Query 034452
Match_columns 94
No_of_seqs 101 out of 110
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 03:01:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034452.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034452hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14705 Costars: Costars; PDB 100.0 4.3E-45 9.2E-50 243.2 1.9 77 1-79 1-77 (77)
2 KOG3376 Uncharacterized conser 100.0 1E-39 2.2E-44 254.3 6.9 91 1-91 77-168 (249)
3 smart00833 CobW_C Cobalamin sy 75.0 0.8 1.7E-05 28.6 -0.3 52 26-79 4-59 (92)
4 PF11848 DUF3368: Domain of un 73.8 2.2 4.8E-05 25.3 1.4 21 46-67 5-25 (48)
5 PHA02092 hypothetical protein 70.2 2.6 5.6E-05 29.8 1.3 31 2-37 17-47 (108)
6 PF07683 CobW_C: Cobalamin syn 60.3 1.5 3.3E-05 27.6 -1.3 51 26-78 4-57 (94)
7 PRK08535 translation initiatio 59.2 17 0.00037 28.9 4.2 68 4-81 100-179 (310)
8 PF10117 McrBC: McrBC 5-methyl 52.9 49 0.0011 25.3 5.7 64 4-71 188-254 (321)
9 TIGR00511 ribulose_e2b2 ribose 52.4 27 0.00058 27.7 4.3 68 4-81 95-174 (301)
10 PF03979 Sigma70_r1_1: Sigma-7 51.4 13 0.00029 23.9 2.0 21 42-62 5-25 (82)
11 TIGR03454 partition_RepB plasm 46.8 29 0.00063 28.3 3.7 29 4-32 85-122 (325)
12 PF01008 IF-2B: Initiation fac 46.7 31 0.00068 26.0 3.7 68 4-81 87-166 (282)
13 PF14330 DUF4387: Domain of un 45.9 27 0.00059 24.4 3.0 31 8-45 2-32 (99)
14 PF12563 Hemolysin_N: Hemolyti 42.3 15 0.00032 28.5 1.4 65 23-87 76-145 (187)
15 PRK13866 plasmid partitioning 39.6 39 0.00084 28.0 3.5 30 3-32 86-124 (336)
16 PF07606 DUF1569: Protein of u 35.4 39 0.00084 24.1 2.6 36 2-37 98-133 (152)
17 PLN00196 alpha-amylase; Provis 35.3 75 0.0016 26.6 4.6 48 22-74 339-386 (428)
18 PF00636 Ribonuclease_3: Ribon 33.5 32 0.00069 22.2 1.7 19 32-50 91-109 (114)
19 PF08438 MMR_HSR1_C: GTPase of 30.9 14 0.0003 26.0 -0.3 15 48-62 35-49 (109)
20 PF02617 ClpS: ATP-dependent C 30.7 31 0.00067 22.0 1.3 21 32-54 10-30 (82)
21 PRK11537 putative GTP-binding 29.4 21 0.00046 28.4 0.4 51 25-77 226-283 (318)
22 TIGR03820 lys_2_3_AblA lysine- 28.1 98 0.0021 26.2 4.1 46 29-76 219-264 (417)
23 PF13350 Y_phosphatase3: Tyros 26.7 33 0.00071 24.0 0.9 48 15-63 3-51 (164)
24 PF00990 GGDEF: GGDEF domain; 26.3 1.4E+02 0.0031 18.7 3.9 32 26-57 123-158 (161)
25 PF10398 DUF2443: Protein of u 25.3 55 0.0012 22.3 1.8 17 2-18 54-70 (79)
26 PRK11041 DNA-binding transcrip 25.1 1.9E+02 0.0041 21.0 4.7 49 9-58 11-66 (309)
27 PF03932 CutC: CutC family; I 24.5 1.3E+02 0.0027 23.0 3.8 46 4-55 68-113 (201)
28 PTZ00174 phosphomannomutase; P 24.0 56 0.0012 24.2 1.8 26 31-58 14-39 (247)
29 PRK08333 L-fuculose phosphate 23.6 1.3E+02 0.0028 21.6 3.6 34 1-34 2-36 (184)
30 PRK12482 flagellar motor prote 22.9 53 0.0012 26.4 1.6 32 33-64 69-100 (287)
31 PF04385 FAINT: Domain of unkn 22.7 61 0.0013 18.3 1.5 16 58-73 37-52 (78)
32 PF04696 Pinin_SDK_memA: pinin 22.4 77 0.0017 22.4 2.2 16 40-55 10-25 (131)
33 PF13986 DUF4224: Domain of un 22.4 1E+02 0.0022 18.3 2.4 19 11-29 21-42 (47)
34 PF05334 DUF719: Protein of un 22.3 18 0.0004 27.7 -1.1 35 3-37 142-178 (181)
35 PF02994 Transposase_22: L1 tr 22.2 70 0.0015 26.2 2.2 19 47-65 263-281 (370)
36 PF09079 Cdc6_C: CDC6, C termi 21.6 2E+02 0.0042 18.0 3.8 60 25-88 13-84 (85)
37 KOG0972 Huntingtin interacting 21.6 59 0.0013 27.6 1.6 30 3-32 313-342 (384)
38 TIGR00524 eIF-2B_rel eIF-2B al 21.1 1.7E+02 0.0038 23.3 4.2 73 4-81 98-186 (303)
39 cd06303 PBP1_LuxPQ_Quorum_Sens 20.6 1.1E+02 0.0023 22.2 2.6 39 46-87 202-251 (280)
40 PF07855 DUF1649: Protein of u 20.5 1.4E+02 0.0031 21.7 3.3 29 2-30 55-87 (163)
41 PRK14447 acylphosphatase; Prov 20.3 59 0.0013 21.6 1.1 26 49-74 23-56 (95)
42 PRK04235 hypothetical protein; 20.1 89 0.0019 23.8 2.2 30 2-31 23-56 (196)
No 1
>PF14705 Costars: Costars; PDB: 2L2O_A 2KRH_A.
