Query 007121
Match_columns 617
No_of_seqs 133 out of 228
Neff 3.2
Searched_HMMs 46136
Date Thu Mar 28 19:13:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007121hhsearch_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 99.6 1.6E-15 3.5E-20 133.0 4.2 116 29-151 1-144 (146)
2 cd06167 LabA_like LabA_like pr 99.1 1.3E-10 2.8E-15 104.1 8.5 118 29-149 2-146 (149)
3 PF14418 OHA: OST-HTH Associat 99.1 9.5E-12 2.1E-16 105.2 1.2 59 550-609 9-70 (75)
4 TIGR00288 conserved hypothetic 98.8 2.8E-08 6.1E-13 95.0 11.8 121 24-151 19-154 (160)
5 COG1432 Uncharacterized conser 95.1 0.043 9.3E-07 53.1 6.0 59 99-157 106-165 (181)
6 KOG0260 RNA polymerase II, lar 84.3 61 0.0013 40.9 18.4 15 104-118 1323-1337(1605)
7 KOG0260 RNA polymerase II, lar 76.5 1.1E+02 0.0023 38.9 16.9 7 29-35 1210-1216(1605)
8 cd05014 SIS_Kpsf KpsF-like pro 74.3 16 0.00035 31.9 7.5 49 103-152 47-98 (128)
9 cd05013 SIS_RpiR RpiR-like pro 68.1 45 0.00096 28.7 8.8 85 65-150 14-109 (139)
10 TIGR03127 RuMP_HxlB 6-phospho 64.8 52 0.0011 30.9 9.2 87 64-151 30-122 (179)
11 cd05005 SIS_PHI Hexulose-6-pho 64.1 56 0.0012 30.9 9.3 87 65-152 34-126 (179)
12 PRK07334 threonine dehydratase 60.2 29 0.00063 37.4 7.5 92 41-133 302-402 (403)
13 COG0794 GutQ Predicted sugar p 59.2 60 0.0013 33.1 9.0 100 48-151 26-136 (202)
14 TIGR00393 kpsF KpsF/GutQ famil 49.2 59 0.0013 32.2 7.1 87 65-152 1-98 (268)
15 PRK11337 DNA-binding transcrip 44.8 1.5E+02 0.0032 30.2 9.3 85 66-151 142-237 (292)
16 PRK11543 gutQ D-arabinose 5-ph 44.8 1.2E+02 0.0026 31.1 8.7 86 65-151 43-139 (321)
17 PF04263 TPK_catalytic: Thiami 44.7 50 0.0011 30.7 5.4 65 69-133 38-121 (123)
18 PF01380 SIS: SIS domain SIS d 43.9 57 0.0012 28.2 5.4 48 103-151 53-103 (131)
19 PRK01045 ispH 4-hydroxy-3-meth 41.6 1E+02 0.0022 33.1 7.8 83 50-137 15-123 (298)
20 PLN02625 uroporphyrin-III C-me 41.6 2.2E+02 0.0048 29.1 9.9 88 8-98 21-128 (263)
21 COG0547 TrpD Anthranilate phos 41.5 1.1E+02 0.0023 33.5 8.0 63 74-136 132-223 (338)
22 cd08502 PBP2_NikA_DppA_OppA_li 41.1 27 0.00058 37.5 3.5 34 470-503 254-287 (472)
23 PRK14820 NADH dehydrogenase su 40.1 27 0.00059 35.0 3.1 30 431-463 137-166 (180)
24 PRK11302 DNA-binding transcrip 39.9 1.6E+02 0.0034 29.6 8.5 86 65-152 129-225 (284)
25 PRK11557 putative DNA-binding 39.2 1.8E+02 0.0039 29.3 8.8 86 65-151 129-225 (278)
26 PRK11869 2-oxoacid ferredoxin 38.9 87 0.0019 33.1 6.7 92 44-138 13-116 (280)
27 cd04908 ACT_Bt0572_1 N-termina 38.2 89 0.0019 24.9 5.3 51 80-132 16-66 (66)
28 COG4634 Uncharacterized protei 38.1 54 0.0012 31.0 4.5 62 77-139 8-80 (113)
29 PRK14814 NADH dehydrogenase su 36.5 36 0.00077 34.4 3.3 27 430-459 136-162 (186)
30 TIGR02177 PorB_KorB 2-oxoacid: 36.0 87 0.0019 33.2 6.2 90 44-138 6-109 (287)
31 PF07582 AP_endonuc_2_N: AP en 35.4 34 0.00073 28.3 2.5 21 52-72 3-23 (55)
32 KOG1610 Corticosteroid 11-beta 34.6 53 0.0011 35.8 4.4 46 101-146 25-73 (322)
33 PF02401 LYTB: LytB protein; 34.3 1.8E+02 0.0038 30.9 8.1 84 49-137 12-121 (281)
34 KOG2972 Uncharacterized conser 33.0 1.6E+02 0.0034 31.6 7.3 83 49-131 135-231 (276)
35 PRK15482 transcriptional regul 32.9 3.1E+02 0.0067 27.9 9.4 86 65-151 136-232 (285)
36 PRK15473 cbiF cobalt-precorrin 32.6 4.2E+02 0.0092 26.9 10.3 88 8-98 14-116 (257)
37 PRK14818 NADH dehydrogenase su 32.4 42 0.00091 33.7 3.1 23 101-123 67-91 (173)
38 KOG3154 Uncharacterized conser 31.6 1E+02 0.0022 32.5 5.8 65 30-97 44-110 (263)
39 PF14258 DUF4350: Domain of un 31.0 1.9E+02 0.0041 23.5 6.2 49 84-133 12-69 (70)
40 TIGR00216 ispH_lytB (E)-4-hydr 30.8 1.9E+02 0.0041 30.8 7.7 71 52-140 42-126 (280)
41 PRK12360 4-hydroxy-3-methylbut 30.6 2E+02 0.0043 30.7 7.8 86 50-137 15-126 (281)
42 cd05008 SIS_GlmS_GlmD_1 SIS (S 30.5 2.9E+02 0.0063 24.0 7.7 48 103-151 46-96 (126)
43 KOG2236 Uncharacterized conser 29.5 3.3E+02 0.0072 31.4 9.6 20 285-305 415-434 (483)
44 PRK14816 NADH dehydrogenase su 29.4 43 0.00093 33.8 2.6 24 101-124 78-103 (182)
45 PRK08136 glycosyl transferase 29.3 2E+02 0.0043 31.0 7.6 60 78-137 140-229 (317)
46 PRK14815 NADH dehydrogenase su 28.9 47 0.001 33.6 2.7 25 100-124 69-95 (183)
47 PF03709 OKR_DC_1_N: Orn/Lys/A 28.9 79 0.0017 28.5 4.0 53 80-132 7-70 (115)
48 cd04882 ACT_Bt0572_2 C-termina 28.9 97 0.0021 23.7 4.0 51 80-131 14-65 (65)
49 cd04883 ACT_AcuB C-terminal AC 28.6 1.7E+02 0.0037 23.1 5.5 52 80-131 16-69 (72)
50 PF10073 DUF2312: Uncharacteri 28.1 18 0.00039 31.8 -0.2 41 444-490 6-48 (74)
51 PLN02641 anthranilate phosphor 28.1 2.3E+02 0.005 30.8 7.9 62 75-136 131-221 (343)
52 PRK11866 2-oxoacid ferredoxin 27.6 1.5E+02 0.0033 31.3 6.3 87 44-138 12-115 (279)
53 PRK06136 uroporphyrin-III C-me 27.6 2.9E+02 0.0063 27.4 8.0 88 8-98 9-116 (249)
54 PRK13371 4-hydroxy-3-methylbut 26.8 2.9E+02 0.0062 31.0 8.5 92 42-136 45-166 (387)
55 COG2359 SpoVS Stage V sporulat 26.7 64 0.0014 29.0 2.9 57 39-98 4-65 (87)
56 PRK08349 hypothetical protein; 25.7 73 0.0016 30.9 3.4 31 106-136 3-33 (198)
57 PF00496 SBP_bac_5: Bacterial 25.1 51 0.0011 33.4 2.4 31 472-502 210-240 (374)
58 cd08519 PBP2_NikA_DppA_OppA_li 24.9 52 0.0011 35.2 2.5 34 469-502 247-280 (469)
59 cd08491 PBP2_NikA_DppA_OppA_li 24.8 51 0.0011 35.4 2.4 33 470-502 237-269 (473)
60 PRK01045 ispH 4-hydroxy-3-meth 24.8 3.4E+02 0.0075 29.2 8.4 16 80-95 78-93 (298)
61 cd06281 PBP1_LacI_like_5 Ligan 24.8 2.7E+02 0.0058 26.8 7.0 17 48-64 15-31 (269)
62 smart00645 Pept_C1 Papain fami 24.6 92 0.002 29.7 3.8 54 439-492 26-79 (174)
63 cd08496 PBP2_NikA_DppA_OppA_li 24.4 58 0.0013 34.7 2.7 87 473-564 243-338 (454)
64 KOG2947 Carbohydrate kinase [C 24.4 1.2E+02 0.0025 32.8 4.7 57 51-111 44-102 (308)
65 COG1737 RpiR Transcriptional r 24.2 4.8E+02 0.01 27.0 9.1 82 69-151 133-227 (281)
66 COG3233 Predicted deacetylase 24.1 1.2E+02 0.0025 31.9 4.6 48 82-134 26-74 (233)
67 PRK00188 trpD anthranilate pho 23.9 2.9E+02 0.0062 29.6 7.7 60 78-137 134-222 (339)
68 PRK06411 NADH dehydrogenase su 23.7 67 0.0015 32.4 2.8 27 431-460 139-165 (183)
69 PRK11867 2-oxoglutarate ferred 23.5 1.3E+02 0.0027 31.8 4.9 91 39-137 20-124 (286)
70 PRK14813 NADH dehydrogenase su 23.5 69 0.0015 32.5 2.9 28 430-460 132-159 (189)
71 cd05710 SIS_1 A subgroup of th 23.2 5.4E+02 0.012 22.9 8.3 48 103-151 47-97 (120)
72 PRK12360 4-hydroxy-3-methylbut 23.2 3.7E+02 0.0081 28.7 8.2 17 79-95 80-96 (281)
73 PRK10892 D-arabinose 5-phospha 22.7 3.5E+02 0.0077 27.9 7.9 86 65-151 48-144 (326)
74 PRK11382 frlB fructoselysine-6 22.6 7.3E+02 0.016 26.3 10.3 99 53-153 34-144 (340)
75 cd07995 TPK Thiamine pyrophosp 22.6 2.4E+02 0.0052 27.8 6.3 39 57-98 34-72 (208)
76 TIGR01957 nuoB_fam NADH-quinon 22.4 73 0.0016 30.9 2.7 26 100-125 53-80 (145)
77 cd06297 PBP1_LacI_like_12 Liga 22.3 3.4E+02 0.0073 26.4 7.2 70 48-134 15-85 (269)
78 PRK14101 bifunctional glucokin 22.2 4.1E+02 0.0089 30.6 9.0 83 66-150 470-563 (638)
79 cd01542 PBP1_TreR_like Ligand- 22.1 3.9E+02 0.0085 25.3 7.5 70 48-134 15-85 (259)
80 PRK05778 2-oxoglutarate ferred 21.9 1.8E+02 0.0039 31.0 5.7 89 44-137 23-125 (301)
81 cd00995 PBP2_NikA_DppA_OppA_li 21.8 66 0.0014 33.6 2.4 30 473-502 248-277 (466)
82 cd08498 PBP2_NikA_DppA_OppA_li 21.7 76 0.0016 34.1 2.9 29 474-502 259-287 (481)
83 COG1576 Uncharacterized conser 21.4 3.9E+02 0.0085 26.6 7.4 41 115-155 84-126 (155)
84 cd05006 SIS_GmhA Phosphoheptos 21.0 6.6E+02 0.014 23.7 8.7 50 102-152 100-152 (177)
85 TIGR02764 spore_ybaN_pdaB poly 21.0 5.1E+02 0.011 24.6 8.0 86 45-133 74-187 (191)
86 cd01712 ThiI ThiI is required 20.9 1.1E+02 0.0025 28.7 3.6 30 106-135 2-31 (177)
87 PF10965 DUF2767: Protein of u 20.8 1.4E+02 0.0031 26.1 3.8 54 439-492 10-66 (69)
88 cd08517 PBP2_NikA_DppA_OppA_li 20.4 73 0.0016 33.9 2.5 29 474-502 257-285 (480)
89 cd08512 PBP2_NikA_DppA_OppA_li 20.4 75 0.0016 33.9 2.6 32 470-501 259-290 (476)
90 cd08492 PBP2_NikA_DppA_OppA_li 20.1 92 0.002 33.2 3.1 28 474-501 261-288 (484)
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=99.56 E-value=1.6e-15 Score=133.00 Aligned_cols=116 Identities=31% Similarity=0.484 Sum_probs=80.6
Q ss_pred ceEEEEeccCCCCCCC---CChhhHHHHHHHHHHhcCcccce-EEEEEecCCCC-chHHHHHhhhcCceeeeccC-----
Q 007121 29 KTSVWWDIENCQVPKN---CDPHTIAQNISSALVKMNYCGPV-SISAYGDTNRI-PASVQHALSSTGIALNHVPA----- 98 (617)
Q Consensus 29 kTsVFWDIENCPVP~G---~da~~Va~nIr~ALrklGY~GPV-SIrAYGDls~i-p~~Vl~aLsSSGIsLiHVPa----- 98 (617)
+|+||||+|||..+.+ +++..+...|++ .|++ .+++|++...- .....++|...||.+.+++.
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 666666655554 5667 79999994321 24677899999999988752
Q ss_pred -----------------CCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEEec-cCCCChhHHhhccceEe
Q 007121 99 -----------------VDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWL 151 (617)
Q Consensus 99 -----------------lDNPpPANIMLISGDrDFS~aLs~LR~RGYNILLAq-P~~aS~~L~aaA~~vWl 151 (617)
....+++++||||||.||.+++..|+.+|++|.++. +..++..|..+|+.++.
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 GGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVRKLRERGKRVIVVGAEDSASEALRSAADEFIS 144 (146)
T ss_dssp --S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHHHHHHH--EEEEEE-GGGS-HHHHHHSSEEEE
T ss_pred cccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHHHHHHcCCEEEEEEeCCCCCHHHHHhcCEEEe
Confidence 223445999999999999999999999999999998 56789999999997654
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=99.15 E-value=1.3e-10 Score=104.06 Aligned_cols=118 Identities=22% Similarity=0.209 Sum_probs=88.3
Q ss_pred ceEEEEeccCCCCCCCCCh--hhHHHHHHHHHHhcCcccce-EEEEEecCCC--CchHHHHHhhhcCceeeecc-----C
Q 007121 29 KTSVWWDIENCQVPKNCDP--HTIAQNISSALVKMNYCGPV-SISAYGDTNR--IPASVQHALSSTGIALNHVP-----A 98 (617)
Q Consensus 29 kTsVFWDIENCPVP~G~da--~~Va~nIr~ALrklGY~GPV-SIrAYGDls~--ip~~Vl~aLsSSGIsLiHVP-----a 98 (617)
+++||||.||+..-..... ..-...+...+.+. +.+ ..++|++... ......++|...|+.+++++ .
