CCCCceEEEEeCCcchHHHHHHHhhcCCeEEEeccCCCCh
Q 006692 107 KILVDMLFWAVD--NPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHKASA 158 (635)
Q Consensus 107 kMLVDML~WAlD--NPpPANIMLISGDrDFS~aL~~LReRGYNILLAqP~~AS~ 158 (635)
.-.+.+|+. +-+|.++++ -||.-|..+|.-=| .|+.+||+.|-..+.
T Consensus 96 ---~~~fr~Al~~m~l~~~~vvm-VGDqL~TDVlggnr-~G~~tIlV~Pl~~~d 144 (175)
T COG2179 96 ---GRAFRRALKEMNLPPEEVVM-VGDQLFTDVLGGNR-AGMRTILVEPLVAPD 144 (175)
T ss_pred ---HHHHHHHHHHcCCChhHEEE-Ecchhhhhhhcccc-cCcEEEEEEEecccc
Confidence 112333433 334444333 38988888765433 588888888865543
No 59
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=25.71 E-value=1.1e+02 Score=30.01 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=35.5
Q ss_pred HHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEecc
Q 006692 84 HALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQP 153 (635)
Q Consensus 84 ~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAqP 153 (635)
+.|...||..+.+|. - -||..|-.-+..+.. . -..++|+|+|+||.-++ ..+.+|.+..+
T Consensus 93 ~~l~~~gi~~~~~~g-~--EADDvIatla~~~~~-~--~~~v~IvS~DkD~~QLv----~~~~~V~~~~~ 152 (169)
T PF02739_consen 93 ELLEALGIPVLEVPG-Y--EADDVIATLAKKASE-E--GFEVIIVSGDKDLLQLV----DENVNVYLLDP 152 (169)
T ss_dssp HHHHHTTSEEEEETT-B---HHHHHHHHHHHHHH-T--TCEEEEE-SSGGGGGGT----CS-TSEEEEET
T ss_pred HHHHHCCCCEecCCC-C--cHHHHHHHHHhhhcc-C--CCEEEEEcCCCCHHHhc----CCCceEEEeec
Confidence 345567988888763 2 255555444444432 2 35799999999987544 33456766655
No 60
>PRK10294 6-phosphofructokinase 2; Provisional
Probab=25.21 E-value=5.6e+02 Score=26.22 Aligned_cols=43 Identities=14% Similarity=0.225 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeec
Q 006692 51 AQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHV 96 (635)
Q Consensus 51 a~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihV 96 (635)
.-|+-.+|.++|.. ...+.+.|| .+-..+++.|...||.+.++
T Consensus 41 ~~NvA~~l~~lG~~-~~~i~~vG~--~~g~~i~~~l~~~gv~~~~~ 83 (309)
T PRK10294 41 GINVARAIAHLGGS-ATAIFPAGG--ATGEHLVSLLADENVPVATV 83 (309)
T ss_pred HHHHHHHHHHcCCC-eEEEEEecC--ccHHHHHHHHHHcCCCceEE
Confidence 45667778888763 124556676 45566888999999986665
No 61
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=25.20 E-value=1.6e+02 Score=31.02 Aligned_cols=72 Identities=17% Similarity=0.270 Sum_probs=44.6
Q ss_pred ceEEE-EEecCCCCCCCCChhhhHHHHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhh--------cCCceeec-cC
Q 006692 29 KTSVW-WDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSS--------TGIALNHV-PA 98 (635)
Q Consensus 29 kTAVF-WDIENCPVPsG~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsS--------SGIsLihV-Pa 98 (635)
.++|| --+||+.-|. -+-..+..-++..|.++.-.+.|.|+.+||.+.+|.++++++.. .|+.|.-+ ..