Probab=100.00 E-value=4.3e-45 Score=243.24 Aligned_cols=77 Identities=57% Similarity=0.880 Sum_probs=68.9
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCCceeeeeeccccccchhhHHHHHHHHHHHHHhcCceeecceeecccccCceEEEec
Q 034452 1 MNVEEEVERLKEEIQRLGKIQPDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDGELLLQGVHDNVEITLK 79 (94)
Q Consensus 1 m~V~~Ei~~L~~~I~~~G~~~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGEmL~Qg~dD~V~I~Ll 79 (94)
|||++||++||++|+++|++++||+++||||+|| ++|+||||||||||+||||||+|+|+|||||||+||||+||||
T Consensus 1 ~~V~~EI~~L~~~I~~~G~~~~~g~~~V~FG~LF--~~~~~i~eaLvG~L~~ArK~~~V~FeGE~L~Qg~dD~V~I~LL 77 (77)
T PF14705_consen 1 MHVDREILELCEIIKRLGTKDADGKYSVTFGVLF--ERYANISEALVGTLLRARKHKLVDFEGEMLLQGRDDDVDITLL 77 (77)
T ss_dssp -GCHCCCHHHHHHHHHH-CCGCTSSEEEEHHHHH--HHHCTTTTTHHHHHHHHHCTTSEE-SSS--STCCCTT-EEEE-
T ss_pred CcHHHHHHHHHHHHHHhCCCCCCCCEeeehhHHH--HHHHHHHHHHHHHHHHHHhcCceeeccceecCCCCCCEeEEeC
Confidence 8999999999999999999999999999999999 5889999999999999999999999999999999999999997
No 2
>KOG3376 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1e-39 Score=254.25 Aligned_cols=91 Identities=45% Similarity=0.614 Sum_probs=87.5
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCC-ceeeeeeccccccchhhHHHHHHHHHHHHHhcCceeecceeecccccCceEEEec
Q 034452 1 MNVEEEVERLKEEIQRLGKIQPDG-SYKVTFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDGELLLQGVHDNVEITLK 79 (94)
Q Consensus 1 m~V~~Ei~~L~~~I~~~G~~~~dG-~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGEmL~Qg~dD~V~I~Ll 79 (94)
|||++||+.||++|+++|.+..|| ++.|+||+||+||+|+||||||||||+||||||||+|+||||+||+||||+||||
T Consensus 77 ~hV~rEi~~L~E~I~s~g~~e~dg~k~~V~FGvLFn~y~csniseklVGtL~~Ark~kiV~feGEmL~Qr~~D~v~ItLl 156 (249)
T KOG3376|consen 77 MHVDREILGLCEEIHSEGSPEKDGKKKEVKFGVLFNIYECSNISEKLVGTLLRARKRKIVHFEGEMLLQRVDDDVIITLL 156 (249)
T ss_pred cCccHHHHHHHHHHhhccCccCCCceeEEeeeEEeechhhhhhHHHHHHhhhhccccceeecccchhhcccccceeEEec
Confidence 899999999999999999999999 8999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchhHhHhh
Q 034452 80 PPPPQPLAVAAA 91 (94)
Q Consensus 80 ~~~~~~~~~~~~ 91 (94)
+++.++++.+.|
T Consensus 157 ~~~~~~~e~~ta 168 (249)
T KOG3376|consen 157 KSWREIREEPTA 168 (249)
T ss_pred cCchhhhhhhhh
Confidence 999999975443
No 3
>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.
Probab=74.96 E-value=0.8 Score=28.62 Aligned_cols=52 Identities=17% Similarity=0.215 Sum_probs=35.9
Q ss_pred eeeeeeccccccchhhHHHHHHHHHHHHHhcCceeecce----eecccccCceEEEec
Q 034452 26 YKVTFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDGE----LLLQGVHDNVEITLK 79 (94)
Q Consensus 26 ~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGE----mL~Qg~dD~V~I~Ll 79 (94)
+++++-.-|+-.+.....+++.+-+.|+ +|++.+.|. +.+|++++...++-.
T Consensus 4 ~~~~~~~~~~~~~l~~~l~~l~~~i~R~--KG~v~~~~~~~~~~~~q~v~~~~~~~~~ 59 (92)
T smart00833 4 FVYRARRPFHPQRLLAALDELPEGVLRA--KGFFWLASRPDLPGVLSGAGGRLRIEPA 59 (92)
T ss_pred EEEecCCCCCHHHHHHHHHhccCCeEEE--EEEEEeCCCCCeEEEEEccCCeeEcccC
Confidence 3455566666556666666666666666 489999765 689999998777643
No 4
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=73.81 E-value=2.2 Score=25.32 Aligned_cols=21 Identities=33% Similarity=0.502 Sum_probs=16.0
Q ss_pred HHHHHHHHHhcCceeecceeec
Q 034452 46 LVGTLRAAKKRKFLTYDGELLL 67 (94)
Q Consensus 46 LVGtL~~ArK~~lV~FeGEmL~ 67 (94)
-+|+|..|+++|+++ +-+.++
T Consensus 5 TlGiL~~Ak~~GlI~-~~~~~l 25 (48)
T PF11848_consen 5 TLGILLLAKRRGLIS-EVKPLL 25 (48)
T ss_pred hHHHHHHHHHcCChh-hHHHHH
Confidence 379999999999998 433333
No 5
>PHA02092 hypothetical protein
Probab=70.22 E-value=2.6 Score=29.80 Aligned_cols=31 Identities=35% Similarity=0.583 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHHHhcCCCCCCCceeeeeecccccc
Q 034452 2 NVEEEVERLKEEIQRLGKIQPDGSYKVTFGVLFHDD 37 (94)
Q Consensus 2 ~V~~Ei~~L~~~I~~~G~~~~dG~~~V~FG~LF~~~ 37 (94)
.|++|+-+|--.++.+|..|.| |||.||...
T Consensus 17 gvekely~l~~~mn~igannqd-----t~gklfktk 47 (108)
T PHA02092 17 GVEKELYELYTSMNAIGANNQD-----TFGKLFKTK 47 (108)
T ss_pred cHHHHHHHHHHHHhhhcccCch-----hHHHHHHHH
Confidence 4889999999999999987755 799999854
No 6
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=60.34 E-value=1.5 Score=27.63 Aligned_cols=51 Identities=22% Similarity=0.313 Sum_probs=29.9
Q ss_pred eeeeeeccccccchhhHHHHHHHHHHHHHhcCceeecce---eecccccCceEEEe
Q 034452 26 YKVTFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDGE---LLLQGVHDNVEITL 78 (94)
Q Consensus 26 ~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGE---mL~Qg~dD~V~I~L 78 (94)
+++.+-.-|+.++.....+..-+.+.|| +|++.++|+ +++|++.+...+.-
T Consensus 4 ~~~~~~~p~~~~~l~~~l~~~~~~vlR~--KG~v~~~~~~~~~~~q~v~~~~~~~~ 57 (94)
T PF07683_consen 4 VTFEFDRPFDPERLEAWLQELPGDVLRA--KGIVWVADGPRRLVFQGVGGRYDIEP 57 (94)
T ss_dssp EEEEESS-B-HHHHHHHHHHTTTTEEEE--EEEE-BTT-SEEEEEEEETTEEEEE-
T ss_pred EEEEeCCCCCHHHHHHHHHhCCCCEEEE--EEEEEeCCcCeEEEEEeeCCEEEecc
Confidence 4455555665444444444433334333 589999887 88999999999983
No 7
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=59.19 E-value=17 Score=28.90 Aligned_cols=68 Identities=21% Similarity=0.216 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHhcCCC-CCCCceeeeeeccccccchhhHHHHHHHHHHHHHhc----Cceeecceeecccc-------c
Q 034452 4 EEEVERLKEEIQRLGKI-QPDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKR----KFLTYDGELLLQGV-------H 71 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~-~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~----~lV~FeGEmL~Qg~-------d 71 (94)
.+|+.+-++.|-++|.. -.||....|+| + |..+.+.|+.|.++ .++-=|+...+||+ .