T Consensus 2 r~~ifiD~~Nl~~~~~~~~~~~~d~~~l~~~~~~~---~~~~~~r~y~~~~~~~~~~~~~~~L~~~g~~~~~~~~~~~~~ 78 (149)
T cd06167 2 RVAVFIDGENLYYSLRDLGGKRFDYRKLLEFLRDG---GEIVLARAYGNWTSPERQRGFLDALRRLGFEPIQKPLRTRGS 78 (149)
T ss_pred eEEEEEeHHHHHHHHHHhcCCCcCHHHHHHHHHhC---CeEEEEEEEEecCCchhHHHHHHHHHHCCcEEEEEcceecCC
Confidence 6899999999975221110 11122233333321 444 6899999874 45678899999999999988 2
Q ss_pred ----------------CCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEEeccC-CCChhHHhhccce
Q 007121 99 ----------------VDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSV 149 (617)
Q Consensus 99 ----------------lDNPpPANIMLISGDrDFS~aLs~LR~RGYNILLAqP~-~aS~~L~aaA~~v 149 (617)
.....++.|||+|||.||.+++..||++|.+|+++.+. ..|..|..+|+.+
T Consensus 79 ~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d~f 146 (149)
T cd06167 79 GKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSRELRKAADRF 146 (149)
T ss_pred cccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCCcc
Confidence 11237899999999999999999999999999999987 7889999988844
No 3
>PF14418 OHA: OST-HTH Associated domain
Probab=99.15 E-value=9.5e-12 Score=105.24 Aligned_cols=59 Identities=36% Similarity=0.451 Sum_probs=53.9
Q ss_pred hhhhHHHHHHHHhh---hhhhhhhhhHHHHHHHhhccceeeecCCCCceeeEEEEeeecCCCC
Q 007121 550 SQCRYEAALILKNS---CLPELALGEILKILNMVITPKKWIIHHQSGWQPVTITLAEYKSDSG 609 (617)
Q Consensus 550 s~~ry~aa~ilk~~---cl~~~algdvlqil~~~i~~kkw~~~h~sgwqp~~i~~~~~~~~~~ 609 (617)
+.|||++|..||+. ||+++.||+|++|++|.|..|||+ +|+++|+|+.++..++++..+
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 999999999888877766543
No 4
>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=98.84 E-value=2.8e-08 Score=94.99 Aligned_cols=121 Identities=16% Similarity=0.144 Sum_probs=92.5
Q ss_pred hhcCCceEEEEeccCCCCCCCCChhhHHHHHHHHHHhcCcccceE-EEEEecCCCCchHHHHHhhhcCceeeeccC----
Q 007121 24 QYVTAKTSVWWDIENCQVPKNCDPHTIAQNISSALVKMNYCGPVS-ISAYGDTNRIPASVQHALSSTGIALNHVPA---- 98 (617)
Q Consensus 24 rya~AkTsVFWDIENCPVP~G~da~~Va~nIr~ALrklGY~GPVS-IrAYGDls~ip~~Vl~aLsSSGIsLiHVPa---- 98 (617)
+--.-+++||-|.+|.. +..+. .+ ...|...|.+ .|.++ -++||++... ...++.|...|++.+....
T Consensus 19 ~~~~~riAvfID~~Nv~-~~~~~-~d-~~~i~~~ls~---~G~i~~~R~Y~~a~a~-~~l~~~l~~~Gf~pv~~kG~~Dv 91 (160)
T TIGR00288 19 RKGEKKIGLLVDGPNML-RKEFN-ID-LDEIREILSE---YGDIKIGKVLLNQYAS-DKLIEAVVNQGFEPIIVAGDVDV 91 (160)
T ss_pred cCCCCcEEEEEeCCccC-hhhhc-cC-HHHHHHHHHh---cCCeEEEEEEechhcc-HHHHHHHHHCCceEEEecCcccH
Confidence 33356799999999996 22221 11 3455666655 57676 5899996433 4678899999999765443
Q ss_pred ---------CCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEEec-cCCCChhHHhhccceEe
Q 007121 99 ---------VDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVWL 151 (617)
Q Consensus 99 ---------lDNPpPANIMLISGDrDFS~aLs~LR~RGYNILLAq-P~~aS~~L~aaA~~vWl 151 (617)
+-.+.-++|+|+|||.||.+++.+||++|..|+++. +..++..|..+|+.++.
T Consensus 92 ~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~acd~FI~ 154 (160)
T TIGR00288 92 RMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNSADIAII 154 (160)
T ss_pred HHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHhcCeEEe
Confidence 225788999999999999999999999999999999 44688999999997765
No 5
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=95.13 E-value=0.043 Score=53.12 Aligned_cols=59 Identities=25% Similarity=0.215 Sum_probs=51.0
Q ss_pred CCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEEeccC-CCChhHHhhccceEeehhhhc
Q 007121 99 VDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAKSVWLWTSLVA 157 (617)
Q Consensus 99 lDNPpPANIMLISGDrDFS~aLs~LR~RGYNILLAqP~-~aS~~L~aaA~~vWlWeSLLa 157 (617)
.+++.-.+++|+|||.||.+++..++.+|..|+++.-. ..|..|..+|+.+..-.++..
T Consensus 106 ~~~~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~~s~~L~~~aD~~i~L~~~~~ 165 (181)
T COG1432 106 ADKKNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAADYYIDLKSLEE 165 (181)
T ss_pred hcccCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCCcCHHHHHHhhcceEEchhhhh
Confidence 46788999999999999999999999999999999854 578889999998777666544
No 6
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=84.31 E-value=61 Score=40.86 Aligned_cols=15 Identities=27% Similarity=0.184 Sum_probs=8.5
Q ss_pred CceEEEEeCCcchHH
Q 007121 104 PSNYLLISGDRDFSN 118 (617)
Q Consensus 104 PANIMLISGDrDFS~ 118 (617)
+--..+|+.|-.+.+
T Consensus 1323 ~e~~~vi~f~gsyVn 1337 (1605)
T KOG0260|consen 1323 RELLNVISFDGSYVN 1337 (1605)
T ss_pred hhhhheEeecccchh
Confidence 344566777765543
No 7
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=76.50 E-value=1.1e+02 Score=38.91 Aligned_cols=7 Identities=0% Similarity=0.126 Sum_probs=3.0
Q ss_pred ceEEEEe
Q 007121 29 KTSVWWD 35 (617)
Q Consensus 29 kTsVFWD 35 (617)
...+||.
T Consensus 1210 d~~~i~~ 1216 (1605)
T KOG0260|consen 1210 DLACIFS 1216 (1605)
T ss_pred CCceeec
Confidence 3444443
No 8
>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=74.33 E-value=16 Score=31.94 Aligned_cols=49 Identities=20% Similarity=0.179 Sum_probs=36.2
Q ss_pred CCceEEEEeCC---cchHHHHHHHhcCCCeEEEeccCCCChhHHhhccceEee
Q 007121 103 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLW 152 (617)
Q Consensus 103 pPANIMLISGD---rDFS~aLs~LR~RGYNILLAqP~~aS~~L~aaA~~vWlW 152 (617)
+-+.+++||-. ++...++..+|++|-.|+++.....+ +|...|+..+..
T Consensus 47 ~~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~~~s-~la~~ad~~l~~ 98 (128)
T cd05014 47 PGDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNS-TLAKLSDVVLDL 98 (128)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCC-chhhhCCEEEEC
Confidence 44667888854 47888999999999999999875543 566667755554
No 9
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=68.13 E-value=45 Score=28.71 Aligned_cols=85 Identities=14% Similarity=0.114 Sum_probs=54.4
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC-------C-CCCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA-------V-DNPAPSNYLLISGDR---DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa-------l-DNPpPANIMLISGDr---DFS~aLs~LR~RGYNILLA 133 (617)
+.|-|.+.|....+-......|...|.....++. + .-.+.+-+++||-.. +...++..++++|-.|+++
T Consensus 14 ~~i~i~g~g~s~~~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iS~~g~~~~~~~~~~~a~~~g~~iv~i 93 (139)
T cd05013 14 RRIYIFGVGSSGLVAEYLAYKLLRLGKPVVLLSDPHLQLMSAANLTPGDVVIAISFSGETKETVEAAEIAKERGAKVIAI 93 (139)
T ss_pred CEEEEEEcCchHHHHHHHHHHHHHcCCceEEecCHHHHHHHHHcCCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEE
Confidence 4566666665444445566677777776655544 1 124456777888554 4666788889999999999
Q ss_pred ccCCCChhHHhhccceE
Q 007121 134 QPHKASAPLVAAAKSVW 150 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vW 150 (617)
..... .+|...++.++
T Consensus 94 T~~~~-~~l~~~~d~~i 109 (139)
T cd05013 94 TDSAN-SPLAKLADIVL 109 (139)
T ss_pred cCCCC-ChhHHhcCEEE
Confidence 87544 35555566443
No 10
>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=64.79 E-value=52 Score=30.92 Aligned_cols=87 Identities=13% Similarity=0.087 Sum_probs=58.1
Q ss_pred ccceEEEEEecCCCCchHHHHHhhhcCceeeeccC--CC-CCCCceEEEEeCC---cchHHHHHHHhcCCCeEEEeccCC
Q 007121 64 CGPVSISAYGDTNRIPASVQHALSSTGIALNHVPA--VD-NPAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHK 137 (617)
Q Consensus 64 ~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--lD-NPpPANIMLISGD---rDFS~aLs~LR~RGYNILLAqP~~ 137 (617)
.+.|-|.+.|.-..+-..+...|...|+....+.. .. -.+-+.+++||.. ++...++..++++|-.|+++....
T Consensus 30 a~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~~~~~~~~~Dv~I~iS~sG~t~~~i~~~~~ak~~g~~ii~IT~~~ 109 (179)
T TIGR03127 30 AKRIFVAGAGRSGLVGKAFAMRLMHLGFNVYVVGETTTPSIKKGDLLIAISGSGETESLVTVAKKAKEIGATVAAITTNP 109 (179)
T ss_pred CCEEEEEecCHHHHHHHHHHHHHHhCCCeEEEeCCcccCCCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCC
Confidence 45666666665444444566677788887765544 22 2345677888854 467778888999999999998655
Q ss_pred CChhHHhhccceEe
Q 007121 138 ASAPLVAAAKSVWL 151 (617)
Q Consensus 138 aS~~L~aaA~~vWl 151 (617)
.+ +|...|+.++.
T Consensus 110 ~s-~la~~ad~~l~ 122 (179)
T TIGR03127 110 ES-TLGKLADVVVE 122 (179)
T ss_pred CC-chHHhCCEEEE
Confidence 53 56666775554
No 11
>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=64.08 E-value=56 Score=30.86 Aligned_cols=87 Identities=17% Similarity=0.193 Sum_probs=57.5
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC--C-CCCCCceEEEEeCC---cchHHHHHHHhcCCCeEEEeccCCC
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA--V-DNPAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKA 138 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--l-DNPpPANIMLISGD---rDFS~aLs~LR~RGYNILLAqP~~a 138 (617)
..|-|.+.|.-..+-......|...|+....+.. . .-.+-+.+++||-. ++...++..++++|-.|+++.....
T Consensus 34 ~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~~~~~~~~~D~vI~iS~sG~t~~~i~~~~~ak~~g~~iI~IT~~~~ 113 (179)
T cd05005 34 KRIFVYGAGRSGLVAKAFAMRLMHLGLNVYVVGETTTPAIGPGDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPD 113 (179)
T ss_pred CeEEEEecChhHHHHHHHHHHHHhCCCeEEEeCCCCCCCCCCCCEEEEEcCCCCcHHHHHHHHHHHHCCCeEEEEECCCC
Confidence 4566666665443444556677778887766554 2 22455677888855 4677788888999999999986544
Q ss_pred ChhHHhhccceEee
Q 007121 139 SAPLVAAAKSVWLW 152 (617)
Q Consensus 139 S~~L~aaA~~vWlW 152 (617)
+ +|...|+.++..
T Consensus 114 s-~la~~ad~~l~~ 126 (179)
T cd05005 114 S-PLAKLADVVVVI 126 (179)
T ss_pred C-chHHhCCEEEEe
Confidence 3 566667755553
No 12
>PRK07334 threonine dehydratase; Provisional
Probab=60.24 E-value=29 Score=37.41 Aligned_cols=92 Identities=14% Similarity=0.188 Sum_probs=62.9
Q ss_pred CCCC-CChhhHHHHHHHHHHhcCcccceEEEEEecCCCCchHHHHHhhhcCceeeeccCC-C------CCCCceEEEEeC
Q 007121 41 VPKN-CDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAV-D------NPAPSNYLLISG 112 (617)
Q Consensus 41 VP~G-~da~~Va~nIr~ALrklGY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPal-D------NPpPANIMLISG 112 (617)
++.| .+...+..-+..+|...||.-.+.|.+.-... +-.++...|++.++.+..+-.- + .....+|.|=..
T Consensus 302 ~~ggn~d~~~l~~il~~~l~~~~y~v~l~I~~~dr~G-lL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~ 380 (403)
T PRK07334 302 LSGGNIDTRLLANVLLRGLVRAGRLARLRVDIRDRPG-ALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETR 380 (403)
T ss_pred ECCCCCCHHHHHHHHHHHHHhCCCEEEEEEEeCCCCC-HHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeC
Confidence 3544 57778888888899888885445555554333 3468889999999998877641 1 122233333334
Q ss_pred Cc-chHHHHHHHhcCCCeEEEe
Q 007121 113 DR-DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 113 Dr-DFS~aLs~LR~RGYNILLA 133 (617)
|+ .+..++.+|+..||-|-|+
T Consensus 381 d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 381 DAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred CHHHHHHHHHHHHHcCCeeEeC
Confidence 54 6889999999999998875
No 13
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=59.16 E-value=60 Score=33.12 Aligned_cols=100 Identities=20% Similarity=0.196 Sum_probs=72.5
Q ss_pred hhHHHHHHHHHHhcCcccceEEEEEecCCCCchHHHHHhhhcCceeeecc-----CCCCC---CCceEEEEeCCc---ch
Q 007121 48 HTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP-----AVDNP---APSNYLLISGDR---DF 116 (617)
Q Consensus 48 ~~Va~nIr~ALrklGY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVP-----alDNP---pPANIMLISGDr---DF 116 (617)
..+.+.++..++ ..|.|-+.-.|.--.+-+.+--.|.++|.....|- +-|-| +-+-+++||+.. +.
T Consensus 26 ~~~~~a~~~i~~---~~gkv~V~G~GkSG~Igkk~Aa~L~s~G~~a~fv~p~ea~hgdlg~i~~~DvviaiS~SGeT~el 102 (202)
T COG0794 26 EDFVRAVELILE---CKGKVFVTGVGKSGLIGKKFAARLASTGTPAFFVGPAEALHGDLGMITPGDVVIAISGSGETKEL 102 (202)
T ss_pred HHHHHHHHHHHh---cCCcEEEEcCChhHHHHHHHHHHHHccCCceEEecCchhccCCccCCCCCCEEEEEeCCCcHHHH
Confidence 344555555554 37889888888877777777778999999877775 33332 457889999874 57
Q ss_pred HHHHHHHhcCCCeEEEeccCCCChhHHhhccceEe
Q 007121 117 SNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 117 S~aLs~LR~RGYNILLAqP~~aS~~L~aaA~~vWl 151 (617)
..++..++.+|-.|+.+.....| .|...|+.++.
T Consensus 103 ~~~~~~aK~~g~~liaiT~~~~S-sLak~aDvvl~ 136 (202)
T COG0794 103 LNLAPKAKRLGAKLIAITSNPDS-SLAKAADVVLV 136 (202)
T ss_pred HHHHHHHHHcCCcEEEEeCCCCC-hHHHhcCeEEE
Confidence 78888999999999988765554 57777776655
No 14
>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=49.24 E-value=59 Score=32.18 Aligned_cols=87 Identities=21% Similarity=0.159 Sum_probs=54.4
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC--------CCCCCCceEEEEeCC---cchHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA--------VDNPAPSNYLLISGD---RDFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--------lDNPpPANIMLISGD---rDFS~aLs~LR~RGYNILLA 133 (617)
|.|-|.+.|.-..+.......|...|+...++.. ..-.+-+-+++||-. ++...++..++++|..|+.+
T Consensus 1 ~rI~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~d~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~i 80 (268)
T TIGR00393 1 GKLVIVGIGKSGLIGKKIVATFASTGTPSFFLHPTEAMHGDLGMVEPNDVVLMISYSGESLELLNLIPHLKRLSHKIIAF 80 (268)
T ss_pred CcEEEEecChHHHHHHHHHHHHHhcCCceEEeCHhHHhhcccCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEE
Confidence 4455555553333334555566677776655543 112345677888854 46778899999999999999
Q ss_pred ccCCCChhHHhhccceEee
Q 007121 134 QPHKASAPLVAAAKSVWLW 152 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vWlW 152 (617)
.....+ +|...|+..+.+
T Consensus 81 T~~~~s-~l~~~~d~~l~~ 98 (268)
T TIGR00393 81 TGSPNS-SLARAADYVLDI 98 (268)
T ss_pred ECCCCC-cccccCCEEEEc
Confidence 875543 455566655554
No 15
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=44.84 E-value=1.5e+02 Score=30.17 Aligned_cols=85 Identities=18% Similarity=0.164 Sum_probs=56.9
Q ss_pred ceEEEEEecCCCCchHHHHHhhhcCceeeeccC--------CCCCCCceEEEEeCC---cchHHHHHHHhcCCCeEEEec
Q 007121 66 PVSISAYGDTNRIPASVQHALSSTGIALNHVPA--------VDNPAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQ 134 (617)
Q Consensus 66 PVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--------lDNPpPANIMLISGD---rDFS~aLs~LR~RGYNILLAq 134 (617)
.|-|.++|.-..+...+...|...|+....+.. ..-.+-+-+++||.. ++...++...+.+|-.|+++.