T Consensus 74 ~lTvYaFS~eN~~R~~-~Ev~~Lm~L~~~~l~~~~~~~~irv~~iG~~~~lp~~~~~~~~~~e~~T~~~~~~~Lnia~~Y 152 (256)
T PRK14828 74 VVTLYLLSTDNLGRPS-EELNPLLDIIEDVVRQLAPDGRWRVRHVGSLDLLPAPSANRLKEAEEATVGNDGIKVNVAVGY 152 (256)
T ss_pred EEEEEEEEhhhcCCCH-HHHHHHHHHHHHHHHHHHHhCCeEEEEECChhhCCHHHHHHHHHHHHhhcCCCCcEEEEEecC
Confidence 34444 3578887663 12223444455555554334578999999999999998887753 45555553 44
Q ss_pred CCc
Q 006692 99 GVK 101 (635)
Q Consensus 99 G~K 101 (635)
|.+
T Consensus 153 ggr 155 (256)
T PRK14828 153 GGR 155 (256)
T ss_pred CCH
Confidence 444
No 62
>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=25.08 E-value=1.8e+02 Score=28.36 Aligned_cols=44 Identities=20% Similarity=0.347 Sum_probs=29.0
Q ss_pred hcCCceeeccCCCcchhhhHHHHHHHHhhhcCCC-CceEEEEeCCcchHHH
Q 006692 88 STGIALNHVPAGVKDASDKKILVDMLFWAVDNPA-PSNYLLISGDRDFSNA 137 (635)
Q Consensus 88 SSGIsLihVPaG~KDAADkkMLVDML~WAlDNPp-PANIMLISGDrDFS~a 137 (635)
..||++++.+.|. .||..|. +++. +... +..++|+|+|......
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 3799999987654 5776544 3332 3333 6899999999755443
No 63
>PRK07334 threonine dehydratase; Provisional
Probab=24.82 E-value=2e+02 Score=31.50 Aligned_cols=94 Identities=16% Similarity=0.173 Sum_probs=58.8
Q ss_pred CChhhhHHHHHHHHHhcCccCceEEEEEe-cCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCc
Q 006692 45 CDPHTIAQNISSALVKMNYCGPVSISAYG-DTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPS 123 (635)
Q Consensus 45 ~da~~Va~NIrsAL~klGY~GpVTIrAYG-Dls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPA 123 (635)
.+...+..-+...|...||. +.|...+ |...+-.++...|...++.+..+-.. ++...+ .+....-
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 46777777788888888884 4444443 34445578888999999998877321 100000 0011123
Q ss_pred eEEEEeCC-cchHHHHHHHhhcCCeEEEe
Q 006692 124 NYLLISGD-RDFSNALHQLRMRRYNILLA 151 (635)
Q Consensus 124 NIMLISGD-rDFS~aL~~LReRGYNILLA 151 (635)
+|.|-..| ..+..++.+||..||.+-++
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 64
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=24.19 E-value=4.6e+02 Score=26.50 Aligned_cols=94 Identities=12% Similarity=0.151 Sum_probs=54.0
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCC---cchHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGD---RDFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGD---rDFS~aL~~L 141 (635)
.+|.|.+.|-...+-..+...|...|+...... |..+. . +. +..-.+-+.+++||-- .+...++...
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 345555555332232334444666787665531 11111 1 11 1122345677888854 3566778888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEEe
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWLW 170 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWlW 170 (635)
+++|-.|+++.. . ..+|...|+.++.-
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 34688888877664
No 65
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=24.01 E-value=4.6e+02 Score=24.73 Aligned_cols=51 Identities=10% Similarity=0.045 Sum_probs=35.4
Q ss_pred CCCceEEEEeCC---cchHHHHHHHhhcCCeEEEeccCCCChhHHhhcCeEEEec
Q 006692 120 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 171 (635)
Q Consensus 120 PpPANIMLISGD---rDFS~aL~~LReRGYNILLAqP~~AS~~L~aaAd~vWlWe 171 (635)
.+-+-+++||.. .+-..++..++++|-.|+.+.... ..+|...|+.++.-.