T Consensus 100 ~~e~~~~~~~I~~~a~~~i~~g~~ILT~~--~--------S~tv~~~l~~A~~~~k~~~V~v~EsrP~~~G~~~a~~L~~ 169 (310)
T PRK08535 100 IESSENAVEKIGEIGAKRIRDGDVIMTHC--N--------SSAALSVIKTAHEQGKDIEVIATETRPRNQGHITAKELAE 169 (310)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCEEEEeC--C--------cHHHHHHHHHHHHCCCeEEEEEecCCchhhHHHHHHHHHH
Confidence 35666667777777753 36788888888 2 56788899988644 34556888888886 3
Q ss_pred CceEEEecCC
Q 034452 72 DNVEITLKPP 81 (94)
Q Consensus 72 D~V~I~Ll~~ 81 (94)
.++++|+..+
T Consensus 170 ~GI~vtlI~D 179 (310)
T PRK08535 170 YGIPVTLIVD 179 (310)
T ss_pred CCCCEEEEeh
Confidence 5777777654
No 8
>PF10117 McrBC: McrBC 5-methylcytosine restriction system component; InterPro: IPR019292 Members of this family of prokaryotic proteins modify the specificity of mcrB restriction by expanding the range of modified sequences that are restricted [, ]. It does not bind DNA.
Probab=52.88 E-value=49 Score=25.34 Aligned_cols=64 Identities=19% Similarity=0.178 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHhcCCC-CCCCceeeeeeccccccchhhHHHHHHHHHHHH--HhcCceeecceeeccccc
Q 034452 4 EEEVERLKEEIQRLGKI-QPDGSYKVTFGVLFHDDRCANIFEALVGTLRAA--KKRKFLTYDGELLLQGVH 71 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~-~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~A--rK~~lV~FeGEmL~Qg~d 71 (94)
.+.+..+|..|=+.-.+ ..+|. .-.||=||+ -+.+||+-|+.++++ ....-|.+++..-|....
T Consensus 188 Y~~~~~la~liL~~~~~~~~~g~-~~~~~fl~d---M~~LFE~fV~~~l~~~~~~~~~v~~q~~~~~~~~~ 254 (321)
T PF10117_consen 188 YKPALRLARLILEGQSPSDSNGS-NQAFSFLFD---MNRLFEKFVAKLLRKRLPQDWKVKFQYSSPFLLDQ 254 (321)
T ss_pred HHHHHHHHHHHHhccCcccCCCC-ccceeeeeh---HHHHHHHHHHHHHHHHhCCCceEeecccceeeccc
Confidence 56788899988776433 33444 477888885 489999999988883 344566777665554433
No 9
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=52.41 E-value=27 Score=27.74 Aligned_cols=68 Identities=19% Similarity=0.220 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHhcCCC-CCCCceeeeeeccccccchhhHHHHHHHHHHHHHhc----Cceeecceeeccccc-------
Q 034452 4 EEEVERLKEEIQRLGKI-QPDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKR----KFLTYDGELLLQGVH------- 71 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~-~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~----~lV~FeGEmL~Qg~d------- 71 (94)
.+|+.+-++.|-++|.. -.||...+|+| + |..+.+.|+.|.++ .++-=|+..++||+.
T Consensus 95 ~~e~~~a~~~I~~~a~~~i~~g~~ILT~~--~--------S~tv~~~l~~a~~~~~~f~V~v~EsrP~~~G~~~a~~L~~ 164 (301)
T TIGR00511 95 INQSDKAQERIGEIGAKRIRDGDVVMTHC--N--------SEAALSVIKTAFEQGKDIEVIATETRPRKQGHITAKELRD 164 (301)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCEEEEEC--C--------cHHHHHHHHHHHHcCCcEEEEEecCCCcchHHHHHHHHHH
Confidence 45667777777777743 36788888887 2 46778888888544 345558888888863
Q ss_pred CceEEEecCC
Q 034452 72 DNVEITLKPP 81 (94)
Q Consensus 72 D~V~I~Ll~~ 81 (94)
.++++||..+
T Consensus 165 ~gI~vtlI~D 174 (301)
T TIGR00511 165 YGIPVTLIVD 174 (301)
T ss_pred CCCCEEEEeh
Confidence 6778887654
No 10
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=51.43 E-value=13 Score=23.92 Aligned_cols=21 Identities=38% Similarity=0.564 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHhcCceeec
Q 034452 42 IFEALVGTLRAAKKRKFLTYD 62 (94)
Q Consensus 42 i~e~LVGtL~~ArK~~lV~Fe 62 (94)
..+++--.+.++|++|+|+|+
T Consensus 5 ~~~~i~~Li~~gK~~G~lT~~ 25 (82)
T PF03979_consen 5 YEEAIKKLIEKGKKKGYLTYD 25 (82)
T ss_dssp HHHHHHHHHHHHHHHSS-BHH
T ss_pred hHHHHHHHHHHHhhcCcCCHH
Confidence 356677788999999999985
No 11
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=46.81 E-value=29 Score=28.31 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhcCCC---------CCCCceeeeeec
Q 034452 4 EEEVERLKEEIQRLGKI---------QPDGSYKVTFGV 32 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~---------~~dG~~~V~FG~ 32 (94)
+.++.+|++-|++.|.. ..+|+|.|-||.
T Consensus 85 ~~~~~eL~~SIr~~Gq~~PIlVR~~p~~~grY~ii~G~ 122 (325)
T TIGR03454 85 DEAFADLVESIRENGQQVPILVRPHPEAEGRYQIAYGH 122 (325)
T ss_pred HHHHHHHHHHHHHhCCcCCeEEEECCCCCCCEEEEeCH
Confidence 47899999999999963 245888888886
No 12
>PF01008 IF-2B: Initiation factor 2 subunit family; InterPro: IPR000649 Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. The eukaryotic translation initiation factor EIF-2B is a complex made up of five different subunits, alpha, beta, gamma, delta and epsilon, and catalyses the exchange of EIF-2-bound GDP for GTP. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes and also contains a subfamily of proteins in eukaryotes, archaeae (e.g. Pyrococcus furiosus), or eubacteria such as Bacillus subtilis and Thermotoga maritima. Many of these proteins were initially annotated as putative translation initiation factors despite the fact that there is no evidence for the requirement of an IF2 recycling factor in prokaryotic translation initiation. Recently, one of these proteins from B. subtilis has been functionally characterised as a 5-methylthioribose-1-phosphate isomerase (MTNA) []. This enzyme participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthioribulose-1-phosphate []. The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species.; GO: 0044237 cellular metabolic process; PDB: 1VB5_A 1T5O_D 3A11_E 3VM6_C 1W2W_A 1T9K_A 3ECS_B 2YRF_A 2YVK_B 2A0U_A ....