T Consensus 142 ~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dl~I~iS~sG~t~~~~~~~~~ak~~g~~ii~IT 221 (292)
T PRK11337 142 QRDLYGAGGSAAIARDVQHKFLRIGVRCQAYDDAHIMLMSAALLQEGDVVLVVSHSGRTSDVIEAVELAKKNGAKIICIT 221 (292)
T ss_pred eEEEEEecHHHHHHHHHHHHHhhCCCeEEEcCCHHHHHHHHhcCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEe
Confidence 455666665444444556677788887765554 122456677888865 367778888899999999998
Q ss_pred cCCCChhHHhhccceEe
Q 007121 135 PHKASAPLVAAAKSVWL 151 (617)
Q Consensus 135 P~~aS~~L~aaA~~vWl 151 (617)
....+ +|...|+.++.
T Consensus 222 ~~~~s-~la~~ad~~l~ 237 (292)
T PRK11337 222 NSYHS-PIAKLADYVIC 237 (292)
T ss_pred CCCCC-hhHHhCCEEEE
Confidence 75544 56666775554
No 16
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=44.77 E-value=1.2e+02 Score=31.11 Aligned_cols=86 Identities=26% Similarity=0.262 Sum_probs=61.4
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC--------CCCCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA--------VDNPAPSNYLLISGDR---DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--------lDNPpPANIMLISGDr---DFS~aLs~LR~RGYNILLA 133 (617)
+.|-|.+.|.-..+...+...|...|+...++.. ..-.+.+-+++||... +...++..++++|-.|+.+
T Consensus 43 ~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~d~~i~iS~sG~t~~~~~~~~~ak~~g~~vI~i 122 (321)
T PRK11543 43 GKVVVSGIGKSGHIGKKIAATLASTGTPAFFVHPAEALHGDLGMIESRDVMLFISYSGGAKELDLIIPRLEDKSIALLAM 122 (321)
T ss_pred CcEEEEecChhHHHHHHHHHHHHcCCCceeecChHHHhhCCcCccCCCCEEEEEeCCCCcHHHHHHHHHHHHcCCeEEEE
Confidence 3577777775555556677788889987765543 1234557788888653 6677888889999999999
Q ss_pred ccCCCChhHHhhccceEe
Q 007121 134 QPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vWl 151 (617)
.....+ +|...|+.++.
T Consensus 123 T~~~~s-~la~~ad~~l~ 139 (321)
T PRK11543 123 TGKPTS-PLGLAAKAVLD 139 (321)
T ss_pred ECCCCC-hhHHhCCEEEE
Confidence 876554 57777886654
No 17
>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=44.68 E-value=50 Score=30.65 Aligned_cols=65 Identities=25% Similarity=0.424 Sum_probs=40.9
Q ss_pred EEEEecCCCCchHHHHHhhhcCceeeeccC------------CCCCCCceEEEEe--CCc---chHH--HHHHHhcCCCe
Q 007121 69 ISAYGDTNRIPASVQHALSSTGIALNHVPA------------VDNPAPSNYLLIS--GDR---DFSN--ALHQLRMRRYN 129 (617)
Q Consensus 69 IrAYGDls~ip~~Vl~aLsSSGIsLiHVPa------------lDNPpPANIMLIS--GDr---DFS~--aLs~LR~RGYN 129 (617)
-.+.||+..+..++++.+.+.|+.+++.|. +....+..|+++- |.| -++. +|.++.+++.+
T Consensus 38 d~iiGDfDSi~~~~~~~~~~~~~~~~~~p~kD~TD~e~Al~~~~~~~~~~i~v~Ga~GgR~DH~lanl~~l~~~~~~~~~ 117 (123)
T PF04263_consen 38 DLIIGDFDSISPEVLEFYKSKGVEIIHFPEKDYTDLEKALEYAIEQGPDEIIVLGALGGRFDHTLANLNLLYKYKKRGIK 117 (123)
T ss_dssp SEEEC-SSSS-HHHHHHHHHCTTEEEEE-STTS-HHHHHHHHHHHTTTSEEEEES-SSSSHHHHHHHHHHHHHHHTTTSE
T ss_pred CEEEecCCCCChHHHHHHHhhccceecccccccCHHHHHHHHHHHCCCCEEEEEecCCCcHHHHHHHHHHHHHHHHcCCe
Confidence 458899999999999999999999999996 2223444444443 222 2333 34444557888
Q ss_pred EEEe
Q 007121 130 ILLA 133 (617)
Q Consensus 130 ILLA 133 (617)
|+|+
T Consensus 118 i~li 121 (123)
T PF04263_consen 118 IVLI 121 (123)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 8776
No 18
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=43.94 E-value=57 Score=28.20 Aligned_cols=48 Identities=19% Similarity=0.235 Sum_probs=33.1
Q ss_pred CCceEEEEeCCc---chHHHHHHHhcCCCeEEEeccCCCChhHHhhccceEe
Q 007121 103 APSNYLLISGDR---DFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 103 pPANIMLISGDr---DFS~aLs~LR~RGYNILLAqP~~aS~~L~aaA~~vWl 151 (617)
+-+.+++||-.. +....+..++++|-.|+++..... .+|...++.++.
T Consensus 53 ~~d~vi~is~sg~~~~~~~~~~~ak~~g~~vi~iT~~~~-~~l~~~ad~~l~ 103 (131)
T PF01380_consen 53 PDDLVIIISYSGETRELIELLRFAKERGAPVILITSNSE-SPLARLADIVLY 103 (131)
T ss_dssp TTEEEEEEESSSTTHHHHHHHHHHHHTTSEEEEEESSTT-SHHHHHSSEEEE
T ss_pred ccceeEeeeccccchhhhhhhHHHHhcCCeEEEEeCCCC-CchhhhCCEEEE
Confidence 345677777543 667788888899999988876544 356666665444
No 19
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=41.64 E-value=1e+02 Score=33.07 Aligned_cols=83 Identities=17% Similarity=0.253 Sum_probs=50.2
Q ss_pred HHHHHHHHHHhc-CcccceEEEEEecCCCCchHHHHHhhhcCceeeeccCCCCCCCceEEEEeCC------------c--
Q 007121 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAVDNPAPSNYLLISGD------------R-- 114 (617)
Q Consensus 50 Va~nIr~ALrkl-GY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPalDNPpPANIMLISGD------------r-- 114 (617)
|.++|+.+.+.+ .+.++ |..||++-+= ..+.+.|.+.||..++-. +.-+....|+|+.= +
T Consensus 15 V~rAi~~a~~~~~~~~~~--iytlG~iIHN-~~vv~~L~~~GV~~v~~~--~~v~~~~~ViirAHGv~~~~~~~~~~~g~ 89 (298)
T PRK01045 15 VDRAIEIVERALEKYGAP--IYVRHEIVHN-RYVVERLEKKGAIFVEEL--DEVPDGAIVIFSAHGVSPAVREEAKERGL 89 (298)
T ss_pred HHHHHHHHHHHHHhcCCC--eEEEecCccC-HHHHHHHHHCCCEEecCc--ccCCCCCEEEEeCCCCCHHHHHHHHHCCC
Confidence 556666654432 22233 6889998765 468899999999877522 21111335666641 0
Q ss_pred ---c----h----HHHHHHHhcCCCeEEEeccCC
Q 007121 115 ---D----F----SNALHQLRMRRYNILLAQPHK 137 (617)
Q Consensus 115 ---D----F----S~aLs~LR~RGYNILLAqP~~ 137 (617)
| | -..+.++..+||.|+++.-.+
T Consensus 90 ~viDaTCP~V~k~~~~v~~~~~~Gy~vvi~G~~~ 123 (298)
T PRK01045 90 TVIDATCPLVTKVHKEVARMSREGYEIILIGHKG 123 (298)
T ss_pred eEEeCCCccchHHHHHHHHHHhCCCEEEEEeCCC
Confidence 1 1 234566677999999997543
No 20
>PLN02625 uroporphyrin-III C-methyltransferase
Probab=41.56 E-value=2.2e+02 Score=29.06 Aligned_cols=88 Identities=17% Similarity=0.108 Sum_probs=55.1
Q ss_pred ccccCCCCCccchhhhhhcCCceEEEEec----------cCCCC---C--CCC---ChhhHHHHHHHHHHhcCcccceEE
Q 007121 8 TVTASVSAPMASTAERQYVTAKTSVWWDI----------ENCQV---P--KNC---DPHTIAQNISSALVKMNYCGPVSI 69 (617)
Q Consensus 8 ~~~~~~~~~~t~~ae~rya~AkTsVFWDI----------ENCPV---P--~G~---da~~Va~nIr~ALrklGY~GPVSI 69 (617)
|+|-|++..-|-++......|.+-+..+. .++.+ . .++ ....+...|...+++ ...|.+
T Consensus 21 G~GpGdp~~LTl~a~~~l~~ADvI~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~---g~~Vvv 97 (263)
T PLN02625 21 GTGPGDPDLLTLKALRLLQTADVVLYDRLVSPDILDLVPPGAELLYVGKRGGYHSRTQEEIHELLLSFAEA---GKTVVR 97 (263)
T ss_pred EeCCCChHHhHHHHHHHHhcCCEEEEeCcCCHHHHHhcCCCCEEEecCCcCCccccCHHHHHHHHHHHHHC---CCeEEE
Confidence 56777777889999999999999888654 11110 0 011 122344444444443 236778
Q ss_pred EEEecCCCC--chHHHHHhhhcCceeeeccC
Q 007121 70 SAYGDTNRI--PASVQHALSSTGIALNHVPA 98 (617)
Q Consensus 70 rAYGDls~i--p~~Vl~aLsSSGIsLiHVPa 98 (617)
-+.||-.-. ...+++.|...|+.+.-+|.
T Consensus 98 l~~GDP~~ys~~~~l~~~l~~~~~~veiiPG 128 (263)
T PLN02625 98 LKGGDPLVFGRGGEEMDALRKNGIPVTVVPG 128 (263)
T ss_pred EcCCCchhhhhHHHHHHHHHHCCCCEEEECC
Confidence 889996543 23456778888988888886
No 21
>COG0547 TrpD Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=41.50 E-value=1.1e+02 Score=33.52 Aligned_cols=63 Identities=27% Similarity=0.348 Sum_probs=47.3
Q ss_pred cCCCCchHHHHHhhhcCceeeeccC--------------------------CCCCCCceEEEEe-CCcchHHHHH-HHhc
Q 007121 74 DTNRIPASVQHALSSTGIALNHVPA--------------------------VDNPAPSNYLLIS-GDRDFSNALH-QLRM 125 (617)
Q Consensus 74 Dls~ip~~Vl~aLsSSGIsLiHVPa--------------------------lDNPpPANIMLIS-GDrDFS~aLs-~LR~ 125 (617)
++..-++.+++.|.+.||...+.|. +-||......||. -+++|...+. -|+.
T Consensus 132 ~l~~~~e~~~~~l~~~g~~FlfAp~~hp~~k~v~~vR~~LG~RTifN~LGPL~NPa~~~~qliGV~~p~~~~~~A~~l~~ 211 (338)
T COG0547 132 NLELSPEQAARALEETGIGFLFAPAYHPAMKHVAPVRKELGVRTIFNLLGPLLNPARAKLQLIGVYHPELVELLAEALRL 211 (338)
T ss_pred CCCCCHHHHHHHHHhcCeEEEEccccCHHHHHHHHHHHHcCCCchHHhhccccCCCCCCceEEEEeCHHHHHHHHHHHHH
Confidence 4455567788899999999988885 6789887777777 6788876544 5666
Q ss_pred CC-CeEEEeccC
Q 007121 126 RR-YNILLAQPH 136 (617)
Q Consensus 126 RG-YNILLAqP~ 136 (617)
.| .+.++++-.
T Consensus 212 LG~~ralvV~G~ 223 (338)
T COG0547 212 LGVERALVVHGL 223 (338)
T ss_pred hCcceEEEEECC
Confidence 77 688888764
No 22
>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=41.07 E-value=27 Score=37.48 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=28.3
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCCc
Q 007121 470 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGAL 503 (617)
Q Consensus 470 irygd~~~~~~dvkkale~ai~~~~vv~~~~g~~ 503 (617)
+....+-+.+.+|||||..||-.++|+++.+|..
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 23
>PRK14820 NADH dehydrogenase subunit B; Provisional
Probab=40.07 E-value=27 Score=35.03 Aligned_cols=30 Identities=13% Similarity=0.120 Sum_probs=22.8
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhccccCCCC
Q 007121 431 QGRLTPSEYVQGLIGVILLALNTLKIERVVPSE 463 (617)
Q Consensus 431 ~g~~~~s~~~qgli~~il~al~~lk~eki~pte 463 (617)
+|||+. ++.+++.|+.+++.++.|++-+..
T Consensus 137 PGCPP~---Pe~il~~l~~l~~~i~~~~~~~~~ 166 (180)
T PRK14820 137 PGCPPR---PEQIIDGVMRVQELVKNESLRRRN 166 (180)
T ss_pred cCCCCC---HHHHHHHHHHHHHHHhhccccccC
Confidence 889884 556788888888988888775543
No 24
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=39.90 E-value=1.6e+02 Score=29.56 Aligned_cols=86 Identities=12% Similarity=0.142 Sum_probs=54.7
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC--------CCCCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA--------VDNPAPSNYLLISGDR---DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--------lDNPpPANIMLISGDr---DFS~aLs~LR~RGYNILLA 133 (617)
..|-|.+.|--..+.......|...|+....... ..-.+-+.+++||-.. +...++...+++|-.|+++
T Consensus 129 ~~I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~D~vI~iS~sG~t~~~~~~~~~ak~~g~~vI~I 208 (284)
T PRK11302 129 KKISFFGLGASAAVAHDAQNKFFRFNVPVVYFDDIVMQRMSCMNSSDGDVVVLISHTGRTKSLVELAQLARENGATVIAI 208 (284)
T ss_pred CeEEEEEcchHHHHHHHHHHHHHhcCCceEecCCHHHHHHHHHhCCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEE
Confidence 3444555553333333444556778887765544 1224457788888554 5677888888999999999
Q ss_pred ccCCCChhHHhhccceEee
Q 007121 134 QPHKASAPLVAAAKSVWLW 152 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vWlW 152 (617)
.. . ..+|...|+.++.-
T Consensus 209 T~-~-~s~l~~~ad~~l~~ 225 (284)
T PRK11302 209 TS-A-GSPLAREATLALTL 225 (284)
T ss_pred CC-C-CChhHHhCCEEEec
Confidence 96 3 34688888866553
No 25
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=39.17 E-value=1.8e+02 Score=29.28 Aligned_cols=86 Identities=14% Similarity=0.096 Sum_probs=56.1
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC-------C-CCCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA-------V-DNPAPSNYLLISGDR---DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa-------l-DNPpPANIMLISGDr---DFS~aLs~LR~RGYNILLA 133 (617)
..|-|.+.|.-..+...+...|...|+....... + .-.+.+-+++||-.. +...++..++++|-.|+++
T Consensus 129 ~~I~i~G~G~s~~~A~~~~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dv~I~iS~sg~~~~~~~~~~~ak~~ga~iI~I 208 (278)
T PRK11557 129 RRIILTGIGASGLVAQNFAWKLMKIGINAVAERDMHALLATVQALSPDDLLLAISYSGERRELNLAADEALRVGAKVLAI 208 (278)
T ss_pred CeEEEEecChhHHHHHHHHHHHhhCCCeEEEcCChHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHHcCCCEEEE
Confidence 3455666664434445566778888987765443 1 234567778888554 5567788889999999999
Q ss_pred ccCCCChhHHhhccceEe
Q 007121 134 QPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vWl 151 (617)
.....+ +|...|+.++.
T Consensus 209 T~~~~s-~la~~ad~~l~ 225 (278)
T PRK11557 209 TGFTPN-ALQQRASHCLY 225 (278)
T ss_pred cCCCCC-chHHhCCEEEE
Confidence 875543 45556665543
No 26
>PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=38.88 E-value=87 Score=33.09 Aligned_cols=92 Identities=20% Similarity=0.291 Sum_probs=55.1
Q ss_pred CCChhhHHHHHHHHHHhcCcccceEEEEEecCCCCchHHHHHhhhcCceeee---ccC-----CCCCCCceEEEEeCCcc
Q 007121 44 NCDPHTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNH---VPA-----VDNPAPSNYLLISGDRD 115 (617)
Q Consensus 44 G~da~~Va~nIr~ALrklGY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiH---VPa-----lDNPpPANIMLISGDrD 115 (617)
||-=+.|...|.+||.++|.... ....+.|...... ....+...++.-.| +|. +-+| -..+|.|+||.+
T Consensus 13 GCg~~~i~~~~~~a~~~l~~~p~-d~ivvsdiG~~~~-~~~~~~~~~~~~~mG~alp~AiGaklA~p-d~~VVai~GDG~ 89 (280)
T PRK11869 13 GCGNFGIRNALMKALSELNLKPR-QVVIVSGIGQAAK-MPHYINVNGFHTLHGRAIPAATAVKATNP-ELTVIAEGGDGD 89 (280)
T ss_pred CCCCHHHHHHHHHHHHHcCCCCC-CEEEEeCchHhhh-HHHHccCCCCCcccccHHHHHHHHHHHCC-CCcEEEEECchH
Confidence 77778899999999999987543 2233344333211 22223322221111 111 4444 368999999999
Q ss_pred hHH----HHHHHhcCCCeEEEeccCCC
Q 007121 116 FSN----ALHQLRMRRYNILLAQPHKA 138 (617)
Q Consensus 116 FS~----aLs~LR~RGYNILLAqP~~a 138 (617)
|.. .|....+|+.+|+++.-.+.