T Consensus 78 ~~~D~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~-~s~l~~~ad~~l~~~ 131 (154)
T TIGR00441 78 QKGDVLLGISTSGNSKNVLKAIEAAKDKGMKTITLAGKD-GGKMAGLADIELRVP 131 (154)
T ss_pred CCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCC-CCchhhhCCEEEEeC
Confidence 445678888865 356677888899999999887533 345667777666543
No 66
>KOG3154 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.51 E-value=1.1e+02 Score=32.43 Aligned_cols=66 Identities=21% Similarity=0.443 Sum_probs=46.5
Q ss_pred eEEEEEecCCCCCCCCChhhhHH-HHHHHHHhcCccCceEEEEEecCCCCChhHHHHhhhcCCceeecc
Q 006692 30 TSVWWDIENCQVPKNCDPHTIAQ-NISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (635)
Q Consensus 30 TAVFWDIENCPVPsG~da~~Va~-NIrsAL~klGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVP 97 (635)
....||++-|- |.-+++..++. +..+.|+.-.-.|=|.++-.|+.. ++...++-+...|+.+++|.
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 34579999997 77888876654 455666544334557777777754 44556777888999999873
No 67
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=23.42 E-value=7.2e+02 Score=25.08 Aligned_cols=99 Identities=11% Similarity=0.054 Sum_probs=52.3
Q ss_pred hhHHHHHHHHHhcCccCc-----------eEEEEEe-cCCC-----CChhHHHHhhhcCCceeeccCCCcchhhhHHHHH
Q 006692 49 TIAQNISSALVKMNYCGP-----------VSISAYG-DTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILVD 111 (635)
Q Consensus 49 ~Va~NIrsAL~klGY~Gp-----------VTIrAYG-Dls~-----ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVD 111 (635)
.....|..+.+++||.-. -+|-... ++.. +-..+.+++...|+.+..+.... +. + -..+
T Consensus 33 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~-~~-~--~~~~ 108 (328)
T PRK11303 33 KTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDD-QP-D--NEMR 108 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCC-CH-H--HHHH
Confidence 466778899999999531 1222221 2221 22345566777888877654322 11 1 1112
Q ss_pred HHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEec
Q 006692 112 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 152 (635)
Q Consensus 112 ML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAq 152 (635)
++.+.... ..+-+++.+.+..-...+..|...+..|+++.
T Consensus 109 ~~~~l~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~v~ 148 (328)
T PRK11303 109 CAEHLLQR-QVDALIVSTSLPPEHPFYQRLQNDGLPIIALD 148 (328)
T ss_pred HHHHHHHc-CCCEEEEcCCCCCChHHHHHHHhcCCCEEEEC
Confidence 33332222 34556665543333455677777788887775
No 68
>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=23.11 E-value=59 Score=33.32 Aligned_cols=31 Identities=29% Similarity=0.545 Sum_probs=25.3
Q ss_pred cCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 006692 490 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (635)
Q Consensus 490 ygd~~~~~~dvkkale~ai~~~~vv~~~~g~ 520 (635)
...+-+.+.+|||||..||.++++++..++.
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 69
>PRK06411 NADH dehydrogenase subunit B; Validated
Probab=22.99 E-value=70 Score=32.40 Aligned_cols=27 Identities=15% Similarity=0.068 Sum_probs=15.1
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhccccC
Q 006692 449 QGRLTPSEYVQGLIGVILLALNTLKIERVV 478 (635)
Q Consensus 449 ~g~~~~s~~~q~li~~il~al~~lk~eki~ 478 (635)
+|||+. ++.+++.|+..++.++.|+..
T Consensus 139 PGCPP~---Pe~il~~l~~l~~~i~~~~~~ 165 (183)
T PRK06411 139 PGCPPR---PEALLYGILKLQKKIRQSERE 165 (183)
T ss_pred CCCCCC---HHHHHHHHHHHHHHHhccccc
Confidence 666663 334555556666666655443
No 70
>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=22.81 E-value=58 Score=35.33 Aligned_cols=33 Identities=33% Similarity=0.440 Sum_probs=27.5
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 006692 488 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (635)
Q Consensus 488 irygd~~~~~~dvkkale~ai~~~~vv~~~~g~ 520 (635)
+....+.+.+..|||||..||-++.++++.++.