Probab=46.75 E-value=31 Score=26.05 Aligned_cols=68 Identities=24% Similarity=0.351 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHhcCCC-CCCCceeeeeeccccccchhhHHHHHHHHHHHHHhcC----ceeecceeecccc-------c
Q 034452 4 EEEVERLKEEIQRLGKI-QPDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKRK----FLTYDGELLLQGV-------H 71 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~-~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~----lV~FeGEmL~Qg~-------d 71 (94)
.+|+..-.+.|-+++.+ -.||...+||| + |..+...|+.|++.| ++-=|+...+||+ .
T Consensus 87 ~~e~~~~~~~I~~~~~~~I~~~~~ILT~~--~--------S~~v~~~l~~a~~~~~~~~V~v~es~P~~eG~~~a~~L~~ 156 (282)
T PF01008_consen 87 LDEIEQAREKIADHASELINDGDTILTHG--Y--------SSTVERFLLSAKKKGKKFRVIVLESRPYNEGRLMAKELAE 156 (282)
T ss_dssp HHHHHHHHHHHHHHHHCCC-TTEEEEEES------------SHHHHHHHHHHHTTEEEEEEEE--TTTTHHHTHHHHHHH
T ss_pred HhHHHHHHHHHHHHHHHhccCCeEEEEeC--C--------chHHHHHHHHHHHcCCeEEEEEccCCcchhhhhHHHHhhh
Confidence 35667777777777754 47899999999 2 566888999998865 5555677666762 3
Q ss_pred CceEEEecCC
Q 034452 72 DNVEITLKPP 81 (94)
Q Consensus 72 D~V~I~Ll~~ 81 (94)
..+++++..+
T Consensus 157 ~gi~v~~i~d 166 (282)
T PF01008_consen 157 AGIPVTLIPD 166 (282)
T ss_dssp TT-EEEEE-G
T ss_pred cceeEEEEec
Confidence 4666666544
No 13
>PF14330 DUF4387: Domain of unknown function (DUF4387)
Probab=45.85 E-value=27 Score=24.40 Aligned_cols=31 Identities=26% Similarity=0.614 Sum_probs=22.9
Q ss_pred HHHHHHHHhcCCCCCCCceeeeeeccccccchhhHHHH
Q 034452 8 ERLKEEIQRLGKIQPDGSYKVTFGVLFHDDRCANIFEA 45 (94)
Q Consensus 8 ~~L~~~I~~~G~~~~dG~~~V~FG~LF~~~~~~~i~e~ 45 (94)
.+||..|++ || -|-+++||-.+|.+ ...||+
T Consensus 2 ~dla~vIRS---KN-AGPf~lT~DI~F~~---~e~Y~~ 32 (99)
T PF14330_consen 2 SDLAKVIRS---KN-AGPFELTFDIIFKD---KEAYER 32 (99)
T ss_pred HHHHHHHhc---cC-CCCcEEEEEEEECC---HHHHHH
Confidence 467788875 43 68899999999986 344554
No 14
>PF12563 Hemolysin_N: Hemolytic toxin N terminal; InterPro: IPR022220 This domain family is found in bacteria, and is approximately 190 amino acids in length. The family is found in association with PF07968 from PFAM, PF00652 from PFAM. This family is a bacterial virulence factor - hemolysin - which forms pores in erythrocytes and causes them to lyse. ; PDB: 1XEZ_A 3O44_I.
Probab=42.29 E-value=15 Score=28.49 Aligned_cols=65 Identities=18% Similarity=0.212 Sum_probs=23.1
Q ss_pred CCceeeeeeccccc---cchhhHHHHHHHHHHHHHhcCceeecceeecccccC--ceEEEecCCCCchhH
Q 034452 23 DGSYKVTFGVLFHD---DRCANIFEALVGTLRAAKKRKFLTYDGELLLQGVHD--NVEITLKPPPPQPLA 87 (94)
Q Consensus 23 dG~~~V~FG~LF~~---~~~~~i~e~LVGtL~~ArK~~lV~FeGEmL~Qg~dD--~V~I~Ll~~~~~~~~ 87 (94)
+-+|-|-|-.+=+. .++..-|.+..|+--.+-=-=+-.|.|||||-.-+| |+.|.+|+.....++
T Consensus 76 ~krylvDFS~iede~~k~~aq~~~r~~~G~sF~~dfiiITehKGeLLFTPld~~dD~~~~~lEa~~~~~s 145 (187)
T PF12563_consen 76 NKRYLVDFSQIEDEEEKAQAQAKFRKQYGLSFDSDFIIITEHKGELLFTPLDDADDPNILLLEAKRSKRS 145 (187)
T ss_dssp --EEEEE-TT--SHHHHHHHHHHHHHHHS-B--SSEEEEEEETTEEEEEEESS-----------------
T ss_pred CCeEEEEccccCChHHHHHHHHHHHHHhCcCccCCEEEEEcccCcEeecCCCCcCCCChhhccCCccccc
Confidence 44566777666432 122233333444332222222457999999998776 899999987766555
No 15
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=39.60 E-value=39 Score=27.98 Aligned_cols=30 Identities=27% Similarity=0.630 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHhcCCC---------CCCCceeeeeec
Q 034452 3 VEEEVERLKEEIQRLGKI---------QPDGSYKVTFGV 32 (94)
Q Consensus 3 V~~Ei~~L~~~I~~~G~~---------~~dG~~~V~FG~ 32 (94)
.+.++.+|.+-|++.|.. ..+|+|.+-||.
T Consensus 86 ~d~~~~eL~~SI~~~Gq~~PIlVRp~p~~~grY~li~G~ 124 (336)
T PRK13866 86 VDPKFEQLEASISQEGQQVPILVRPHPEAAGRYQIVYGR 124 (336)
T ss_pred ccHHHHHHHHHHHHhCCcCCeEEEECCCCCCCEEEEecH
Confidence 457899999999999963 135889998886
No 16
>PF07606 DUF1569: Protein of unknown function (DUF1569); InterPro: IPR011463 This entry represents a family of hypothetical proteins identified in Rhodopirellula baltica and other bacteria.