T Consensus 90 ~~~iG~~eL~tA~r~nl~i~~IV~NN~ 116 (280)
T PRK11869 90 MYAEGGNHLIHAIRRNPDITVLVHNNQ 116 (280)
T ss_pred HhhCcHHHHHHHHHhCcCcEEEEEECH
Confidence 875 35555568888888865543
No 27
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=38.20 E-value=89 Score=24.93 Aligned_cols=51 Identities=25% Similarity=0.310 Sum_probs=32.2
Q ss_pred hHHHHHhhhcCceeeeccCCCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEE
Q 007121 80 ASVQHALSSTGIALNHVPAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILL 132 (617)
Q Consensus 80 ~~Vl~aLsSSGIsLiHVPalDNPpPANIMLISGDrDFS~aLs~LR~RGYNILL 132 (617)
.++.+.|...||.+..+-.......+.+.+.+ .|...+...|++.||.|.|
T Consensus 16 a~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~--~~~~~~~~~L~~~G~~v~~ 66 (66)
T cd04908 16 AAVTEILSEAGINIRALSIADTSEFGILRLIV--SDPDKAKEALKEAGFAVKL 66 (66)
T ss_pred HHHHHHHHHCCCCEEEEEEEecCCCCEEEEEE--CCHHHHHHHHHHCCCEEEC
Confidence 45677788888877655432211134444444 3345788899999999864
No 28
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.14 E-value=54 Score=31.03 Aligned_cols=62 Identities=19% Similarity=0.221 Sum_probs=43.5
Q ss_pred CCchHHHHHhhhcCceeeeccC-----------CCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEEeccCCCC
Q 007121 77 RIPASVQHALSSTGIALNHVPA-----------VDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHKAS 139 (617)
Q Consensus 77 ~ip~~Vl~aLsSSGIsLiHVPa-----------lDNPpPANIMLISGDrDFS~aLs~LR~RGYNILLAqP~~aS 139 (617)
+++..+.+-|..+||+-+|+-. ++.-.-.+.||+|.|.|| ..|..+...-..|+.+.-.+.+
T Consensus 8 ~Lp~rlad~l~~~g~e~~h~r~lg~~da~D~EI~a~A~~~~~iivTkDsDF-~~la~~~G~Ppki~wLr~gNvs 80 (113)
T COG4634 8 QLPPRLADWLPMAGIEAVHWRDLGLRDATDIEIWAYARRNNRIIVTKDSDF-ADLALTLGSPPKIVWLRCGNVS 80 (113)
T ss_pred CCChHHHHHhhhcccceeeecccCcCCCccHHHHHHHHhcCcEEEEcCccH-HHHHHHcCCCCeEEEEEecCCC
Confidence 3667778888888877777654 223344689999999999 4555555566678877655544
No 29
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=36.54 E-value=36 Score=34.41 Aligned_cols=27 Identities=11% Similarity=0.208 Sum_probs=20.2
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccc
Q 007121 430 TQGRLTPSEYVQGLIGVILLALNTLKIERV 459 (617)
Q Consensus 430 ~~g~~~~s~~~qgli~~il~al~~lk~eki 459 (617)
-+|||+. ++.+++.|+..+..+|.|.+
T Consensus 136 IPGCPP~---Pe~il~~l~~L~~~i~~~~~ 162 (186)
T PRK14814 136 VPGCPPR---PEAILDALVKLQTKLKTQGL 162 (186)
T ss_pred ecCCCCC---HHHHHHHHHHHHHHHhcccc
Confidence 4899995 45577777888888887755
No 30
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes.
Probab=36.04 E-value=87 Score=33.21 Aligned_cols=90 Identities=22% Similarity=0.379 Sum_probs=52.3
Q ss_pred CCChhhHHHHHHHHHHhcCcccceE--EEEEecCCCCchHHHHHhhhcCceeee---ccC-----CCCCCCceEEEEeCC
Q 007121 44 NCDPHTIAQNISSALVKMNYCGPVS--ISAYGDTNRIPASVQHALSSTGIALNH---VPA-----VDNPAPSNYLLISGD 113 (617)
Q Consensus 44 G~da~~Va~nIr~ALrklGY~GPVS--IrAYGDls~ip~~Vl~aLsSSGIsLiH---VPa-----lDNPpPANIMLISGD 113 (617)
||--+.|...|.+||.++|....=+ +.-.|...+.+ ..|...|+.-.| +|. +-+| -..||.|+||
T Consensus 6 GCg~~~i~~~~~~a~~~l~~~p~d~iivsdiGc~~~~~----~~l~~~~~~t~mG~alPaAiGaklA~P-d~~VVai~GD 80 (287)
T TIGR02177 6 GCGDFGILSALQRALAELNLDPEQVVVVSGIGCSAKTP----HYVNVNGFHGLHGRALPVATGIKLANP-HLKVIVVGGD 80 (287)
T ss_pred CCCChHHHHHHHHHHHHhcCCCCCEEEEECCCcccccC----CeEecCCcccccccHHHHHHHHHHHCC-CCcEEEEeCc
Confidence 7777889999999999988754322 22223322222 223333332111 111 3444 3689999999
Q ss_pred cchH----HHHHHHhcCCCeEEEeccCCC
Q 007121 114 RDFS----NALHQLRMRRYNILLAQPHKA 138 (617)
Q Consensus 114 rDFS----~aLs~LR~RGYNILLAqP~~a 138 (617)
.+|. .-|....+|+-+|+++.-.+.
T Consensus 81 G~f~~mg~~eL~tA~r~nl~I~vIVlNN~ 109 (287)
T TIGR02177 81 GDLYGIGGNHFVAAGRRNVDITVIVHDNQ 109 (287)
T ss_pred hHHHhccHHHHHHHHHhCcCeEEEEEECH
Confidence 9973 334445567888877754443
No 31
>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=35.40 E-value=34 Score=28.33 Aligned_cols=21 Identities=38% Similarity=0.392 Sum_probs=14.2
Q ss_pred HHHHHHHHhcCcccceEEEEE
Q 007121 52 QNISSALVKMNYCGPVSISAY 72 (617)
Q Consensus 52 ~nIr~ALrklGY~GPVSIrAY 72 (617)
..|-++|+..||.|+|+|--=
T Consensus 3 ~~i~~~L~~~GYdG~~siE~E 23 (55)
T PF07582_consen 3 KRIFSALREIGYDGWLSIEHE 23 (55)
T ss_dssp HHHHHHHHHTT--SEEEE---
T ss_pred HHHHHHHHHcCCCceEEEEee
Confidence 467899999999999998643
No 32
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=34.58 E-value=53 Score=35.77 Aligned_cols=46 Identities=17% Similarity=0.361 Sum_probs=34.6
Q ss_pred CCCCceEEEEeC-CcchHHHHH-HHhcCCCeEEEeccCC-CChhHHhhc
Q 007121 101 NPAPSNYLLISG-DRDFSNALH-QLRMRRYNILLAQPHK-ASAPLVAAA 146 (617)
Q Consensus 101 NPpPANIMLISG-DrDFS~aLs-~LR~RGYNILLAqP~~-aS~~L~aaA 146 (617)
.+.+...||||| |..|-..|. +|-++||+|+-.|... ..+.|...+
T Consensus 25 ~~~~~k~VlITGCDSGfG~~LA~~L~~~Gf~V~Agcl~~~gae~L~~~~ 73 (322)
T KOG1610|consen 25 DSLSDKAVLITGCDSGFGRLLAKKLDKKGFRVFAGCLTEEGAESLRGET 73 (322)
T ss_pred cccCCcEEEEecCCcHHHHHHHHHHHhcCCEEEEEeecCchHHHHhhhh
Confidence 355678999998 789988766 7888999999999543 445566544
No 33
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. 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 [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=34.34 E-value=1.8e+02 Score=30.95 Aligned_cols=84 Identities=18% Similarity=0.305 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHhcC-cccceEEEEEecCCCCchHHHHHhhhcCceeeeccCCCCCCCceEEEEeCC------------c-
Q 007121 49 TIAQNISSALVKMN-YCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAVDNPAPSNYLLISGD------------R- 114 (617)
Q Consensus 49 ~Va~nIr~ALrklG-Y~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPalDNPpPANIMLISGD------------r- 114 (617)
-|.++|+.+.+.+- +.+ -|..||++-+= ..+.+.|...||..++-. +.-+....|+|+.= +
T Consensus 12 GV~rAi~~a~~~~~~~~~--~vy~lG~iIHN-~~vv~~L~~~Gv~~v~~~--~~~~~g~~ViirAHGv~~~~~~~l~~~g 86 (281)
T PF02401_consen 12 GVKRAIEIAEEALEEYPG--PVYTLGPIIHN-PQVVERLEKRGVKVVDDI--DEVPEGDTVIIRAHGVPPEVYEELKERG 86 (281)
T ss_dssp HHHHHHHHHHHHCCCHSS---EEECS-SSS--HHHHHHHHHCTEEEESSG--CGS-TTEEEEE-TT---HHHHHHHHHTT
T ss_pred cHHHHHHHHHHHHHhcCC--CEEEecCcccC-HHHHHHHHHCCCEEecCc--cccCCCCEEEEeCCCCCHHHHHHHHHcC
Confidence 36777887777653 333 67888998764 478899999999875433 22224556777742 1
Q ss_pred ----c----hH----HHHHHHhcCCCeEEEeccCC
Q 007121 115 ----D----FS----NALHQLRMRRYNILLAQPHK 137 (617)
Q Consensus 115 ----D----FS----~aLs~LR~RGYNILLAqP~~ 137 (617)
| |. ..+.++..+||.|+++.-.+
T Consensus 87 ~~viDaTCP~V~k~~~~v~~~~~~Gy~iviiG~~~ 121 (281)
T PF02401_consen 87 LEVIDATCPFVKKIHKIVRKYAKEGYQIVIIGDKN 121 (281)
T ss_dssp EEEEE---HHHHHHHHHHHHHHHCT-EEEEES-TT
T ss_pred CEEEECCChhHHHHHHHHHHHHhcCCEEEEECCCC
Confidence 1 21 24555667999999998644
No 34
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.03 E-value=1.6e+02 Score=31.63 Aligned_cols=83 Identities=17% Similarity=0.292 Sum_probs=50.4
Q ss_pred hHHHHHHHHHHhcCcccceEEEEEecCCC----Cc-----hHHH--HHhhhcCceeeeccC--CCCCCCce-EEEEeCCc
Q 007121 49 TIAQNISSALVKMNYCGPVSISAYGDTNR----IP-----ASVQ--HALSSTGIALNHVPA--VDNPAPSN-YLLISGDR 114 (617)
Q Consensus 49 ~Va~nIr~ALrklGY~GPVSIrAYGDls~----ip-----~~Vl--~aLsSSGIsLiHVPa--lDNPpPAN-IMLISGDr 114 (617)
+-+..||.+|.++|=.--...+..-|... ++ ++++ +++.+-+.....-|. +|...-.+ |-+|+...
T Consensus 135 r~~~~iRs~~nk~GG~s~~~~r~~FdkKG~Vv~V~~~~~dk~vL~ie~ie~~A~d~~~~~~~e~d~eeer~~fkiv~e~s 214 (276)
T KOG2972|consen 135 RAASSIRSIFNKHGGASASGVRFLFDKKGVVVNVPPEKRDKDVLNIEAIEAGAEDIVAEPVLEIDEEEEREEFKIVTEPS 214 (276)
T ss_pred HHHHHHHHHHHHcCCcccccceeEEeccceEEecChhhcchhhhhHHHHHhcccccccCcccccccccccceeEEEeccc
Confidence 45668999999976100111222222221 22 2222 234444555544444 55555555 89999999
Q ss_pred chHHHHHHHhcCCCeEE
Q 007121 115 DFSNALHQLRMRRYNIL 131 (617)
Q Consensus 115 DFS~aLs~LR~RGYNIL 131 (617)
++..+.+.||.+||+|.
T Consensus 215 sl~qV~~~Lr~~G~~i~ 231 (276)
T KOG2972|consen 215 SLNQVAHKLRSKGFEIK 231 (276)
T ss_pred hHHHHHHHhhcCCceee
Confidence 99999999999999998
No 35
>PRK15482 transcriptional regulator MurR; Provisional
Probab=32.94 E-value=3.1e+02 Score=27.91 Aligned_cols=86 Identities=13% Similarity=0.079 Sum_probs=56.6
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC-------CC-CCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA-------VD-NPAPSNYLLISGDR---DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa-------lD-NPpPANIMLISGDr---DFS~aLs~LR~RGYNILLA 133 (617)
..|-|.+.|.-..+-..+...|...|..+..... .. -.+-+.+++||-.. +...++...+++|-.|+++
T Consensus 136 ~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dv~i~iS~sg~t~~~~~~~~~a~~~g~~iI~I 215 (285)
T PRK15482 136 PFIQITGLGGSALVGRDLSFKLMKIGYRVACEADTHVQATVSQALKKGDVQIAISYSGSKKEIVLCAEAARKQGATVIAI 215 (285)
T ss_pred CeeEEEEeChhHHHHHHHHHHHHhCCCeeEEeccHhHHHHHHhcCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEE
Confidence 3456666665444445566677888877655432 12 23457788888654 6677888888999999999
Q ss_pred ccCCCChhHHhhccceEe
Q 007121 134 QPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vWl 151 (617)
.....+ +|...|+.++.
T Consensus 216 T~~~~s-~la~~ad~~l~ 232 (285)
T PRK15482 216 TSLADS-PLRRLAHFTLD 232 (285)
T ss_pred eCCCCC-chHHhCCEEEE
Confidence 865554 56666775554
No 36
>PRK15473 cbiF cobalt-precorrin-4 C(11)-methyltransferase; Provisional
Probab=32.65 E-value=4.2e+02 Score=26.93 Aligned_cols=88 Identities=14% Similarity=0.172 Sum_probs=58.6
Q ss_pred ccccCCCCCccchhhhhhcCCceEEEEe-------ccCCCC------CCCCChhhHHHHHHHHHHhcCcccceEEEEEec
Q 007121 8 TVTASVSAPMASTAERQYVTAKTSVWWD-------IENCQV------PKNCDPHTIAQNISSALVKMNYCGPVSISAYGD 74 (617)
Q Consensus 8 ~~~~~~~~~~t~~ae~rya~AkTsVFWD-------IENCPV------P~G~da~~Va~nIr~ALrklGY~GPVSIrAYGD 74 (617)
|+|-|++-.-|.++......|.+-+..+ .+-++. ....+...+...|+..+++ ...|.+-+-||
T Consensus 14 G~GpG~~~~lT~~A~~~L~~advv~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~---g~~Vv~L~sGD 90 (257)
T PRK15473 14 GAGPGDKELITLKGYRLLQQAQVVIYAGSLINTELLDYCPAQAECHDSAELHLEQIIDLMEAGVKA---GKTVVRLQTGD 90 (257)
T ss_pred EeCCCChHHhhHHHHHHHHhCCEEEEecccCCHHHHhhcCCCCEEEecCCCCHHHHHHHHHHHHHC---CCeEEEEeCcC
Confidence 5566777788999999999999988876 222221 0112334556666665543 23577777899
Q ss_pred CCCCc--hHHHHHhhhcCceeeeccC
Q 007121 75 TNRIP--ASVQHALSSTGIALNHVPA 98 (617)
Q Consensus 75 ls~ip--~~Vl~aLsSSGIsLiHVPa 98 (617)
-.-+. ..+.++|...||.+.-+|.