T Consensus 237 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 269 (473)
T cd08491 237 IDAQIPPLDDVRVRKALNLAIDRDGIVGALFGG 269 (473)
T ss_pred ecCCCCcccCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 334467788999999999999999999987653
No 71
>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=22.74 E-value=8e+02 Score=24.77 Aligned_cols=100 Identities=9% Similarity=0.074 Sum_probs=54.2
Q ss_pred hhHHHHHHHHHhcCccCc-----------eEEEEE-ecCCC-----CChhHHHHhhhcCCceeeccCCCcchhhhHHHHH
Q 006692 49 TIAQNISSALVKMNYCGP-----------VSISAY-GDTNR-----IPASVQHALSSTGIALNHVPAGVKDASDKKILVD 111 (635)
Q Consensus 49 ~Va~NIrsAL~klGY~Gp-----------VTIrAY-GDls~-----ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVD 111 (635)
+....|..+.+++||.-. -+|-.. .++.. +-..+.+++...|..+..+...........+
T Consensus 32 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~~~~~--- 108 (327)
T TIGR02417 32 ETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDDNPDQEKVV--- 108 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHH---
Confidence 466789999999999532 122222 23222 2234556677889888776543211111122
Q ss_pred HHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeEEEecc
Q 006692 112 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQP 153 (635)
Q Consensus 112 ML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNILLAqP 153 (635)
+.....+ ..+-+++...+......+..|+..+..|+++..
T Consensus 109 -~~~l~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~ 148 (327)
T TIGR02417 109 -IENLLAR-QVDALIVASCMPPEDAYYQKLQNEGLPVVALDR 148 (327)
T ss_pred -HHHHHHc-CCCEEEEeCCCCCChHHHHHHHhcCCCEEEEcc
Confidence 2222222 245566665544234567778878888887753
No 72
>PRK14813 NADH dehydrogenase subunit B; Provisional
Probab=22.67 E-value=73 Score=32.52 Aligned_cols=27 Identities=19% Similarity=0.338 Sum_probs=21.1
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhccccC
Q 006692 449 QGRLTPSEYVQGLIGVILLALNTLKIERVV 478 (635)
Q Consensus 449 ~g~~~~s~~~q~li~~il~al~~lk~eki~ 478 (635)
|||||. ++.+|+-||.+++.++.|++.
T Consensus 133 PGCPP~---PeaIl~gl~~l~~~i~~~~~~ 159 (189)
T PRK14813 133 PGCPPR---PEALIGGLMKVQELIRMEQIG 159 (189)
T ss_pred cCCCCC---HHHHHHHHHHHHHHHHhcccc
Confidence 899984 566778888888888887653
No 73
>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=22.56 E-value=61 Score=35.04 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=27.5
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 006692 487 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (635)
Q Consensus 487 cirygd~~~~~~dvkkale~ai~~~~vv~~~~g~ 520 (635)
++..-.+-+....|||||..||-++.|+++.++.
T Consensus 247 ~~N~~~~~~~d~~vRkAl~~aiDr~~i~~~~~~g 280 (469)
T cd08519 247 VFNVNQPPLDNLAVRQALAYLIDRDLIVNRVYYG 280 (469)
T ss_pred EEeCCCCCCCCHHHHHHHHHHcCHHHHHHHHHhc
Confidence 3444556778899999999999999999987543
No 74
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=22.42 E-value=1.1e+02 Score=29.54 Aligned_cols=54 Identities=15% Similarity=0.087 Sum_probs=41.1
Q ss_pred chhhHHHHHHHHHhhhhccccCCCCccccchhhcCCCCCCCchHHHHHHHHHHh
Q 006692 457 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGEPKHRNTDVRKALNCAIEQ 510 (635)
Q Consensus 457 ~~q~li~~il~al~~lk~eki~pte~ni~dcirygd~~~~~~dvkkale~ai~~ 510 (635)
..-..+.+|-.++.+...+.+.-+|+.+.||.++++-.-.+=+..+||+.++++
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 555666666666666666788999999999999844334577889999988877
No 75
>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=22.28 E-value=67 Score=34.52 Aligned_cols=87 Identities=22% Similarity=0.232 Sum_probs=48.3
Q ss_pred CCCCCCCchHHHHHHHHHHhhHHHHhhcCCcc----eeecCCCccceeeccCCCCCCCcHHHHHHHHHHHcCcc---chh
Q 006692 491 GEPKHRNTDVRKALNCAIEQHMVIKRSLGALP----LYVPKNEKLWNCENLYGNPNQYPKEVWDRIQKFLTSSS---GRS 563 (635)
Q Consensus 491 gd~~~~~~dvkkale~ai~~~~vv~~~~g~~~----l~~~kne~lwkcvn~~~~~~~~pk~~~d~i~~fl~s~~---g~s 563 (635)
..+.+.+..|||||..||..+.++++.++..- -++.... .|-..++.. .|+ --.++-++.|.-+. |-.