Probab=35.44 E-value=39 Score=24.14 Aligned_cols=36 Identities=36% Similarity=0.425 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHHHhcCCCCCCCceeeeeecccccc
Q 034452 2 NVEEEVERLKEEIQRLGKIQPDGSYKVTFGVLFHDD 37 (94)
Q Consensus 2 ~V~~Ei~~L~~~I~~~G~~~~dG~~~V~FG~LF~~~ 37 (94)
+.+.|...|.+.|.+.+..+.+.....-||.|-.++
T Consensus 98 d~~~~~~~L~~~i~~f~~~~~~~~~Hp~FG~Lt~ee 133 (152)
T PF07606_consen 98 DFEEEKERLIEAIQRFQAHPGELAPHPFFGKLTKEE 133 (152)
T ss_pred CHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCHHH
Confidence 567899999999999987655666678999998654
No 17
>PLN00196 alpha-amylase; Provisional
Probab=35.31 E-value=75 Score=26.55 Aligned_cols=48 Identities=15% Similarity=0.225 Sum_probs=32.7
Q ss_pred CCCceeeeeeccccccchhhHHHHHHHHHHHHHhcCceeecceeecccccCce
Q 034452 22 PDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDGELLLQGVHDNV 74 (94)
Q Consensus 22 ~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGEmL~Qg~dD~V 74 (94)
.+|..+|-+|..|... ....+-.|..+||..=+.-.|+.-..-.+|+|
T Consensus 339 ~pG~P~IyYg~~~~~~-----~~~~i~~Li~~Rk~~~~~~~g~~~~~~a~~d~ 386 (428)
T PLN00196 339 HPGNPCIFYDHFFDWG-----LKEEIAALVSIRNRNGITPTSELRIMEADADL 386 (428)
T ss_pred CCCcceEeeCCCcCcc-----HHHHHHHHHHHHHhCCCcCCccEEEEEecCCE
Confidence 4788999999999743 44577888899998755554554444444443
No 18
>PF00636 Ribonuclease_3: Ribonuclease III domain; InterPro: IPR000999 Prokaryotic ribonuclease III (3.1.26.3 from EC) (gene rnc) [] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related to a number of proteins including []: Saccharomyces cerevisiae (Baker's yeast) protein pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites Caenorhabditis elegans hypothetical protein F26E4.13 Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346 yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c ; GO: 0003723 RNA binding, 0004525 ribonuclease III activity, 0006396 RNA processing; PDB: 2GSL_A 2NUE_B 1YYO_A 2NUF_A 1YZ9_A 1JFZ_A 1YYW_C 1RC5_B 1YYK_B 1RC7_A ....
Probab=33.52 E-value=32 Score=22.25 Aligned_cols=19 Identities=32% Similarity=0.620 Sum_probs=15.0
Q ss_pred ccccccchhhHHHHHHHHH
Q 034452 32 VLFHDDRCANIFEALVGTL 50 (94)
Q Consensus 32 ~LF~~~~~~~i~e~LVGtL 50 (94)
.......++++||+++|.+
T Consensus 91 ~~~~~k~laD~~EAliGAi 109 (114)
T PF00636_consen 91 QVLPPKVLADVFEALIGAI 109 (114)
T ss_dssp SSHHHHHHHHHHHHHHHHH
T ss_pred cCCccHHHHHHHHHHHHHH
Confidence 3445567899999999976
No 19
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=30.87 E-value=14 Score=25.95 Aligned_cols=15 Identities=33% Similarity=0.375 Sum_probs=7.7
Q ss_pred HHHHHHHhcCceeec
Q 034452 48 GTLRAAKKRKFLTYD 62 (94)
Q Consensus 48 GtL~~ArK~~lV~Fe 62 (94)
=.|++|+|.|+|+|.
T Consensus 35 l~Lr~a~k~g~I~Y~ 49 (109)
T PF08438_consen 35 LALRKAAKAGLIDYI 49 (109)
T ss_dssp HHHHS-SSS----S-
T ss_pred HHHHHHHHCCCEEeC
Confidence 369999999999985
No 20
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=30.74 E-value=31 Score=22.00 Aligned_cols=21 Identities=33% Similarity=0.645 Sum_probs=16.8
Q ss_pred ccccccchhhHHHHHHHHHHHHH
Q 034452 32 VLFHDDRCANIFEALVGTLRAAK 54 (94)
Q Consensus 32 ~LF~~~~~~~i~e~LVGtL~~Ar 54 (94)
.|+||+ .|-|+-++..|.++=
T Consensus 10 vL~NDe--~ht~~~Vi~~L~~~~ 30 (82)
T PF02617_consen 10 VLWNDE--VHTFEQVIDVLRRVF 30 (82)
T ss_dssp EEE--S--SSBHHHHHHHHHHHC
T ss_pred EEEcCC--CCCHHHHHHHHHHHH
Confidence 589999 899999999999874
No 21
>PRK11537 putative GTP-binding protein YjiA; Provisional
Probab=29.37 E-value=21 Score=28.41 Aligned_cols=51 Identities=27% Similarity=0.361 Sum_probs=31.7
Q ss_pred ceeeeeeccccccchhhHHHHHH----HHHHHHHhcCceeecce---eecccccCceEEE
Q 034452 25 SYKVTFGVLFHDDRCANIFEALV----GTLRAAKKRKFLTYDGE---LLLQGVHDNVEIT 77 (94)
Q Consensus 25 ~~~V~FG~LF~~~~~~~i~e~LV----GtL~~ArK~~lV~FeGE---mL~Qg~dD~V~I~ 77 (94)
.+++++-..|+-.+.....+.++ +-+ -|=+|++.+.|+ +++||+.....+.
T Consensus 226 s~~~~~~~p~~~~~l~~~L~~l~~~~~~~i--~R~KG~v~~~~~~~~~~~q~v~~~~~~~ 283 (318)
T PRK11537 226 SIVVELDYPVDISEVSRVMENLLLESADKL--LRYKGMLWIDGEPNRLLFQGVQRLYSAD 283 (318)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHhCCCce--EEeeeEEEeCCCCCEEEEEEehhhcccC
Confidence 45566677776544333344433 223 345699999876 8999998765543
No 22
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=28.07 E-value=98 Score=26.22 Aligned_cols=46 Identities=20% Similarity=0.184 Sum_probs=36.8
Q ss_pred eeeccccccchhhHHHHHHHHHHHHHhcCceeecceeecccccCceEE
Q 034452 29 TFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDGELLLQGVHDNVEI 76 (94)
Q Consensus 29 ~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGEmL~Qg~dD~V~I 76 (94)
.++.=|+-. ..+++...-.+.+-++.|+.-..--.|+.|..|++.+
T Consensus 219 ~v~~h~nhp--~Eit~~a~~Al~~L~~aGI~l~nQsVLLkGVND~~~~ 264 (417)
T TIGR03820 219 WLNTHFNHP--REITASSKKALAKLADAGIPLGNQSVLLAGVNDCPRI 264 (417)
T ss_pred EEEEeCCCh--HhChHHHHHHHHHHHHcCCEEEeeceEECCcCCCHHH
Confidence 334445433 5678899999999999999999999999999998765
No 23
>PF13350 Y_phosphatase3: Tyrosine phosphatase family; PDB: 1YWF_A 2OZ5_B.
Probab=26.72 E-value=33 Score=23.95 Aligned_cols=48 Identities=25% Similarity=0.385 Sum_probs=27.2
Q ss_pred HhcC-CCCCCCceeeeeeccccccchhhHHHHHHHHHHHHHhcCceeecc
Q 034452 15 QRLG-KIQPDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKRKFLTYDG 63 (94)
Q Consensus 15 ~~~G-~~~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeG 63 (94)
+++| .+..||+ .|+-|.||+...-.+++++=.-.|..-.=+.+|||-.