T Consensus 91 P~~yg~~~~l~~~l~~~~i~veiiPG 116 (257)
T PRK15473 91 VSLYGSIREQGEELTKRGIDFQVVPG 116 (257)
T ss_pred chhhhhHHHHHHHHHHCCCCEEEeCC
Confidence 65443 3667788888999888886
No 37
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=32.44 E-value=42 Score=33.65 Aligned_cols=23 Identities=13% Similarity=0.517 Sum_probs=11.4
Q ss_pred CCCCceEEEEeCCc--chHHHHHHH
Q 007121 101 NPAPSNYLLISGDR--DFSNALHQL 123 (617)
Q Consensus 101 NPpPANIMLISGDr--DFS~aLs~L 123 (617)
.|.-|.+|||+|.. .....|.++
T Consensus 67 SPRhADvLlVtG~vT~km~~~l~~~ 91 (173)
T PRK14818 67 SPRQADFMIVAGTLTYKMAERARLL 91 (173)
T ss_pred CcccccEEEEeCcCccccHHHHHHH
Confidence 45555566666652 334444443
No 38
>KOG3154 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.62 E-value=1e+02 Score=32.50 Aligned_cols=65 Identities=22% Similarity=0.463 Sum_probs=47.0
Q ss_pred eEEEEeccCCCCCCCCChhhHHH-HHHHHHHhc-CcccceEEEEEecCCCCchHHHHHhhhcCceeeecc
Q 007121 30 TSVWWDIENCQVPKNCDPHTIAQ-NISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP 97 (617)
Q Consensus 30 TsVFWDIENCPVP~G~da~~Va~-nIr~ALrkl-GY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVP 97 (617)
.-..||++-|- |.-+++.+++. +..+.|+.- +|.| |.++-.|+..- +..-++-+...|+.+++|.
T Consensus 44 ~lamwdf~hCd-pkrCsGkKL~rlglv~~lr~g~kF~G-vVlSP~gk~~v-sp~D~d~v~~~G~avvdCS 110 (263)
T KOG3154|consen 44 RLAMWDFGHCD-PKRCSGKKLARLGLVRNLRVGQKFGG-VVLSPVGKQCV-SPADRDVVERSGAAVVDCS 110 (263)
T ss_pred hhhhhcccCCC-ccccchHHHHhhhhHHHhhccCccCc-eEECCCCCccc-CHHHHHHHHhcCceEEecc
Confidence 44689999997 88999876554 555666542 3544 77777787653 4466777889999999876
No 39
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=30.99 E-value=1.9e+02 Score=23.46 Aligned_cols=49 Identities=20% Similarity=0.299 Sum_probs=29.7
Q ss_pred HHhhhcCceeeeccC----CCCCCCceEEEEeCCcchH--H---HHHHHhcCCCeEEEe
Q 007121 84 HALSSTGIALNHVPA----VDNPAPSNYLLISGDRDFS--N---ALHQLRMRRYNILLA 133 (617)
Q Consensus 84 ~aLsSSGIsLiHVPa----lDNPpPANIMLISGDrDFS--~---aLs~LR~RGYNILLA 133 (617)
+.|.+.|+.+..+-. ++ ..+.++++|..+..+. . .|..+-++|=+++|+
T Consensus 12 ~~L~~~g~~v~~~~~~~~~l~-~~~~tll~i~~~~~~~~~~~~~~l~~~v~~G~~lvl~ 69 (70)
T PF14258_consen 12 QLLEEQGVKVERWRKPYEALE-ADDGTLLVIGPDLRLSEPEEAEALLEWVEAGNTLVLA 69 (70)
T ss_pred HHHHHCCCeeEEecccHHHhC-CCCCEEEEEeCCCCCCchHHHHHHHHHHHcCCEEEEe
Confidence 345555665543322 32 3678899999886665 3 344444588787776
No 40
>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=30.84 E-value=1.9e+02 Score=30.79 Aligned_cols=71 Identities=20% Similarity=0.341 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCc------------ccceEEEEEecCCCCchHHHHHhhhcCceeeeccC--CCCCCCceEEEEeCCcchH
Q 007121 52 QNISSALVKMNY------------CGPVSISAYGDTNRIPASVQHALSSTGIALNHVPA--VDNPAPSNYLLISGDRDFS 117 (617)
Q Consensus 52 ~nIr~ALrklGY------------~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--lDNPpPANIMLISGDrDFS 117 (617)
+.+...|+++|. .+.|-|+|.| ++.+++++|.+.|+.++|... + ..--
T Consensus 42 ~~Vv~~L~~~Gv~~~v~~~~~v~~~~~ViirAHG----v~~~~~~~~~~~gl~viDaTCP~V--------------~kv~ 103 (280)
T TIGR00216 42 PQVVERLRERGVFFFLEDLDEVAAGDTVIIRAHG----VPPEVREELEKKGLEVIDATCPLV--------------TKVH 103 (280)
T ss_pred HHHHHHHHHCCCEEeecCcccCCCCCEEEEeCCC----CCHHHHHHHHHCCCeEEeCCCccc--------------HHHH
Q ss_pred HHHHHHhcCCCeEEEeccCCCCh
Q 007121 118 NALHQLRMRRYNILLAQPHKASA 140 (617)
Q Consensus 118 ~aLs~LR~RGYNILLAqP~~aS~ 140 (617)
..+.++..+||.|+++.-....+
T Consensus 104 ~~v~~~~~~Gy~iiiiG~~~HpE 126 (280)
T TIGR00216 104 NAVKKYAKEGYHVILIGKKNHPE 126 (280)
T ss_pred HHHHHHHhCCCEEEEEeCCCCCe
No 41
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=30.63 E-value=2e+02 Score=30.69 Aligned_cols=86 Identities=17% Similarity=0.312 Sum_probs=51.7
Q ss_pred HHHHHHHHHHhc-CcccceEEEEEecCCCCchHHHHHhhhcCceeeeccCCCCCCCceEEEEeCC------------c--
Q 007121 50 IAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPAVDNPAPSNYLLISGD------------R-- 114 (617)
Q Consensus 50 Va~nIr~ALrkl-GY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPalDNPpPANIMLISGD------------r-- 114 (617)
|.++|+.+.+.+ .+.| -.|..||++-+= ..+.+.|.+.||..+....++.-+....|+|+.= +
T Consensus 15 V~rAi~~a~~~~~~~~~-~~vy~lG~iVHN-~~Vv~~L~~~Gv~~v~~~~~~~v~~~~~ViirAHGv~~~~~~~~~~~g~ 92 (281)
T PRK12360 15 VKRAIDTAYDEIEKNDG-KKIYTLGPLIHN-NQVVSDLEEKGVKTIEESEIDSLKEGDVVIIRSHGVSKKVYKDLKDKGL 92 (281)
T ss_pred HHHHHHHHHHHHHhcCC-CCeEEecCCcCC-HHHHHHHHHCcCEEECcCchhhCCCCCEEEEeCCCCCHHHHHHHHHCCC
Confidence 556666654432 2323 246899998765 4788999999998872222222122335566631 0
Q ss_pred ---c----h----HHHHHHHhcCCCeEEEeccCC
Q 007121 115 ---D----F----SNALHQLRMRRYNILLAQPHK 137 (617)
Q Consensus 115 ---D----F----S~aLs~LR~RGYNILLAqP~~ 137 (617)
| | -..+.++..+||.|+++.-.+
T Consensus 93 ~viDaTCP~V~k~~~~v~~~~~~Gy~iviiG~~~ 126 (281)
T PRK12360 93 EIIDATCPFVKKIQNIVEEYYNKGYSIIIVGDKN 126 (281)
T ss_pred eEEeCCCccchHHHHHHHHHHhCCCEEEEEcCCC
Confidence 1 1 235667778999999997543
No 42
>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=30.49 E-value=2.9e+02 Score=24.02 Aligned_cols=48 Identities=17% Similarity=0.087 Sum_probs=34.1
Q ss_pred CCceEEEEeCC---cchHHHHHHHhcCCCeEEEeccCCCChhHHhhccceEe
Q 007121 103 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 103 pPANIMLISGD---rDFS~aLs~LR~RGYNILLAqP~~aS~~L~aaA~~vWl 151 (617)
+.+-+++||-. ++...++..++++|..|+.+..... .+|...|+..+.
T Consensus 46 ~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~~~-s~la~~ad~~l~ 96 (126)
T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVVG-STLAREADYVLY 96 (126)
T ss_pred CCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECCCC-ChHHHhCCEEEE
Confidence 45567788854 3567788889999999999986544 367776775443
No 43
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.53 E-value=3.3e+02 Score=31.35 Aligned_cols=20 Identities=30% Similarity=0.448 Sum_probs=11.1
Q ss_pred CccccCCCCCCCCCCCCCCCC
Q 007121 285 NFRNQHLLRPNNFPMQPNFPQ 305 (617)
Q Consensus 285 ~~~~~~~~rp~~~~~~~~~~~ 305 (617)
-+||+.|.-|. |+|++||.+
T Consensus 415 q~qNyppp~p~-f~m~~~hP~ 434 (483)
T KOG2236|consen 415 QQQNYPPPSPS-FPMFQPHPP 434 (483)
T ss_pred ccCCCCCCCCC-CCccCCCCC
Confidence 34455555555 777755543
No 44
>PRK14816 NADH dehydrogenase subunit B; Provisional
Probab=29.42 E-value=43 Score=33.78 Aligned_cols=24 Identities=17% Similarity=0.480 Sum_probs=12.3
Q ss_pred CCCCceEEEEeCCc--chHHHHHHHh
Q 007121 101 NPAPSNYLLISGDR--DFSNALHQLR 124 (617)
Q Consensus 101 NPpPANIMLISGDr--DFS~aLs~LR 124 (617)
.|.-+.++||+|.. .....|.++.
T Consensus 78 sPRhADvllVtG~VT~~m~~~l~~~~ 103 (182)
T PRK14816 78 SPRQADMIMVCGTITNKMAPVLKRLY 103 (182)
T ss_pred CCCcceEEEEecCCcchhHHHHHHHH
Confidence 34456666666653 3334444443
No 45
>PRK08136 glycosyl transferase family protein; Provisional
Probab=29.29 E-value=2e+02 Score=30.99 Aligned_cols=60 Identities=17% Similarity=0.151 Sum_probs=40.5
Q ss_pred CchHHHHHhhhcCceeeeccC--------------------------CCCC--CCceEEEEe-CCcchHHHHHH-HhcCC
Q 007121 78 IPASVQHALSSTGIALNHVPA--------------------------VDNP--APSNYLLIS-GDRDFSNALHQ-LRMRR 127 (617)
Q Consensus 78 ip~~Vl~aLsSSGIsLiHVPa--------------------------lDNP--pPANIMLIS-GDrDFS~aLs~-LR~RG 127 (617)
.+.++.+.|.+.||...+.|. +-|| .-+...||. -++++...+.. |+..|
T Consensus 140 ~~~~~~~~l~~~g~~fl~ap~~hPa~~~~~~vR~~LG~RT~fN~lgpL~NP~~a~~~~~v~Gv~~~~~~~~~a~~l~~lg 219 (317)
T PRK08136 140 HADQAQAKLAEGQPAFIPVGVLCPPLARLLALRWRMGVRNSAHTLAKLATPFAEGAALRLSSYTHPEYRDRLAEFFSDIG 219 (317)
T ss_pred CHHHHHHHHHhcCeEEEEhHHhCHHHHHHHHHHHHhCCCCHHHHHHHhcCccccCCCeEEEeeeChHHHHHHHHHHHHcC
Confidence 345667778889998887664 6688 344554444 46777766665 66667
Q ss_pred CeEEEeccCC
Q 007121 128 YNILLAQPHK 137 (617)
Q Consensus 128 YNILLAqP~~ 137 (617)
++.++++-..
T Consensus 220 ~~alvv~G~~ 229 (317)
T PRK08136 220 ARALLMRGTE 229 (317)
T ss_pred CCEEEEEcCC
Confidence 8888888643
No 46
>PRK14815 NADH dehydrogenase subunit B; Provisional
Probab=28.93 E-value=47 Score=33.58 Aligned_cols=25 Identities=12% Similarity=0.359 Sum_probs=13.9
Q ss_pred CCCCCceEEEEeCCcc--hHHHHHHHh
Q 007121 100 DNPAPSNYLLISGDRD--FSNALHQLR 124 (617)
Q Consensus 100 DNPpPANIMLISGDrD--FS~aLs~LR 124 (617)
..|..+.++||+|..- ....|.++.
T Consensus 69 ~SPR~ADillVtG~VT~~m~~~l~r~y 95 (183)
T PRK14815 69 FSPRQADVMIVAGTVTYKMALAVRRIY 95 (183)
T ss_pred CCCccccEEEEeCcCchhhHHHHHHHH
Confidence 3456666777777643 334555444
No 47
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=28.88 E-value=79 Score=28.50 Aligned_cols=53 Identities=19% Similarity=0.299 Sum_probs=37.3
Q ss_pred hHHHHHhhhcCceeeeccC-------CCCCCCceEEEEeCC----cchHHHHHHHhcCCCeEEE
Q 007121 80 ASVQHALSSTGIALNHVPA-------VDNPAPSNYLLISGD----RDFSNALHQLRMRRYNILL 132 (617)
Q Consensus 80 ~~Vl~aLsSSGIsLiHVPa-------lDNPpPANIMLISGD----rDFS~aLs~LR~RGYNILL 132 (617)
.++.++|...|++++.+.. +.+-+...-+||+-| .....+|..+|.|+++|-+
T Consensus 7 ~~l~~~L~~~~~~vv~~~~~dd~~~~i~~~~~i~avvi~~d~~~~~~~~~ll~~i~~~~~~iPV 70 (115)
T PF03709_consen 7 RELAEALEQRGREVVDADSTDDALAIIESFTDIAAVVISWDGEEEDEAQELLDKIRERNFGIPV 70 (115)
T ss_dssp HHHHHHHHHTTTEEEEESSHHHHHHHHHCTTTEEEEEEECHHHHHHHHHHHHHHHHHHSTT-EE
T ss_pred HHHHHHHHHCCCEEEEeCChHHHHHHHHhCCCeeEEEEEcccccchhHHHHHHHHHHhCCCCCE
Confidence 4567788888998888887 334444455667777 5667889999998877543
No 48
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.87 E-value=97 Score=23.70 Aligned_cols=51 Identities=18% Similarity=0.283 Sum_probs=31.4
Q ss_pred hHHHHHhhhcCceeeeccCCCCC-CCceEEEEeCCcchHHHHHHHhcCCCeEE
Q 007121 80 ASVQHALSSTGIALNHVPAVDNP-APSNYLLISGDRDFSNALHQLRMRRYNIL 131 (617)
Q Consensus 80 ~~Vl~aLsSSGIsLiHVPalDNP-pPANIMLISGDrDFS~aLs~LR~RGYNIL 131 (617)
.++...|...|+.+.++-...+. .-...+.+.-|. ...++..|++.||.|+
T Consensus 14 ~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~-~~~~~~~L~~~G~~v~ 65 (65)
T cd04882 14 HEILQILSEEGINIEYMYAFVEKKGGKALLIFRTED-IEKAIEVLQERGVELV 65 (65)
T ss_pred HHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCC-HHHHHHHHHHCCceEC
Confidence 45667788888877655432222 112333444332 6688899999999875
No 49
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.63 E-value=1.7e+02 Score=23.06 Aligned_cols=52 Identities=13% Similarity=0.206 Sum_probs=32.5
Q ss_pred hHHHHHhhhcCceeeeccCCCC--CCCceEEEEeCCcchHHHHHHHhcCCCeEE
Q 007121 80 ASVQHALSSTGIALNHVPAVDN--PAPSNYLLISGDRDFSNALHQLRMRRYNIL 131 (617)
Q Consensus 80 ~~Vl~aLsSSGIsLiHVPalDN--PpPANIMLISGDrDFS~aLs~LR~RGYNIL 131 (617)
..+.+.|...||.+..+-.... ..-+.++|-....+...++..|+++||.|+
T Consensus 16 ~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v~ 69 (72)
T cd04883 16 ADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEVL 69 (72)
T ss_pred HHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCeee
Confidence 3566778888888766543222 222333333332455589999999999876
No 50
>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=28.10 E-value=18 Score=31.81 Aligned_cols=41 Identities=29% Similarity=0.435 Sum_probs=30.9
Q ss_pred HHHHHHHHhhhhccccCCCCccccchhh--cCCCCCCCchHHHHHHHHH
Q 007121 444 IGVILLALNTLKIERVVPSEANITDCIR--YGEPKHRNTDVRKALNCAI 490 (617)
Q Consensus 444 i~~il~al~~lk~eki~pte~ni~dcir--ygd~~~~~~dvkkale~ai 490 (617)
++.++.=++-|..|| +.|+|+|+ |.++|..|||+| +|.-.|
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 444443
No 51
>PLN02641 anthranilate phosphoribosyltransferase
Probab=28.06 E-value=2.3e+02 Score=30.80 Aligned_cols=62 Identities=16% Similarity=0.248 Sum_probs=41.3
Q ss_pred CCCCchHHHHHhhhcCceeeeccC--------------------------CCCCCCceEEEEe-CCcchHHHHH-HHhcC
Q 007121 75 TNRIPASVQHALSSTGIALNHVPA--------------------------VDNPAPSNYLLIS-GDRDFSNALH-QLRMR 126 (617)
Q Consensus 75 ls~ip~~Vl~aLsSSGIsLiHVPa--------------------------lDNPpPANIMLIS-GDrDFS~aLs-~LR~R 126 (617)
+..-++++.+.|...||...+.|. +-||..+...||. -+++|...+. -|+..