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 111111110 121 13456666676442 222
Q ss_pred h-h-hhhhhhHHHHHHHHhhh
Q 006692 564 A-I-MASQCRYEAALILKNSC 582 (635)
Q Consensus 564 ~-i-~~s~~ry~aa~~lk~~c 582 (635)
. | ....-+-+.|.+|+.++
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 76
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.15 E-value=3.1e+02 Score=29.62 Aligned_cols=27 Identities=15% Similarity=0.455 Sum_probs=24.7
Q ss_pred ce-EEEEeCCcchHHHHHHHhhcCCeEE
Q 006692 123 SN-YLLISGDRDFSNALHQLRMRRYNIL 149 (635)
Q Consensus 123 AN-IMLISGDrDFS~aL~~LReRGYNIL 149 (635)
.+ |-+|+...++..+.+.||.+||+|.
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 77
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit. This model describes the B chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. The quinone is plastoquinone in Synechocystis (where the chain is designated K) and in chloroplast, where NADH may be replaced by NADPH. In the methanogenic archaeal genus Methanosarcina, NADH is replaced by F420H2.
Probab=22.00 E-value=75 Score=31.00 Aligned_cols=42 Identities=14% Similarity=0.309 Sum_probs=25.8
Q ss_pred HHHHHhh----hcCCCCceEEEEeCCc--chHHHHHHHhhc--CCeEEEe
Q 006692 110 VDMLFWA----VDNPAPSNYLLISGDR--DFSNALHQLRMR--RYNILLA 151 (635)
Q Consensus 110 VDML~WA----lDNPpPANIMLISGDr--DFS~aL~~LReR--GYNILLA 151 (635)
.|+-.|. ...|..+.++||+|.. .....|.++++. .-.++++
T Consensus 41 ~D~erfG~i~~~~sPr~aDvllVtG~vt~~~~~~l~~~~e~~p~pk~VIA 90 (145)
T TIGR01957 41 YDLDRFGSEVFRASPRQADVMIVAGTVTKKMAPALRRLYDQMPEPKWVIS 90 (145)
T ss_pred ccHHHhCCceecCCCCcceEEEEecCCcHHHHHHHHHHHHhccCCceEEE
Confidence 4555554 2457779999999974 456666666654 3344443
No 78
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=21.88 E-value=5.1e+02 Score=26.54 Aligned_cols=112 Identities=16% Similarity=0.057 Sum_probs=56.0
Q ss_pred EEEEEec--CCCCC-CCCChhhhHHHHHHHHHhcCccCceEEEEEecCCC-C----ChhHHHHhhhcCCceee--ccCCC
Q 006692 31 SVWWDIE--NCQVP-KNCDPHTIAQNISSALVKMNYCGPVSISAYGDTNR-I----PASVQHALSSTGIALNH--VPAGV 100 (635)
Q Consensus 31 AVFWDIE--NCPVP-sG~da~~Va~NIrsAL~klGY~GpVTIrAYGDls~-i----p~~vl~aLsSSGIsLih--VPaG~ 100 (635)
.||+|-. .+.++ -+.|-+..+..+...|.++|++ +|-+-. +.... . -..++++|...|+.+.. +-.+.