T Consensus 3 RDlGg~~~~~g~-~ir~g~lyRS~~l~~lt~~d~~~L~~lgI~tIiDLRs 51 (164)
T PF13350_consen 3 RDLGGYPTADGR-RIRPGRLYRSGNLSNLTEADLERLRELGIRTIIDLRS 51 (164)
T ss_dssp EEGGGTST-----TS-TTSEEEES--TT--HHHHHHHHHTT--EEEE-S-
T ss_pred cccCCCCcccee-eecCCcEEecCCcCcCCHHHHHHHHhCCCCEEEECCC
Confidence 4566 3566787 8999999999888899999777777666677788743
No 24
>PF00990 GGDEF: GGDEF domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [,]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [].; PDB: 3IGN_A 3BRE_B 3EZU_A 3ICL_B 3PJX_A 3PJW_A 3HVW_A 3HVA_B 3I5C_B 3I5B_B ....
Probab=26.33 E-value=1.4e+02 Score=18.73 Aligned_cols=32 Identities=16% Similarity=0.324 Sum_probs=22.9
Q ss_pred eeeeeeccccc----cchhhHHHHHHHHHHHHHhcC
Q 034452 26 YKVTFGVLFHD----DRCANIFEALVGTLRAAKKRK 57 (94)
Q Consensus 26 ~~V~FG~LF~~----~~~~~i~e~LVGtL~~ArK~~ 57 (94)
+++.+|...-. ..+..+..+.--.|..||+.|
T Consensus 123 ~~~~~G~~~~~~~~~~~~~~ll~~a~~al~~ak~~g 158 (161)
T PF00990_consen 123 LTLSIGIAVYDPNDGQDADELLKKADQALQEAKEQG 158 (161)
T ss_dssp CEEEEEEEEEETSTTSSHHHHHHHHHHHHHHHHHTT
T ss_pred ccccceEEEecCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 67888877653 344566677778888898876
No 25
>PF10398 DUF2443: Protein of unknown function (DUF2443); InterPro: IPR019469 This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of alpha helices. The function is not known. ; PDB: 1ZKE_F.
Probab=25.28 E-value=55 Score=22.30 Aligned_cols=17 Identities=53% Similarity=0.849 Sum_probs=14.3
Q ss_pred CHHHHHHHHHHHHHhcC
Q 034452 2 NVEEEVERLKEEIQRLG 18 (94)
Q Consensus 2 ~V~~Ei~~L~~~I~~~G 18 (94)
++++||.+|.+.|+.+.
T Consensus 54 QideeV~~LKe~IdaLN 70 (79)
T PF10398_consen 54 QIDEEVEKLKEHIDALN 70 (79)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 47899999999998763
No 26
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=25.14 E-value=1.9e+02 Score=20.99 Aligned_cols=49 Identities=18% Similarity=0.170 Sum_probs=31.9
Q ss_pred HHHHHHHhcCCC-C------CCCceeeeeeccccccchhhHHHHHHHHHHHHHhcCc
Q 034452 9 RLKEEIQRLGKI-Q------PDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKKRKF 58 (94)
Q Consensus 9 ~L~~~I~~~G~~-~------~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK~~l 58 (94)
...++++++|-. | ..|+ +-++|.++.+.......+-+-|+..+|+++|+
T Consensus 11 rV~~~a~elgY~pn~~a~~l~~~~-~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~ 66 (309)
T PRK11041 11 RVEQAVLEVGYSPQSLGRNLKRNE-SRTILVIVPDICDPFFSEIIRGIEVTAAEHGY 66 (309)
T ss_pred HHHHHHHHHCCCcCHHHHHhhcCC-CcEEEEEeCCCcCccHHHHHHHHHHHHHHCCC
Confidence 345678899953 3 2233 36889998654223334457799999999885
No 27
>PF03932 CutC: CutC family; InterPro: IPR005627 Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are between 200 and 300 amino acids in length and are found in both eukaryotes and bacteria.; GO: 0005507 copper ion binding, 0055070 copper ion homeostasis; PDB: 2BDQ_A 3IWP_I 1X8C_B 1X7I_A 1TWD_B.
Probab=24.50 E-value=1.3e+02 Score=23.03 Aligned_cols=46 Identities=37% Similarity=0.543 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhcCCCCCCCceeeeeeccccccchhhHHHHHHHHHHHHHh
Q 034452 4 EEEVERLKEEIQRLGKIQPDGSYKVTFGVLFHDDRCANIFEALVGTLRAAKK 55 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~~~dG~~~V~FG~LF~~~~~~~i~e~LVGtL~~ArK 55 (94)
+.|+..+++.|+.+-+-+.|| +-||.|=.+. .|=......|..|-+
T Consensus 68 ~~E~~~M~~dI~~~~~~GadG---~VfG~L~~dg---~iD~~~~~~Li~~a~ 113 (201)
T PF03932_consen 68 DEEIEIMKEDIRMLRELGADG---FVFGALTEDG---EIDEEALEELIEAAG 113 (201)
T ss_dssp HHHHHHHHHHHHHHHHTT-SE---EEE--BETTS---SB-HHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHcCCCe---eEEEeECCCC---CcCHHHHHHHHHhcC
Confidence 578888888888766655565 6788887643 344566666666655
No 28
>PTZ00174 phosphomannomutase; Provisional
Probab=23.98 E-value=56 Score=24.24 Aligned_cols=26 Identities=27% Similarity=0.356 Sum_probs=16.8
Q ss_pred eccccccchhhHHHHHHHHHHHHHhcCc
Q 034452 31 GVLFHDDRCANIFEALVGTLRAAKKRKF 58 (94)
Q Consensus 31 G~LF~~~~~~~i~e~LVGtL~~ArK~~l 58 (94)
|.|++++ ..|++...-+|.+++++|+
T Consensus 14 GTLL~~~--~~is~~~~~ai~~l~~~Gi 39 (247)
T PTZ00174 14 GTLTKPR--NPITQEMKDTLAKLKSKGF 39 (247)
T ss_pred CCCcCCC--CCCCHHHHHHHHHHHHCCC
Confidence 5677665 5677766666777666643
No 29
>PRK08333 L-fuculose phosphate aldolase; Provisional
Probab=23.59 E-value=1.3e+02 Score=21.59 Aligned_cols=34 Identities=18% Similarity=0.268 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHHhcCCC-CCCCceeeeeeccc
Q 034452 1 MNVEEEVERLKEEIQRLGKI-QPDGSYKVTFGVLF 34 (94)
Q Consensus 1 m~V~~Ei~~L~~~I~~~G~~-~~dG~~~V~FG~LF 34 (94)
|++.+||.+.|..+.+.|-- ...|.+++.-|..|
T Consensus 2 ~~~~~~l~~~~~~~~~~gl~~~~~GNiS~R~~~~~ 36 (184)
T PRK08333 2 RNVKAQLVKYSKLAHERGLTAAFGGNLSIRVGNLV 36 (184)
T ss_pred hHHHHHHHHHHHHHHHCCCCcCCCCeEEEEeCCEE
Confidence 56778999999999999964 56689999877544
No 30
>PRK12482 flagellar motor protein MotA; Provisional
Probab=22.87 E-value=53 Score=26.44 Aligned_cols=32 Identities=9% Similarity=0.054 Sum_probs=27.0
Q ss_pred cccccchhhHHHHHHHHHHHHHhcCceeecce
Q 034452 33 LFHDDRCANIFEALVGTLRAAKKRKFLTYDGE 64 (94)
Q Consensus 33 LF~~~~~~~i~e~LVGtL~~ArK~~lV~FeGE 64 (94)
-++..+|.++.+.++.....|||.|++..|.+
T Consensus 69 ~~~~~~y~~~i~~lv~ls~~aRr~GllaLE~~ 100 (287)
T PRK12482 69 EYGVEFQRQLLLLLYELLEMVQEGGLKRLDQH 100 (287)
T ss_pred CCChhhHHHHHHHHHHHHHHHHhcCHHHHHHh
Confidence 34445678899999999999999999999975
No 31
>PF04385 FAINT: Domain of unknown function, DUF529; InterPro: IPR007480 This entry represents a repeated region found in several Theileria parva proteins.The repeat is normally about 70 residues long and contains a conserved aromatic residue in the middle.