T Consensus 131 ~~~~~~~~~~~l~~~g~~fl~a~~~hPa~~~~~~~R~~LG~RT~fN~lgpL~NPa~~~~~v~GV~~~~~~~~~a~al~~l 210 (343)
T PLN02641 131 IDLGPEGVKRCVEEVGIGFMMAPKYHPAMKIVAPVRKKLKVKTVFNILGPMLNPARVPHAVVGVYHESLVEKMAKALQRF 210 (343)
T ss_pred CCCCHHHHHHHHHhcCcEEEechhhCHHHHHHHHHHHHhCCCcHHHHHHHhcCCCCCCceEEeeeCHHHHHHHHHHHHHc
Confidence 333445677888889998887764 5688766666665 4677766555 45666
Q ss_pred CC-eEEEeccC
Q 007121 127 RY-NILLAQPH 136 (617)
Q Consensus 127 GY-NILLAqP~ 136 (617)
|+ ++++++-.
T Consensus 211 G~~~alVv~G~ 221 (343)
T PLN02641 211 GMKRALVVHSE 221 (343)
T ss_pred CCCeEEEEecC
Confidence 76 56676654
No 52
>PRK11866 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=27.65 E-value=1.5e+02 Score=31.29 Aligned_cols=87 Identities=22% Similarity=0.308 Sum_probs=51.1
Q ss_pred CCChhhHHHHHHHHHHhcCcccce--EEEEEecCCCCchHHHHHhhhcCceeeeccC-----------CCCCCCceEEEE
Q 007121 44 NCDPHTIAQNISSALVKMNYCGPV--SISAYGDTNRIPASVQHALSSTGIALNHVPA-----------VDNPAPSNYLLI 110 (617)
Q Consensus 44 G~da~~Va~nIr~ALrklGY~GPV--SIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa-----------lDNPpPANIMLI 110 (617)
||.-+.|...|+++|.++|+.+.= .+...|-...++ ..+...++ |..+ +-+| -.+|+.|
T Consensus 12 GCg~~~il~al~~al~~l~~~~~~~ivvsdiGc~~~~~----~~~~~~~~---~~~~G~alp~A~GaklA~P-d~~VV~i 83 (279)
T PRK11866 12 GCGNYGILEALRKALAELGIPPENVVVVSGIGCSSNLP----EFLNTYGI---HGIHGRVLPIATGVKWANP-KLTVIGY 83 (279)
T ss_pred CCCChHHHHHHHHHHHHhcCCCCCEEEEECCchhhhhh----hhccCCCc---ccccccHHHHHHHHHHHCC-CCcEEEE
Confidence 788888999999999998875432 233333322221 11211111 2222 3444 3789999
Q ss_pred eCCcc-hHH---HHHHHhcCCCeEEEeccCCC
Q 007121 111 SGDRD-FSN---ALHQLRMRRYNILLAQPHKA 138 (617)
Q Consensus 111 SGDrD-FS~---aLs~LR~RGYNILLAqP~~a 138 (617)
+||.| |.- .|.....|+.+|+++.-.+.
T Consensus 84 ~GDG~~f~ig~~eL~tA~rrn~~i~vIV~nN~ 115 (279)
T PRK11866 84 GGDGDGYGIGLGHLPHAARRNVDITYIVSNNQ 115 (279)
T ss_pred ECChHHHHccHHHHHHHHHHCcCcEEEEEECh
Confidence 99996 654 34444557888887765443
No 53
>PRK06136 uroporphyrin-III C-methyltransferase; Reviewed
Probab=27.57 E-value=2.9e+02 Score=27.40 Aligned_cols=88 Identities=16% Similarity=0.109 Sum_probs=55.1
Q ss_pred ccccCCCCCccchhhhhhcCCceEEEEeccC--C--CCCCC--------------CChhhHHHHHHHHHHhcCcccceEE
Q 007121 8 TVTASVSAPMASTAERQYVTAKTSVWWDIEN--C--QVPKN--------------CDPHTIAQNISSALVKMNYCGPVSI 69 (617)
Q Consensus 8 ~~~~~~~~~~t~~ae~rya~AkTsVFWDIEN--C--PVP~G--------------~da~~Va~nIr~ALrklGY~GPVSI 69 (617)
|+|-|++..-|.+|..-...+.+-+++|... . -++.. .....+...|...+++ | ..|.+
T Consensus 9 GvGpGdp~~lT~~A~~~L~~advI~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-g--~~V~~ 85 (249)
T PRK06136 9 GAGPGDPDLITLKGVRLLEQADVVLYDDLVSPEILAYAKPDAELIYVGKRAGRHSTKQEEINRLLVDYARK-G--KVVVR 85 (249)
T ss_pred EECCCChHHHHHHHHHHHhcCCEEEEcCCCCHHHHhhCCCCCEEEeCCCcCCCCCcCHHHHHHHHHHHHHC-C--CeEEE
Confidence 6677788889999999999999999875311 0 01110 0012244444444433 2 25777
Q ss_pred EEEecCCCC--chHHHHHhhhcCceeeeccC
Q 007121 70 SAYGDTNRI--PASVQHALSSTGIALNHVPA 98 (617)
Q Consensus 70 rAYGDls~i--p~~Vl~aLsSSGIsLiHVPa 98 (617)
-+.||-.-. ...+++.|...|+.+.-+|.
T Consensus 86 l~~GDP~~ys~~~~l~~~l~~~~~~veviPG 116 (249)
T PRK06136 86 LKGGDPFVFGRGGEELEALEAAGIPYEVVPG 116 (249)
T ss_pred EeCCCchhhhcHHHHHHHHHHCCCCEEEEcC
Confidence 789996543 33456778888988888886
No 54
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=26.82 E-value=2.9e+02 Score=30.98 Aligned_cols=92 Identities=11% Similarity=0.158 Sum_probs=54.4
Q ss_pred CCCCChhhHHHHHHHHHHhc-CcccceEEEEEecCCCCchHHHHHhhhcCceeeecc----CCCCCCCceEEEEeCCc--
Q 007121 42 PKNCDPHTIAQNISSALVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVP----AVDNPAPSNYLLISGDR-- 114 (617)
Q Consensus 42 P~G~da~~Va~nIr~ALrkl-GY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVP----alDNPpPANIMLISGDr-- 114 (617)
|.|+= +-|.++|..+.+.+ .+.| -.|..+|++-+= ..+.+.|.+.||..+.-. .++.-+....|+|+.=.
T Consensus 45 ~~GFC-~GV~RAI~~a~~~~~~~~~-~~vytlG~IIHN-p~Vv~~L~~~Gv~~v~~~~~~~~~~~v~~~~~VIIrAHGv~ 121 (387)
T PRK13371 45 AFGFC-WGVERAVAMAYETRRHFPD-ERIWITNEIIHN-PSVNQHLREMGVRFIPVEKGVKDFSVVTPGDVVILPAFGAT 121 (387)
T ss_pred CCCCC-ccHHHHHHHHHHHHhhcCC-CCeEEecCCcCC-HHHHHHHHhCCCEEEcCcCcccchhcCCCCCEEEEeCCCCC
Confidence 44543 23666666665432 1222 246888998664 478899999999888632 23332334467777421
Q ss_pred ---------------c----h----HHHHHHHhcCCCeEEEeccC
Q 007121 115 ---------------D----F----SNALHQLRMRRYNILLAQPH 136 (617)
Q Consensus 115 ---------------D----F----S~aLs~LR~RGYNILLAqP~ 136 (617)
| | -..+.++..+||.||++.-.
T Consensus 122 ~~v~~~~~~rgl~iiDATCP~V~kvh~~v~~~~~~Gy~iIIiG~~ 166 (387)
T PRK13371 122 VQEMQLLNEKGCHIVDTTCPWVSKVWNTVEKHKKKDFTSIIHGKY 166 (387)
T ss_pred HHHHHHHHHCCCeEEecCCccchHHHHHHHHHHhCCCEEEEEcCC
Confidence 1 1 12455666788888888743
No 55
>COG2359 SpoVS Stage V sporulation protein SpoVS [Function unknown]
Probab=26.74 E-value=64 Score=29.01 Aligned_cols=57 Identities=28% Similarity=0.471 Sum_probs=42.5
Q ss_pred CCCCCCCChhhHHHHHHHHHHhcCcccceEEEEEec--CCCCchH--H-HHHhhhcCceeeeccC
Q 007121 39 CQVPKNCDPHTIAQNISSALVKMNYCGPVSISAYGD--TNRIPAS--V-QHALSSTGIALNHVPA 98 (617)
Q Consensus 39 CPVP~G~da~~Va~nIr~ALrklGY~GPVSIrAYGD--ls~ip~~--V-l~aLsSSGIsLiHVPa 98 (617)
..|.+.-+|..|+..|-..|++ +|.+.|.|.|- +++--+. + +.-|..+||.|+-+|+
T Consensus 4 LKVsa~S~PnsVAGAlAgvlr~---~g~aEiQAiGagAvNQaVKAiAiaRgflapsGidL~~vPa 65 (87)
T COG2359 4 LKVSAKSNPNSVAGALAGVLRE---RGKAEIQAIGAGAVNQAVKAIAIARGFLAPSGIDLVCVPA 65 (87)
T ss_pred EEeccCCCcchHHHHHHHHHHh---cCceeeeeechHHHHHHHHHHHHHhhccCccCCcEEEeee
Confidence 3455667789999999999998 78899999975 4432121 1 3346789999999998
No 56
>PRK08349 hypothetical protein; Validated
Probab=25.73 E-value=73 Score=30.91 Aligned_cols=31 Identities=16% Similarity=0.081 Sum_probs=27.5
Q ss_pred eEEEEeCCcchHHHHHHHhcCCCeEEEeccC
Q 007121 106 NYLLISGDRDFSNALHQLRMRRYNILLAQPH 136 (617)
Q Consensus 106 NIMLISGDrDFS~aLs~LR~RGYNILLAqP~ 136 (617)
.++++||-.|=+-++..|..+||+|+.++-.
T Consensus 3 ~vvllSGG~DS~v~~~~l~~~g~~v~av~~d 33 (198)
T PRK08349 3 AVALLSSGIDSPVAIYLMLRRGVEVYPVHFR 33 (198)
T ss_pred EEEEccCChhHHHHHHHHHHcCCeEEEEEEe
Confidence 5899999999999999998999999988754
No 57
>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=25.12 E-value=51 Score=33.39 Aligned_cols=31 Identities=29% Similarity=0.545 Sum_probs=25.3
Q ss_pred cCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007121 472 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 502 (617)
Q Consensus 472 ygd~~~~~~dvkkale~ai~~~~vv~~~~g~ 502 (617)
...+-+.+.+|||||..||.++++++..++.
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 58
>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=24.85 E-value=52 Score=35.21 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=27.6
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007121 469 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 502 (617)
Q Consensus 469 cirygd~~~~~~dvkkale~ai~~~~vv~~~~g~ 502 (617)
++..-.+-+....|||||..||-.+.|+++.++.
T Consensus 247 ~~N~~~~~~~d~~vRkAl~~aiDr~~i~~~~~~g 280 (469)
T cd08519 247 VFNVNQPPLDNLAVRQALAYLIDRDLIVNRVYYG 280 (469)
T ss_pred EEeCCCCCCCCHHHHHHHHHHcCHHHHHHHHHhc
Confidence 3444556778899999999999999999987543
No 59
>cd08491 PBP2_NikA_DppA_OppA_like_12 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=24.84 E-value=51 Score=35.44 Aligned_cols=33 Identities=33% Similarity=0.440 Sum_probs=27.6
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007121 470 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 502 (617)
Q Consensus 470 irygd~~~~~~dvkkale~ai~~~~vv~~~~g~ 502 (617)
+....+.+.+..|||||..||-++.|+++.++.
T Consensus 237 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 269 (473)
T cd08491 237 IDAQIPPLDDVRVRKALNLAIDRDGIVGALFGG 269 (473)
T ss_pred ecCCCCcccCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 344467788999999999999999999987654
No 60
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=24.82 E-value=3.4e+02 Score=29.16 Aligned_cols=16 Identities=13% Similarity=0.314 Sum_probs=7.8
Q ss_pred hHHHHHhhhcCceeee
Q 007121 80 ASVQHALSSTGIALNH 95 (617)
Q Consensus 80 ~~Vl~aLsSSGIsLiH 95 (617)
.+++++|.+.|+.++|
T Consensus 78 ~~~~~~~~~~g~~viD 93 (298)
T PRK01045 78 PAVREEAKERGLTVID 93 (298)
T ss_pred HHHHHHHHHCCCeEEe
Confidence 3444455555555444
No 61
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=24.79 E-value=2.7e+02 Score=26.80 Aligned_cols=17 Identities=12% Similarity=0.174 Sum_probs=12.3
Q ss_pred hhHHHHHHHHHHhcCcc
Q 007121 48 HTIAQNISSALVKMNYC 64 (617)
Q Consensus 48 ~~Va~nIr~ALrklGY~ 64 (617)
..+...|..++++.||.
T Consensus 15 ~~~~~~i~~~a~~~g~~ 31 (269)
T cd06281 15 AQLFSGAEDRLRAAGYS 31 (269)
T ss_pred HHHHHHHHHHHHHcCCE
Confidence 45677788888887774
No 62
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=24.62 E-value=92 Score=29.74 Aligned_cols=54 Identities=15% Similarity=0.087 Sum_probs=40.9
Q ss_pred chhhHHHHHHHHHhhhhccccCCCCccccchhhcCCCCCCCchHHHHHHHHHHh
Q 007121 439 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGEPKHRNTDVRKALNCAIEQ 492 (617)
Q Consensus 439 ~~qgli~~il~al~~lk~eki~pte~ni~dcirygd~~~~~~dvkkale~ai~~ 492 (617)
..-..+.+|-.++.+...+.+.-+|+.+.||.++++-.-.+=+..+||+.++++
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 455666666666666666788999999999998844334577889999988877
No 63
>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=24.42 E-value=58 Score=34.66 Aligned_cols=87 Identities=22% Similarity=0.232 Sum_probs=48.1
Q ss_pred CCCCCCCchHHHHHHHHHHhhHHHHhhcCCcc----eeecCCCcceeeeccCCCCCCCcHHHHHHHHHHHcCcc---chh
Q 007121 473 GEPKHRNTDVRKALNCAIEQHMVIKRSLGALP----LYVPKNEKLWNCENLYGNPNQYPKEVWDRIQKFLTSSS---GRS 545 (617)
Q Consensus 473 gd~~~~~~dvkkale~ai~~~~vv~~~~g~~~----l~~~kne~lwkcvn~~~n~~~~pk~~~d~i~~fl~s~~---g~s 545 (617)
..+.+.+..|||||..||..+.++++.++..- -++.... .|-..++.. .|+ --.++-++.|.-+. |-.
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 007121 546 A-I-MASQCRYEAALILKNSC 564 (617)
Q Consensus 546 a-i-~~s~~ry~aa~ilk~~c 564 (617)
. | ..+.-+-+.|.+|+.++
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 64
>KOG2947 consensus Carbohydrate kinase [Carbohydrate transport and metabolism]
Probab=24.41 E-value=1.2e+02 Score=32.75 Aligned_cols=57 Identities=25% Similarity=0.468 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCcccceEEEEEecCCC--CchHHHHHhhhcCceeeeccCCCCCCCceEEEEe
Q 007121 51 AQNISSALVKMNYCGPVSISAYGDTNR--IPASVQHALSSTGIALNHVPAVDNPAPSNYLLIS 111 (617)
Q Consensus 51 a~nIr~ALrklGY~GPVSIrAYGDls~--ip~~Vl~aLsSSGIsLiHVPalDNPpPANIMLIS 111 (617)
+.||..+|+.||- ++.| +|-+++ .=+-+++.|++.||.+.|+|--|+.||-.-++|-
T Consensus 44 asNvcTvlrlLG~--~cef--~Gvlsr~~~f~~lLddl~~rgIdishcpftd~~pp~ssiI~~ 102 (308)
T KOG2947|consen 44 ASNVCTVLRLLGA--PCEF--FGVLSRGHVFRFLLDDLRRRGIDISHCPFTDHSPPFSSIIIN 102 (308)
T ss_pred cchHHHHHHHhCC--chhe--eeecccchhHHHHHHHHHhcCCCcccCccccCCCCcceEEEe
Confidence 4578889998775 3443 344444 3356789999999999999986665554444443
No 65
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=24.18 E-value=4.8e+02 Score=27.00 Aligned_cols=82 Identities=17% Similarity=0.190 Sum_probs=56.0
Q ss_pred EEEEe--cCCCCchHHHHHhhhcCceeeeccC--------CCCCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEecc
Q 007121 69 ISAYG--DTNRIPASVQHALSSTGIALNHVPA--------VDNPAPSNYLLISGDR---DFSNALHQLRMRRYNILLAQP 135 (617)
Q Consensus 69 IrAYG--Dls~ip~~Vl~aLsSSGIsLiHVPa--------lDNPpPANIMLISGDr---DFS~aLs~LR~RGYNILLAqP 135 (617)
|..|| --.-+..+....|..-|+....+.. ..-.+-+-+++||-.+ +...++...+++|..||.+..