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 1234444455555666677763 443211 22211 1 13466788888986432 11121
Q ss_pred cch-hhhHHHHHHHHhhhcCCCCceEEEEeCCcchHHHHHHHhhcCCeE
Q 006692 101 KDA-SDKKILVDMLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNI 148 (635)
Q Consensus 101 KDA-ADkkMLVDML~WAlDNPpPANIMLISGDrDFS~aL~~LReRGYNI 148 (635)
-+. .....+. .|...++.| +-++..+|.--..++..|+++|++|
T Consensus 219 ~~~~~~~~~~~---~~l~~~~~~-~ai~~~nd~~A~g~~~al~~~G~~v 263 (346)
T PRK10401 219 PDMQGGEAAMV---ELLGRNLQL-TAVFAYNDNMAAGALTALKDNGIAI 263 (346)
T ss_pred CChHHHHHHHH---HHHcCCCCC-cEEEECCcHHHHHHHHHHHHcCCCC
Confidence 110 1112222 232233434 4566667776678899999998864
No 79
>PRK01254 hypothetical protein; Provisional
Probab=21.86 E-value=1e+02 Score=37.07 Aligned_cols=41 Identities=24% Similarity=0.548 Sum_probs=28.2
Q ss_pred HHHHhhhcCCCCceEEEEeCC-----cchHHHH--HHHhhcCCeE-EEeccC
Q 006692 111 DMLFWAVDNPAPSNYLLISGD-----RDFSNAL--HQLRMRRYNI-LLAQPH 154 (635)
Q Consensus 111 DML~WAlDNPpPANIMLISGD-----rDFS~aL--~~LReRGYNI-LLAqP~ 154 (635)
||-...+|. .-|+||||| ..|..+| +-|...||.| |++||.
T Consensus 31 em~~~Gwd~---~DiilVtGDAYVDHPsFG~AiigR~Le~~G~rVgIiaQPd 79 (707)
T PRK01254 31 EMDQLGWDS---CDIIIVTGDAYVDHPSFGMAIIGRMLEAQGFRVGIIAQPD 79 (707)
T ss_pred HHHHcCCCc---cCEEEEeCcccccCccchHHHHHHHHHHcCCeEEEEeCCC
Confidence 344444443 459999999 3576643 4567799999 778885
No 80
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=21.33 E-value=3.9e+02 Score=33.20 Aligned_cols=39 Identities=26% Similarity=0.446 Sum_probs=21.5
Q ss_pred HHHHhhhhccccCCCCccccch--hhcCCCCCCCchHHHHHHHHH
Q 006692 466 LLALNTLKIERVVPSEANITDC--IRYGEPKHRNTDVRKALNCAI 508 (635)
Q Consensus 466 l~al~~lk~eki~pte~ni~dc--irygd~~~~~~dvkkale~ai 508 (635)
+.-+|-.| |.|++=. -+| ++.-+-++.|-|.=--|++-.
T Consensus 626 Mrr~nW~k---I~p~d~s-~~cFWvkv~Edk~en~dlfakL~~~F 666 (1102)
T KOG1924|consen 626 MRRFNWSK---IVPRDLS-ENCFWVKVNEDKLENDDLFAKLALKF 666 (1102)
T ss_pred cccCCccc---cCccccC-ccceeeecchhhccchHHHHHHHHHh
Confidence 34445554 6676521 245 455677888877644444433
No 81
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=20.10 E-value=5.7e+02 Score=29.73 Aligned_cols=93 Identities=12% Similarity=0.069 Sum_probs=54.4
Q ss_pred CceEEEEEecCCCCChhHHHHhhhcCCceeeccCCCcchhhhHHHHHHHHhhhcCCCCceEEEEeCCc---chHHHHHHH
Q 006692 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPAGVKDASDKKILVDMLFWAVDNPAPSNYLLISGDR---DFSNALHQL 141 (635)
Q Consensus 65 GpVTIrAYGDls~ip~~vl~aLsSSGIsLihVPaG~KDAADkkMLVDML~WAlDNPpPANIMLISGDr---DFS~aL~~L 141 (635)
.+|.|.++|....+-..+...|...|+..+... |..+.. ..+..-.+-+-+++||-.. +...++..+
T Consensus 469 ~rI~i~G~G~S~~~A~~~~~~l~~lg~~~~~~~-------d~~~~~---~~~~~l~~~DvvI~iS~sG~t~e~i~~~~~A 538 (638)
T PRK14101 469 RRIEFYGLGNSNIVAQDAHYKFFRFGIPTIAYG-------DLYMQA---ASAALLGKGDVIVAVSKSGRAPELLRVLDVA 538 (638)
T ss_pred CEEEEEEccHHHHHHHHHHHHHhcCCceEEEcC-------CHHHHH---HHHhcCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 345555555443333445556777787665431 111111 1111223446677788543 466678888
Q ss_pred hhcCCeEEEeccCCCChhHHhhcCeEEE
Q 006692 142 RMRRYNILLAQPHKASAPLVAAAKSVWL 169 (635)
Q Consensus 142 ReRGYNILLAqP~~AS~~L~aaAd~vWl 169 (635)
+++|-.|+++.. . ..+|...|+.++.