Probab=22.71 E-value=61 Score=18.27 Aligned_cols=16 Identities=13% Similarity=0.297 Sum_probs=13.7
Q ss_pred ceeecceeecccccCc
Q 034452 58 FLTYDGELLLQGVHDN 73 (94)
Q Consensus 58 lV~FeGEmL~Qg~dD~ 73 (94)
-|.|.+.++||..++.
T Consensus 37 ~V~~~~~~iW~~~~~~ 52 (78)
T PF04385_consen 37 KVKYGDKTIWKSKSDE 52 (78)
T ss_pred EEEECCEEEEecCCCC
Confidence 4788999999999884
No 32
>PF04696 Pinin_SDK_memA: pinin/SDK/memA/ protein conserved region; InterPro: IPR006786 This conserved region is located adjacent and C-terminal to a N-terminal pinin/SKD domain IPR006787 from INTERPRO. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque []. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing []. MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions [].
Probab=22.40 E-value=77 Score=22.38 Aligned_cols=16 Identities=44% Similarity=0.688 Sum_probs=13.7
Q ss_pred hhHHHHHHHHHHHHHh
Q 034452 40 ANIFEALVGTLRAAKK 55 (94)
Q Consensus 40 ~~i~e~LVGtL~~ArK 55 (94)
-.+|-.|+|||-.+++
T Consensus 10 RRmFG~LlGTL~kf~~ 25 (131)
T PF04696_consen 10 RRMFGGLLGTLQKFKK 25 (131)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 4578899999999987
No 33
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=22.40 E-value=1e+02 Score=18.33 Aligned_cols=19 Identities=32% Similarity=0.373 Sum_probs=15.5
Q ss_pred HHHHHhcCC---CCCCCceeee
Q 034452 11 KEEIQRLGK---IQPDGSYKVT 29 (94)
Q Consensus 11 ~~~I~~~G~---~~~dG~~~V~ 29 (94)
|+.++++|- .++||+..|+
T Consensus 21 ~~~L~~~Gi~~~~~~~G~p~V~ 42 (47)
T PF13986_consen 21 IRWLRRNGIPFVVRADGRPIVT 42 (47)
T ss_pred HHHHHHCCCeeEECCCCCEEee
Confidence 678889996 4799998886
No 34
>PF05334 DUF719: Protein of unknown function (DUF719); InterPro: IPR007998 This family consists of several eukaryotic proteins of unknown function.
Probab=22.25 E-value=18 Score=27.66 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHhcCCCC-CC-Cceeeeeecccccc
Q 034452 3 VEEEVERLKEEIQRLGKIQ-PD-GSYKVTFGVLFHDD 37 (94)
Q Consensus 3 V~~Ei~~L~~~I~~~G~~~-~d-G~~~V~FG~LF~~~ 37 (94)
|-+|-++-.+...+..+.. .. -+..+.||.||++|
T Consensus 142 vLREAKekae~~e~~~~q~~~e~~k~~~hy~~LFD~y 178 (181)
T PF05334_consen 142 VLREAKEKAEELERTAQQVQSERTKKQAHYGMLFDEY 178 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcccHHHHHHHh
Confidence 5566666666644444321 11 22349999999765
No 35
>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition. Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.
Probab=22.22 E-value=70 Score=26.17 Aligned_cols=19 Identities=37% Similarity=0.548 Sum_probs=15.1
Q ss_pred HHHHHHHHhcCceeeccee
Q 034452 47 VGTLRAAKKRKFLTYDGEL 65 (94)
Q Consensus 47 VGtL~~ArK~~lV~FeGEm 65 (94)
.-+|++||+.|-++|.|.-
T Consensus 263 E~IL~aAR~~~~~~~~g~~ 281 (370)
T PF02994_consen 263 EKILKAAREKGQLTYKGKR 281 (370)
T ss_dssp HHHHHHHHHHS-EEETTEE
T ss_pred HHHHHHHHhcCceeeCCCc
Confidence 4579999999999988863
No 36
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=21.61 E-value=2e+02 Score=17.98 Aligned_cols=60 Identities=18% Similarity=0.226 Sum_probs=41.9
Q ss_pred ceeeeeeccccccchhhHHHH----------HHHHHHHHHhcCceeecceeeccc--ccCceEEEecCCCCchhHh
Q 034452 25 SYKVTFGVLFHDDRCANIFEA----------LVGTLRAAKKRKFLTYDGELLLQG--VHDNVEITLKPPPPQPLAV 88 (94)
Q Consensus 25 ~~~V~FG~LF~~~~~~~i~e~----------LVGtL~~ArK~~lV~FeGEmL~Qg--~dD~V~I~Ll~~~~~~~~~ 88 (94)
.-.+++|++++ .|..+.+. +.-.|..-.-.|+|+.+- -..| +.-.-.|.|.-|++.+.++
T Consensus 13 ~~~~~~~~vy~--~Y~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~--~~~G~~~G~~~~~~l~~d~~~v~~a 84 (85)
T PF09079_consen 13 KEEVTTGEVYE--VYEELCESLGVDPLSYRRFSDYLSELEMLGLIESER--KGRGRGRGRTREISLNVDPEDVLEA 84 (85)
T ss_dssp SSSEEHHHHHH--HHHHHHHHTTS----HHHHHHHHHHHHHTTSEEEEE--EE-TT-CTEEEEEEECSSSHHHHHH
T ss_pred CCceeHHHHHH--HHHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe--ecCCCCCCeEEEEEecCCHHHHHhh
Confidence 45899999997 56888874 666788888899997653 3344 3335577788887766543
No 37
>KOG0972 consensus Huntingtin interacting protein 1 (Hip1) interactor Hippi [Signal transduction mechanisms]