T Consensus 133 I~~~G~g~S~~vA~~~~~~l~~ig~~~~~~~d~~~~~~~~~~~~~~Dv~i~iS~sG~t~e~i~~a~~ak~~ga~vIaiT~ 212 (281)
T COG1737 133 IYFFGLGSSGLVASDLAYKLMRIGLNVVALSDTHGQLMQLALLTPGDVVIAISFSGYTREIVEAAELAKERGAKVIAITD 212 (281)
T ss_pred EEEEEechhHHHHHHHHHHHHHcCCceeEecchHHHHHHHHhCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCcEEEEcC
Confidence 55555 2223445677888899998877766 2445556777777543 677788888999999999987
Q ss_pred CCCChhHHhhccceEe
Q 007121 136 HKASAPLVAAAKSVWL 151 (617)
Q Consensus 136 ~~aS~~L~aaA~~vWl 151 (617)
...+ +|...|+.++.
T Consensus 213 ~~~s-pla~~Ad~~L~ 227 (281)
T COG1737 213 SADS-PLAKLADIVLL 227 (281)
T ss_pred CCCC-chhhhhceEEe
Confidence 5544 56666664433
No 66
>COG3233 Predicted deacetylase [General function prediction only]
Probab=24.07 E-value=1.2e+02 Score=31.91 Aligned_cols=48 Identities=17% Similarity=0.231 Sum_probs=33.7
Q ss_pred HHHHhhhcCcee-eeccCCCCCCCceEEEEeCCcchHHHHHHHhcCCCeEEEec
Q 007121 82 VQHALSSTGIAL-NHVPAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ 134 (617)
Q Consensus 82 Vl~aLsSSGIsL-iHVPalDNPpPANIMLISGDrDFS~aLs~LR~RGYNILLAq 134 (617)
+.+++...++++ .-+|...+..| +++|..|+..|++++++||.++|=.
T Consensus 26 ~ide~~~~~~t~lLViPn~~~~~~-----l~~d~rf~~~l~~r~e~Gdel~lHG 74 (233)
T COG3233 26 AIDEYGAQNSTVLLVIPNHANDYP-----LSKDPRFVDLLTEREEEGDELVLHG 74 (233)
T ss_pred HHHHhCCCCceEEEEeeccCCCCC-----cccChHHHHHHHHHHhcCCEEEEec
Confidence 344444455554 45565433333 6789999999999999999999964
No 67
>PRK00188 trpD anthranilate phosphoribosyltransferase; Provisional
Probab=23.95 E-value=2.9e+02 Score=29.63 Aligned_cols=60 Identities=23% Similarity=0.348 Sum_probs=40.4
Q ss_pred CchHHHHHhhhcCceeeeccC--------------------------CCCCCCceEEEEe-CCcchHHHHHH-HhcCCC-
Q 007121 78 IPASVQHALSSTGIALNHVPA--------------------------VDNPAPSNYLLIS-GDRDFSNALHQ-LRMRRY- 128 (617)
Q Consensus 78 ip~~Vl~aLsSSGIsLiHVPa--------------------------lDNPpPANIMLIS-GDrDFS~aLs~-LR~RGY- 128 (617)
.++++.+.|...||...+.|. +-||..+...||. -.++|...+.. |+..|+
T Consensus 134 ~~~~~~~~l~~~g~~fl~a~~~~P~l~~l~~lR~~Lg~Rt~fN~l~~L~NP~~~~~~v~Gv~h~~~~~~~a~~l~~lg~~ 213 (339)
T PRK00188 134 SPEQVARCLEEVGIGFLFAPLYHPAMKHVAPVRKELGIRTIFNLLGPLTNPARPKRQLIGVYSPDLLEPMAEVLKRLGSK 213 (339)
T ss_pred CHHHHHHHHHHcCcEEeeCcccCHHHHHHHHHHHHhCCCCHHHHHHHhcCCCCCCCEEEeecCHHHHHHHHHHHHHhCCC
Confidence 345677778888998887664 5577666666664 45677766665 556777
Q ss_pred eEEEeccCC
Q 007121 129 NILLAQPHK 137 (617)
Q Consensus 129 NILLAqP~~ 137 (617)
++++++-..
T Consensus 214 ~~~vv~G~~ 222 (339)
T PRK00188 214 RALVVHGSD 222 (339)
T ss_pred eEEEEECCC
Confidence 677776544
No 68
>PRK06411 NADH dehydrogenase subunit B; Validated
Probab=23.68 E-value=67 Score=32.37 Aligned_cols=27 Identities=15% Similarity=0.068 Sum_probs=16.9
Q ss_pred CCCCCCccchhhHHHHHHHHHhhhhccccC
Q 007121 431 QGRLTPSEYVQGLIGVILLALNTLKIERVV 460 (617)
Q Consensus 431 ~g~~~~s~~~qgli~~il~al~~lk~eki~ 460 (617)
+|||+. ++.+++.|+..++.++.|+..
T Consensus 139 PGCPP~---Pe~il~~l~~l~~~i~~~~~~ 165 (183)
T PRK06411 139 PGCPPR---PEALLYGILKLQKKIRQSERE 165 (183)
T ss_pred CCCCCC---HHHHHHHHHHHHHHHhccccc
Confidence 777774 344566666667777766544
No 69
>PRK11867 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed
Probab=23.55 E-value=1.3e+02 Score=31.79 Aligned_cols=91 Identities=20% Similarity=0.374 Sum_probs=51.3
Q ss_pred CCCCCCCChhhHHHHHHHHHHhcCcccc--eEEEEEecCCCCchHHHHHhhhcCceeee---ccC-----CCCCCCceEE
Q 007121 39 CQVPKNCDPHTIAQNISSALVKMNYCGP--VSISAYGDTNRIPASVQHALSSTGIALNH---VPA-----VDNPAPSNYL 108 (617)
Q Consensus 39 CPVP~G~da~~Va~nIr~ALrklGY~GP--VSIrAYGDls~ip~~Vl~aLsSSGIsLiH---VPa-----lDNPpPANIM 108 (617)
|| ||.-+.|...|+++|.++|..+. |.+.-.|...+.+ ..+...|+.-.| +|. +-+| -..++
T Consensus 20 Cp---GCg~~~il~~l~~al~~l~~~p~d~vvvsdiGc~~~~~----~~~~~~~~~g~mG~alpaAiGaklA~P-d~~VV 91 (286)
T PRK11867 20 CP---GCGDGSILAALQRALAELGLDPENVAVVSGIGCSGRLP----GYINTYGFHTIHGRALAIATGLKLANP-DLTVI 91 (286)
T ss_pred CC---CCCCHHHHHHHHHHHHHhCCCCCcEEEEeCCccccccC----ccccccchhhhhhcHHHHHHHHHHhCC-CCcEE
Confidence 65 77767799999999999887643 2233333332222 112222221011 111 3343 46899
Q ss_pred EEeCCcc-hHH---HHHHHhcCCCeEEEeccCC
Q 007121 109 LISGDRD-FSN---ALHQLRMRRYNILLAQPHK 137 (617)
Q Consensus 109 LISGDrD-FS~---aLs~LR~RGYNILLAqP~~ 137 (617)
.|+||.+ |.- .|.....++-+|+++--.+
T Consensus 92 ~i~GDG~~f~mg~~eL~tA~r~nl~i~vIV~NN 124 (286)
T PRK11867 92 VVTGDGDALAIGGNHFIHALRRNIDITYILFNN 124 (286)
T ss_pred EEeCccHHHhCCHHHHHHHHHhCCCcEEEEEeC
Confidence 9999997 643 3444445777777765444
No 70
>PRK14813 NADH dehydrogenase subunit B; Provisional
Probab=23.52 E-value=69 Score=32.53 Aligned_cols=28 Identities=18% Similarity=0.326 Sum_probs=22.0
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhccccC
Q 007121 430 TQGRLTPSEYVQGLIGVILLALNTLKIERVV 460 (617)
Q Consensus 430 ~~g~~~~s~~~qgli~~il~al~~lk~eki~ 460 (617)
-+||||. ++.+|+-||.+++.++.|++.
T Consensus 132 IPGCPP~---PeaIl~gl~~l~~~i~~~~~~ 159 (189)
T PRK14813 132 VPGCPPR---PEALIGGLMKVQELIRMEQIG 159 (189)
T ss_pred ccCCCCC---HHHHHHHHHHHHHHHHhcccc
Confidence 3899995 567788888999999987653
No 71
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=23.20 E-value=5.4e+02 Score=22.95 Aligned_cols=48 Identities=19% Similarity=0.167 Sum_probs=34.5
Q ss_pred CCceEEEEeCC---cchHHHHHHHhcCCCeEEEeccCCCChhHHhhccceEe
Q 007121 103 APSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 103 pPANIMLISGD---rDFS~aLs~LR~RGYNILLAqP~~aS~~L~aaA~~vWl 151 (617)
+.+-+++||.. .+-..++..++++|-.|+.+.....+ +|...|+.++.
T Consensus 47 ~~dl~I~iS~SG~t~~~~~~~~~a~~~g~~vi~iT~~~~s-~la~~ad~~l~ 97 (120)
T cd05710 47 EKSVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDS-PLAKLADYVIV 97 (120)
T ss_pred CCcEEEEEeCCCCChHHHHHHHHHHHcCCeEEEEECCCCC-cHHHhCCEEEE
Confidence 34667888854 46778889999999999998875544 46666775544
No 72
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=23.17 E-value=3.7e+02 Score=28.66 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=8.3
Q ss_pred chHHHHHhhhcCceeee
Q 007121 79 PASVQHALSSTGIALNH 95 (617)
Q Consensus 79 p~~Vl~aLsSSGIsLiH 95 (617)
+.+++++|.+.|+.++|
T Consensus 80 ~~~~~~~~~~~g~~viD 96 (281)
T PRK12360 80 SKKVYKDLKDKGLEIID 96 (281)
T ss_pred CHHHHHHHHHCCCeEEe
Confidence 34455555555555543
No 73
>PRK10892 D-arabinose 5-phosphate isomerase; Provisional
Probab=22.69 E-value=3.5e+02 Score=27.92 Aligned_cols=86 Identities=16% Similarity=0.187 Sum_probs=56.9
Q ss_pred cceEEEEEecCCCCchHHHHHhhhcCceeeeccC-------CC-CCCCceEEEEeCC---cchHHHHHHHhcCCCeEEEe
Q 007121 65 GPVSISAYGDTNRIPASVQHALSSTGIALNHVPA-------VD-NPAPSNYLLISGD---RDFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 65 GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa-------lD-NPpPANIMLISGD---rDFS~aLs~LR~RGYNILLA 133 (617)
+.|-|.+.|.-..+-......|...|+....+.. .. -.+.+-+++||-. ++...++..++++|-.|+.+
T Consensus 48 ~~I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~d~~I~iS~sG~t~~~~~~~~~ak~~g~~vi~i 127 (326)
T PRK10892 48 GKVVVMGMGKSGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEILALIPVLKRLHVPLICI 127 (326)
T ss_pred CeEEEEeCcHhHHHHHHHHHHHhcCCceeEEeChHHhhccccccCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCcEEEE
Confidence 4666677774444445667788889988776532 11 2345678888854 46777888899999999998
Q ss_pred ccCCCChhHHhhccceEe
Q 007121 134 QPHKASAPLVAAAKSVWL 151 (617)
Q Consensus 134 qP~~aS~~L~aaA~~vWl 151 (617)
.....+ +|...|+..+.
T Consensus 128 T~~~~s-~la~~ad~~l~ 144 (326)
T PRK10892 128 TGRPES-SMARAADIHLC 144 (326)
T ss_pred ECCCCC-cccccCCEEEE
Confidence 765443 45555664443
No 74
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=22.62 E-value=7.3e+02 Score=26.34 Aligned_cols=99 Identities=14% Similarity=0.139 Sum_probs=56.7
Q ss_pred HHHHHHHhcCcccceEEEEEecCCCCchHHHHHhhh-cCceeeeccC-------CCCCCC-ceEEEEe--CC-cchHHHH
Q 007121 53 NISSALVKMNYCGPVSISAYGDTNRIPASVQHALSS-TGIALNHVPA-------VDNPAP-SNYLLIS--GD-RDFSNAL 120 (617)
Q Consensus 53 nIr~ALrklGY~GPVSIrAYGDls~ip~~Vl~aLsS-SGIsLiHVPa-------lDNPpP-ANIMLIS--GD-rDFS~aL 120 (617)
.|...|.+.++ -.|-|.+.|.-.......+..|.. .++....... ..+..+ +-++.|| |. .|-..++
T Consensus 34 ~~~~~l~~~~~-~~I~~~g~GsS~~aa~~~~~~~~k~~~i~v~~~~~~~~~~~~~~~~~~~~lvI~iS~SGeT~e~i~al 112 (340)
T PRK11382 34 AIVEEMVKRDI-DRIYFVACGSPLNAAQTAKHLADRFSDLQVYAISGWEFCDNTPYRLDDRCAVIGVSDYGKTEEVIKAL 112 (340)
T ss_pred HHHHHHHhCCC-CEEEEEEechHHHHHHHHHHHHHHHcCCCeEEeccHHHHhcCCcCCCCCCEEEEEcCCCCCHHHHHHH
Confidence 34444443233 246677777755433333333322 2433222222 112223 4466776 43 5888999
Q ss_pred HHHhcCCCeEEEeccCCCChhHHhhccceEeeh
Q 007121 121 HQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 153 (617)
Q Consensus 121 s~LR~RGYNILLAqP~~aS~~L~aaA~~vWlWe 153 (617)
..++++|..||.+..... .+|...|+.++...
T Consensus 113 ~~ak~~Ga~~I~IT~~~~-S~L~~~ad~~l~~~ 144 (340)
T PRK11382 113 ELGRACGALTAAFTKRAD-SPITSAAEFSIDYQ 144 (340)
T ss_pred HHHHHcCCeEEEEECCCC-ChHHHhCCEEEEeC
Confidence 999999999998876544 36777788777665
No 75
>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=22.58 E-value=2.4e+02 Score=27.80 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=30.7
Q ss_pred HHHhcCcccceEEEEEecCCCCchHHHHHhhhcCceeeeccC
Q 007121 57 ALVKMNYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPA 98 (617)
Q Consensus 57 ALrklGY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa 98 (617)
.|.++|+.- -.+.||+..++.++++.+.+.|+.+++.|.
T Consensus 34 ~l~~~gi~P---d~iiGDfDSi~~~~~~~~~~~~~~~~~~p~ 72 (208)
T cd07995 34 HLLDLGIVP---DLIIGDFDSISPEVLEYYKSKGVEIIHFPD 72 (208)
T ss_pred HHHHcCCCC---CEEEecCcCCCHHHHHHHHhcCCeEEECCC
Confidence 344455533 347799999999999999999999999987
No 76
>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=22.38 E-value=73 Score=30.90 Aligned_cols=26 Identities=19% Similarity=0.437 Sum_probs=18.7
Q ss_pred CCCCCceEEEEeCCc--chHHHHHHHhc
Q 007121 100 DNPAPSNYLLISGDR--DFSNALHQLRM 125 (617)
Q Consensus 100 DNPpPANIMLISGDr--DFS~aLs~LR~ 125 (617)
..|..+.++||+|.. .....|.++++
T Consensus 53 ~sPr~aDvllVtG~vt~~~~~~l~~~~e 80 (145)
T TIGR01957 53 ASPRQADVMIVAGTVTKKMAPALRRLYD 80 (145)
T ss_pred CCCCcceEEEEecCCcHHHHHHHHHHHH
Confidence 567779999999985 44556666654
No 77
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=22.30 E-value=3.4e+02 Score=26.37 Aligned_cols=70 Identities=14% Similarity=0.119 Sum_probs=37.2
Q ss_pred hhHHHHHHHHHHhcCcccceEEEEEecCCCCchHHH-HHhhhcCceeeeccCCCCCCCceEEEEeCCcchHHHHHHHhcC
Q 007121 48 HTIAQNISSALVKMNYCGPVSISAYGDTNRIPASVQ-HALSSTGIALNHVPAVDNPAPSNYLLISGDRDFSNALHQLRMR 126 (617)
Q Consensus 48 ~~Va~nIr~ALrklGY~GPVSIrAYGDls~ip~~Vl-~aLsSSGIsLiHVPalDNPpPANIMLISGDrDFS~aLs~LR~R 126 (617)
..+...|..++++.||. +.+....+.... .+.+ +.|.+..| +-+++.+.+.+ ...+..|+..