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 4568888886653
No 82
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=20.09 E-value=1.1e+03 Score=26.53 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=32.6
Q ss_pred CCCChhhhHHHHHHHHHh-cCccCceEEEEEecCCCCChhHHHHhhhcCCceeec
Q 006692 43 KNCDPHTIAQNISSALVK-MNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHV 96 (635)
Q Consensus 43 sG~da~~Va~NIrsAL~k-lGY~GpVTIrAYGDls~ip~~vl~aLsSSGIsLihV 96 (635)
..+++..+..-+ .++++ +.......|+..++-..+..+.++.|...||.-+.+
T Consensus 126 s~L~~~~l~~ll-~~i~~~~~l~~~~eitiE~~p~~~t~e~l~~l~~aGvnRiSi 179 (449)
T PRK09058 126 TALSAEDLARLI-TALREYLPLAPDCEITLEGRINGFDDEKADAALDAGANRFSI 179 (449)
T ss_pred ccCCHHHHHHHH-HHHHHhCCCCCCCEEEEEeCcCcCCHHHHHHHHHcCCCEEEe
Confidence 334444444433 33333 333333467888887778888888888889876665
No 83
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=20.01 E-value=75 Score=33.55 Aligned_cols=30 Identities=30% Similarity=0.573 Sum_probs=25.6
Q ss_pred CCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 006692 491 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 520 (635)
Q Consensus 491 gd~~~~~~dvkkale~ai~~~~vv~~~~g~ 520 (635)
..+-+.+.+|||||..||-.+.+++..++.
T Consensus 248 ~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 277 (466)
T cd00995 248 NKPPFDDKRVRQAISYAIDREEIIDAVLGG 277 (466)
T ss_pred CCCCCCCHHHHHHHHHhcCHHHHHHHHHhC
Confidence 345678999999999999999999988653
No 84
>PF10965 DUF2767: Protein of unknown function (DUF2767); InterPro: IPR024493 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.01 E-value=1.5e+02 Score=26.02 Aligned_cols=54 Identities=20% Similarity=0.105 Sum_probs=41.5
Q ss_pred chhhHHHHHHHHHhhhhccccCCCCccccchhhcCC---CCCCCchHHHHHHHHHHh
Q 006692 457 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGE---PKHRNTDVRKALNCAIEQ 510 (635)
Q Consensus 457 ~~q~li~~il~al~~lk~eki~pte~ni~dcirygd---~~~~~~dvkkale~ai~~ 510 (635)
..|..-|||=.|.=.|-.+-.-|+-.+|+|-+|--- .-.+.-+..+|+|.||+.
T Consensus 10 ~Y~EmCRVVGd~Vl~L~~~G~etk~~~Ia~~LrT~l~~~~~kr~~~~~~~me~aI~~ 66 (69)
T PF10965_consen 10 LYQEMCRVVGDAVLELADLGHETKRIVIADVLRTELANGRSKRSELQQQAMELAIDL 66 (69)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHhccccccCHHHHHHHHHHHHH
Confidence 456666677667777778888899999999999743 344566889999999975
Done!