Probab=21.56 E-value=59 Score=27.58 Aligned_cols=30 Identities=33% Similarity=0.490 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCceeeeeec
Q 034452 3 VEEEVERLKEEIQRLGKIQPDGSYKVTFGV 32 (94)
Q Consensus 3 V~~Ei~~L~~~I~~~G~~~~dG~~~V~FG~ 32 (94)
|..|++++.++|.+-|.+-.||...|+..+
T Consensus 313 Vm~e~E~~KqemEe~G~~msDGaplvkIkq 342 (384)
T KOG0972|consen 313 VMDEIEQLKQEMEEQGAKMSDGAPLVKIKQ 342 (384)
T ss_pred HHHHHHHHHHHHHHhcccccCCchHHHHHH
Confidence 778999999999999999999987665443
No 38
>TIGR00524 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=21.13 E-value=1.7e+02 Score=23.32 Aligned_cols=73 Identities=23% Similarity=0.273 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHhcCCC-CCCCceeeeee---ccccccchhhHHHHHHHHHHHHHhcC----ceeecceeeccc-cc---
Q 034452 4 EEEVERLKEEIQRLGKI-QPDGSYKVTFG---VLFHDDRCANIFEALVGTLRAAKKRK----FLTYDGELLLQG-VH--- 71 (94)
Q Consensus 4 ~~Ei~~L~~~I~~~G~~-~~dG~~~V~FG---~LF~~~~~~~i~e~LVGtL~~ArK~~----lV~FeGEmL~Qg-~d--- 71 (94)
.+|..+.++.|-++|.. -.||....|+| .|-.-. +..+.+.|+.|.++| ++-=|+....|| +-
T Consensus 98 ~~e~~~~~~~Ia~~a~~~I~~g~~ILT~~~Sg~lat~~-----~~tv~~~l~~A~~~g~~~~V~v~EsrP~~~G~~~~a~ 172 (303)
T TIGR00524 98 IEEDLETNRKIGENGAKLIKDGDTVLTHCNAGALATSD-----YGTALGVIRSAWEDGKRIRVIACETRPRNQGSRLTAW 172 (303)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCEEEEecCCccccccC-----cchHHHHHHHHHHcCCceEEEECCCCCccchHHHHHH
Confidence 35556677777777743 36788888886 222111 245667888886543 344467777787 32
Q ss_pred ----CceEEEecCC
Q 034452 72 ----DNVEITLKPP 81 (94)
Q Consensus 72 ----D~V~I~Ll~~ 81 (94)
.++++|+.-+
T Consensus 173 ~L~~~gI~vtlI~D 186 (303)
T TIGR00524 173 ELMQDGIDVTLITD 186 (303)
T ss_pred HHHHCCCCEEEECh
Confidence 5677777654
No 39
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=20.56 E-value=1.1e+02 Score=22.25 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcCc------eeecc--e---eecccccCceEEEecCCCCchhH
Q 034452 46 LVGTLRAAKKRKF------LTYDG--E---LLLQGVHDNVEITLKPPPPQPLA 87 (94)
Q Consensus 46 LVGtL~~ArK~~l------V~FeG--E---mL~Qg~dD~V~I~Ll~~~~~~~~ 87 (94)
..|.+.+++++|+ |-|++ + .+..| ....|..+|+.+.-.
T Consensus 202 A~g~l~al~~~G~~~dv~vvg~d~~~~~~~~~~~g---~~~~tv~~~~~~~g~ 251 (280)
T cd06303 202 ALGASDALKELGREDDILINGWGGGSAELDAIQQG---ELDVTVMRMNDDTGV 251 (280)
T ss_pred HHHHHHHHHHcCCCCCcEEEecCCCHHHHHHHHcC---CceEEEecCchHhHH
Confidence 5699999999984 45555 1 22222 344556666655544
No 40
>PF07855 DUF1649: Protein of unknown function (DUF1649); InterPro: IPR012445 This family represents Autophagy-related protein 101.
Probab=20.51 E-value=1.4e+02 Score=21.69 Aligned_cols=29 Identities=10% Similarity=0.327 Sum_probs=22.0
Q ss_pred CHHHHHHHHHHHHHhcCCC----CCCCceeeee
Q 034452 2 NVEEEVERLKEEIQRLGKI----QPDGSYKVTF 30 (94)
Q Consensus 2 ~V~~Ei~~L~~~I~~~G~~----~~dG~~~V~F 30 (94)
.|++.|..|...+.+.+.+ ...|+++|.|
T Consensus 55 ~Id~ki~~f~~~l~~~~~~~~~~~~~gqI~l~F 87 (163)
T PF07855_consen 55 LIDEKINQFIRQLEKHPSKSSNGLGRGQISLQF 87 (163)
T ss_pred HHHHHHHHHHHHHHhCcCccCCCcceEEEEEEE
Confidence 3788999999999887654 2357788877
No 41
>PRK14447 acylphosphatase; Provisional
Probab=20.27 E-value=59 Score=21.65 Aligned_cols=26 Identities=31% Similarity=0.491 Sum_probs=18.9
Q ss_pred HHHHHHhcCceee-----cc---eeecccccCce
Q 034452 49 TLRAAKKRKFLTY-----DG---ELLLQGVHDNV 74 (94)
Q Consensus 49 tL~~ArK~~lV~F-----eG---EmL~Qg~dD~V 74 (94)
+...|+++|+.=| +| |+..||-.+.+
T Consensus 23 ~~~~A~~~gl~G~V~N~~dG~~Vei~~qG~~~~l 56 (95)
T PRK14447 23 MKEVANRNGVRGWVRNRSDGRTVEAVLEGPRDAV 56 (95)
T ss_pred HHHHHhhcCeEEEEEECCCCCEEEEEEEeCHHHH
Confidence 6789999999877 55 56666665544
No 42
>PRK04235 hypothetical protein; Provisional
Probab=20.10 E-value=89 Score=23.83 Aligned_cols=30 Identities=20% Similarity=0.216 Sum_probs=23.9
Q ss_pred CHHHHHHHHHHHHHhcC----CCCCCCceeeeee
Q 034452 2 NVEEEVERLKEEIQRLG----KIQPDGSYKVTFG 31 (94)
Q Consensus 2 ~V~~Ei~~L~~~I~~~G----~~~~dG~~~V~FG 31 (94)
.||..|..|++.|+++- +..+.|+++|--.
T Consensus 23 ~VD~~i~~ll~~INs~~~~~TTSSCSGRIsv~~~ 56 (196)
T PRK04235 23 YVDEDIIPLLDLINSLKNYYTTSSCSGRIGIIEA 56 (196)
T ss_pred CCCHHHHHHHHHHhCCCCeEEccCCcceEEEEec
Confidence 37899999999999876 3568898887544
Done!