T Consensus 15 ~~~~~~i~~~~~~~gy~--~~~~~~~~~~~~-~~~~~~~l~~~~v-------------dgvi~~~~~~~-~~~~~~l~~~ 77 (269)
T cd06297 15 RRLLEGIEGALLEQRYD--LALFPLLSLARL-KRYLESTTLAYLT-------------DGLLLASYDLT-ERLAERRLPT 77 (269)
T ss_pred HHHHHHHHHHHHHCCCE--EEEEeCCCcHHH-HHHHHHHHHhcCC-------------CEEEEecCccC-hHHHHHHhhc
Confidence 56788999999998883 444332221111 1222 23444434 34444444433 2345666666
Q ss_pred CCeEEEec
Q 007121 127 RYNILLAQ 134 (617)
Q Consensus 127 GYNILLAq 134 (617)
|.-|+++.
T Consensus 78 ~iPvv~~~ 85 (269)
T cd06297 78 ERPVVLVD 85 (269)
T ss_pred CCCEEEEc
Confidence 66666664
No 78
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=22.25 E-value=4.1e+02 Score=30.61 Aligned_cols=83 Identities=11% Similarity=0.098 Sum_probs=54.5
Q ss_pred ceEEEEEecCCCCchHHHHHhhhcCceeeeccC--------CCCCCCceEEEEeCCc---chHHHHHHHhcCCCeEEEec
Q 007121 66 PVSISAYGDTNRIPASVQHALSSTGIALNHVPA--------VDNPAPSNYLLISGDR---DFSNALHQLRMRRYNILLAQ 134 (617)
Q Consensus 66 PVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa--------lDNPpPANIMLISGDr---DFS~aLs~LR~RGYNILLAq 134 (617)
.|-|.++|.-..+-......|...|+..+.... ..-.+-+-+++||-.. +...++..++++|-.|+++.
T Consensus 470 rI~i~G~G~S~~~A~~~~~~l~~lg~~~~~~~d~~~~~~~~~~l~~~DvvI~iS~sG~t~e~i~~~~~Ak~~Ga~vIaIT 549 (638)
T PRK14101 470 RIEFYGLGNSNIVAQDAHYKFFRFGIPTIAYGDLYMQAASAALLGKGDVIVAVSKSGRAPELLRVLDVAMQAGAKVIAIT 549 (638)
T ss_pred EEEEEEccHHHHHHHHHHHHHhcCCceEEEcCCHHHHHHHHhcCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEc
Confidence 455555554333444456667778887665443 1224456778888554 56778888889999999999
Q ss_pred cCCCChhHHhhccceE
Q 007121 135 PHKASAPLVAAAKSVW 150 (617)
Q Consensus 135 P~~aS~~L~aaA~~vW 150 (617)
. . ..+|...|+.++
T Consensus 550 ~-~-~spLa~~aD~~L 563 (638)
T PRK14101 550 S-S-NTPLAKRATVAL 563 (638)
T ss_pred C-C-CChhHhhCCEEE
Confidence 7 3 456888888554
No 79
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=22.07 E-value=3.9e+02 Score=25.29 Aligned_cols=70 Identities=9% Similarity=0.107 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHHhcCcccceEEEEEecCCC-CchHHHHHhhhcCceeeeccCCCCCCCceEEEEeCCcchHHHHHHHhcC
Q 007121 48 HTIAQNISSALVKMNYCGPVSISAYGDTNR-IPASVQHALSSTGIALNHVPAVDNPAPSNYLLISGDRDFSNALHQLRMR 126 (617)
Q Consensus 48 ~~Va~nIr~ALrklGY~GPVSIrAYGDls~-ip~~Vl~aLsSSGIsLiHVPalDNPpPANIMLISGDrDFS~aLs~LR~R 126 (617)
..+...|+.++++.||. +.+ .+.+.+. ...+.++.|.+.++. -+++...+. ....+..|+..
T Consensus 15 ~~~~~gi~~~~~~~g~~--~~~-~~~~~~~~~~~~~i~~l~~~~~d-------------gii~~~~~~-~~~~~~~~~~~ 77 (259)
T cd01542 15 SRTVKGILAALYENGYQ--MLL-MNTNFSIEKEIEALELLARQKVD-------------GIILLATTI-TDEHREAIKKL 77 (259)
T ss_pred HHHHHHHHHHHHHCCCE--EEE-EeCCCCHHHHHHHHHHHHhcCCC-------------EEEEeCCCC-CHHHHHHHhcC
Confidence 46888899999988874 332 2222111 112345556666663 233332221 12345555555
Q ss_pred CCeEEEec
Q 007121 127 RYNILLAQ 134 (617)
Q Consensus 127 GYNILLAq 134 (617)
|..|+++.
T Consensus 78 ~ipvv~~~ 85 (259)
T cd01542 78 NVPVVVVG 85 (259)
T ss_pred CCCEEEEe
Confidence 66666653
No 80
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=21.95 E-value=1.8e+02 Score=31.01 Aligned_cols=89 Identities=22% Similarity=0.390 Sum_probs=51.5
Q ss_pred CCChhhHHHHHHHHHHhcCccc-c-eEEEEEecCCCCchHHHHHhhhcCce-ee--eccC-----CCCCCCceEEEEeCC
Q 007121 44 NCDPHTIAQNISSALVKMNYCG-P-VSISAYGDTNRIPASVQHALSSTGIA-LN--HVPA-----VDNPAPSNYLLISGD 113 (617)
Q Consensus 44 G~da~~Va~nIr~ALrklGY~G-P-VSIrAYGDls~ip~~Vl~aLsSSGIs-Li--HVPa-----lDNPpPANIMLISGD 113 (617)
||--+.|...|.++|+++|... . +.+.-.|.....+ ..|...++. ++ -+|. +-+| -..+|.|+||
T Consensus 23 GCg~~~i~~~i~~al~~l~l~p~d~vivsdiG~s~~~~----~yl~~~~~~g~mG~alpaAiGaklA~p-d~~VV~i~GD 97 (301)
T PRK05778 23 GCGNFGILNAIIQALAELGLDPDKVVVVSGIGCSSKIP----GYFLSHGLHTLHGRAIAFATGAKLANP-DLEVIVVGGD 97 (301)
T ss_pred CCCChHHHHHHHHHHHHhcCCCCCEEEEeCCcHhhhhh----hhcccCccchhhccHHHHHHHHHHHCC-CCcEEEEeCc
Confidence 7777889999999999987632 2 2233334332222 123333331 10 1111 3343 4679999999
Q ss_pred cchH----HHHHHHhcCCCeEEEeccCC
Q 007121 114 RDFS----NALHQLRMRRYNILLAQPHK 137 (617)
Q Consensus 114 rDFS----~aLs~LR~RGYNILLAqP~~ 137 (617)
.+|. ..|.....++.+|+++.-.+
T Consensus 98 G~~~~mg~~eL~tA~r~nl~i~vIV~NN 125 (301)
T PRK05778 98 GDLASIGGGHFIHAGRRNIDITVIVENN 125 (301)
T ss_pred cHHHhccHHHHHHHHHHCCCcEEEEEeC
Confidence 9974 23555566777877775444
No 81
>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=21.80 E-value=66 Score=33.61 Aligned_cols=30 Identities=30% Similarity=0.573 Sum_probs=25.6
Q ss_pred CCCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007121 473 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 502 (617)
Q Consensus 473 gd~~~~~~dvkkale~ai~~~~vv~~~~g~ 502 (617)
..+-+.+.+|||||..||-.+.+++..++.
T Consensus 248 ~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 277 (466)
T cd00995 248 NKPPFDDKRVRQAISYAIDREEIIDAVLGG 277 (466)
T ss_pred CCCCCCCHHHHHHHHHhcCHHHHHHHHHhC
Confidence 345678999999999999999999988653
No 82
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=21.68 E-value=76 Score=34.06 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=24.7
Q ss_pred CCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007121 474 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 502 (617)
Q Consensus 474 d~~~~~~dvkkale~ai~~~~vv~~~~g~ 502 (617)
.+-+.+.+|||||..||-.+.++++.++.
T Consensus 259 ~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 287 (481)
T cd08498 259 KNPLKDPRVRQALSLAIDREAIVDRVMRG 287 (481)
T ss_pred CCCCCCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 45578899999999999999999987553
No 83
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=21.45 E-value=3.9e+02 Score=26.58 Aligned_cols=41 Identities=24% Similarity=0.282 Sum_probs=30.8
Q ss_pred chHHHHHHHhcCCCeEEEe--ccCCCChhHHhhccceEeehhh
Q 007121 115 DFSNALHQLRMRRYNILLA--QPHKASAPLVAAAKSVWLWTSL 155 (617)
Q Consensus 115 DFS~aLs~LR~RGYNILLA--qP~~aS~~L~aaA~~vWlWeSL 155 (617)
.|+..|.+++..|-+|.++ .+..-++.+.+.|+..|....|
T Consensus 84 ~fA~~l~~~~~~G~~i~f~IGG~~Gl~~~~~~~a~~~~sls~l 126 (155)
T COG1576 84 EFADFLERLRDDGRDISFLIGGADGLSEAVKARADQVLSLSKL 126 (155)
T ss_pred HHHHHHHHHHhcCCeEEEEEeCcccCCHHHHHHHhhheecccc
Confidence 7999999999988666554 4666788888888866665443
No 84
>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=20.97 E-value=6.6e+02 Score=23.68 Aligned_cols=50 Identities=14% Similarity=0.058 Sum_probs=36.0
Q ss_pred CCCceEEEEeCC---cchHHHHHHHhcCCCeEEEeccCCCChhHHhhccceEee
Q 007121 102 PAPSNYLLISGD---RDFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLW 152 (617)
Q Consensus 102 PpPANIMLISGD---rDFS~aLs~LR~RGYNILLAqP~~aS~~L~aaA~~vWlW 152 (617)
.+.+-+++||.. ++-..++..++++|-.|+.+.....+ +|...|+..+..
T Consensus 100 ~~~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s-~La~~aD~~l~~ 152 (177)
T cd05006 100 QPGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGG-KLLELADIEIHV 152 (177)
T ss_pred CCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCC-chhhhCCEEEEe
Confidence 445677888743 47788899999999999999865544 477777755543
No 85
>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=20.96 E-value=5.1e+02 Score=24.63 Aligned_cols=86 Identities=19% Similarity=0.296 Sum_probs=46.8
Q ss_pred CChhhHHHHHHHH---HHhc-CcccceEEEEEecCCCCchHHHHHhhhcCceeeeccC-----------------CCCCC
Q 007121 45 CDPHTIAQNISSA---LVKM-NYCGPVSISAYGDTNRIPASVQHALSSTGIALNHVPA-----------------VDNPA 103 (617)
Q Consensus 45 ~da~~Va~nIr~A---Lrkl-GY~GPVSIrAYGDls~ip~~Vl~aLsSSGIsLiHVPa-----------------lDNPp 103 (617)
.+...+...|.++ |+++ |..-..-.--||.. ...+++.|.+.|+.++.--- +++-.
T Consensus 74 ~~~~~~~~ei~~~~~~l~~~~g~~~~~fr~P~G~~---~~~~~~~l~~~G~~~v~w~~~~~D~~~~~~~~i~~~~~~~~~ 150 (191)
T TIGR02764 74 LEDEKIKKDILRAQEIIEKLTGKKPTLFRPPSGAF---NKAVLKAAESLGYTVVHWSVDSRDWKNPGVESIVDRVVKNTK 150 (191)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCCEEECCCcCC---CHHHHHHHHHcCCeEEEecCCCCccCCCCHHHHHHHHHhcCC
Confidence 4455555556554 3332 32211112335554 35678888888887654221 23334
Q ss_pred CceEEEEe--CCc-----chHHHHHHHhcCCCeEEEe
Q 007121 104 PSNYLLIS--GDR-----DFSNALHQLRMRRYNILLA 133 (617)
Q Consensus 104 PANIMLIS--GDr-----DFS~aLs~LR~RGYNILLA 133 (617)
|..|+|+= .+. -+..+|..|+.+||.++-+
T Consensus 151 ~g~Iil~Hd~~~~~~t~~~l~~~i~~l~~~Gy~~vtl 187 (191)
T TIGR02764 151 PGDIILLHASDSAKQTVKALPTIIKKLKEKGYEFVTI 187 (191)
T ss_pred CCCEEEEeCCCCcHhHHHHHHHHHHHHHHCCCEEEEH
Confidence 45566555 222 3556788888888887644
No 86
>cd01712 ThiI ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide.
Probab=20.85 E-value=1.1e+02 Score=28.73 Aligned_cols=30 Identities=23% Similarity=0.109 Sum_probs=26.4
Q ss_pred eEEEEeCCcchHHHHHHHhcCCCeEEEecc
Q 007121 106 NYLLISGDRDFSNALHQLRMRRYNILLAQP 135 (617)
Q Consensus 106 NIMLISGDrDFS~aLs~LR~RGYNILLAqP 135 (617)
-++++||-.|=+.++..|+++|++|+.++-
T Consensus 2 vlv~~SGG~DS~~la~ll~~~g~~v~av~~ 31 (177)
T cd01712 2 ALALLSGGIDSPVAAWLLMKRGIEVDALHF 31 (177)
T ss_pred EEEEecCChhHHHHHHHHHHcCCeEEEEEE
Confidence 378999999999999999999999988763
No 87
>PF10965 DUF2767: Protein of unknown function (DUF2767); InterPro: IPR024493 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.76 E-value=1.4e+02 Score=26.08 Aligned_cols=54 Identities=20% Similarity=0.105 Sum_probs=41.3
Q ss_pred chhhHHHHHHHHHhhhhccccCCCCccccchhhcCC---CCCCCchHHHHHHHHHHh
Q 007121 439 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGE---PKHRNTDVRKALNCAIEQ 492 (617)
Q Consensus 439 ~~qgli~~il~al~~lk~eki~pte~ni~dcirygd---~~~~~~dvkkale~ai~~ 492 (617)
..|..-|||=.|.=.|-.+-.-|+-.+|+|-+|--- .-.+.-+..+|+|.||+.
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 456666666666667778888899999999999743 344566889999999975
No 88
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=20.44 E-value=73 Score=33.85 Aligned_cols=29 Identities=21% Similarity=0.461 Sum_probs=25.0
Q ss_pred CCCCCCchHHHHHHHHHHhhHHHHhhcCC
Q 007121 474 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 502 (617)
Q Consensus 474 d~~~~~~dvkkale~ai~~~~vv~~~~g~ 502 (617)
.+-+.+.+|||||..||.++.++++.++.
T Consensus 257 ~~~~~d~~vR~Al~~aidr~~i~~~~~~g 285 (480)
T cd08517 257 NPPLKDVRVRQAIAHAIDRQFIVDTVFFG 285 (480)
T ss_pred CCccCCHHHHHHHHHhcCHHHHHHHHHcC
Confidence 45678899999999999999999988653
No 89
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=20.39 E-value=75 Score=33.87 Aligned_cols=32 Identities=25% Similarity=0.359 Sum_probs=26.8
Q ss_pred hhcCCCCCCCchHHHHHHHHHHhhHHHHhhcC
Q 007121 470 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLG 501 (617)
Q Consensus 470 irygd~~~~~~dvkkale~ai~~~~vv~~~~g 501 (617)
+-...+-+.+..|||||..||.++.+++..++
T Consensus 259 ~N~~~~~~~d~~vR~Al~~aidr~~i~~~~~~ 290 (476)
T cd08512 259 LNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLK 290 (476)
T ss_pred eeCCCCCCCCHHHHHHHHHhcCHHHHHHHHhc
Confidence 33445678899999999999999999998865
No 90
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=20.05 E-value=92 Score=33.23 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=24.3
Q ss_pred CCCCCCchHHHHHHHHHHhhHHHHhhcC
Q 007121 474 EPKHRNTDVRKALNCAIEQHMVIKRSLG 501 (617)
Q Consensus 474 d~~~~~~dvkkale~ai~~~~vv~~~~g 501 (617)
.+-+.+.+|||||-.||-++.|++..++
T Consensus 261 ~~~~~d~~vR~Ai~~aidr~~i~~~~~~ 288 (484)
T cd08492 261 RPPFDDVRVRQALQLAIDREAIVETVFF 288 (484)
T ss_pred CCCCCCHHHHHHHHHhhhHHHHHHHHhc
Confidence 4557789999999999999999988754
Done!