Query 027380
Match_columns 224
No_of_seqs 84 out of 86
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 09:06:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027380.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027380hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13867 SAP30_Sin3_bdg: Sin3 99.8 3.2E-21 6.9E-26 135.4 5.7 53 164-217 1-53 (53)
2 PRK05886 yajC preprotein trans 95.8 0.022 4.8E-07 46.0 5.4 57 27-94 36-93 (109)
3 PF04648 MF_alpha: Yeast matin 94.5 0.013 2.8E-07 31.7 0.4 11 64-74 1-11 (13)
4 PF02037 SAP: SAP domain; Int 93.5 0.14 3E-06 33.1 3.8 35 161-198 1-35 (35)
5 PF10281 Ish1: Putative stress 92.2 0.33 7.3E-06 31.7 4.4 35 163-198 3-38 (38)
6 smart00513 SAP Putative DNA-bi 88.1 1.1 2.5E-05 28.5 4.1 34 162-198 2-35 (35)
7 PRK06531 yajC preprotein trans 77.5 7.5 0.00016 31.7 5.8 53 26-89 33-86 (113)
8 PF07498 Rho_N: Rho terminatio 76.6 3.5 7.6E-05 27.7 3.1 38 160-198 1-38 (43)
9 TIGR00578 ku70 ATP-dependent D 76.4 2.9 6.3E-05 41.6 3.8 37 160-199 548-584 (584)
10 COG1862 YajC Preprotein transl 71.4 5.2 0.00011 31.8 3.4 51 25-86 39-90 (97)
11 PF12949 HeH: HeH/LEM domain; 60.6 10 0.00022 25.2 2.6 33 162-195 2-34 (35)
12 TIGR00739 yajC preprotein tran 58.0 17 0.00036 27.8 3.8 46 27-85 35-82 (84)
13 TIGR00008 infA translation ini 53.7 18 0.00038 27.2 3.3 38 47-85 3-46 (68)
14 PRK05585 yajC preprotein trans 53.7 22 0.00047 28.4 3.9 49 25-86 48-98 (106)
15 PLN02431 ferredoxin--nitrite r 52.5 12 0.00026 37.6 2.8 34 23-56 245-282 (587)
16 PF01077 NIR_SIR: Nitrite and 40.2 32 0.00069 27.6 3.1 42 25-67 39-84 (157)
17 COG2109 BtuR ATP:corrinoid ade 37.8 19 0.00042 32.2 1.6 17 27-43 149-165 (198)
18 PRK09566 nirA ferredoxin-nitri 36.8 44 0.00095 32.6 3.9 35 23-57 174-212 (513)
19 PRK12442 translation initiatio 35.7 48 0.001 26.2 3.3 40 45-85 3-48 (87)
20 PRK09567 nirA ferredoxin-nitri 31.9 38 0.00082 33.9 2.7 34 23-56 220-257 (593)
21 cd01246 PH_oxysterol_bp Oxyste 28.9 45 0.00097 23.3 2.0 29 52-88 2-33 (91)
22 PF00054 Laminin_G_1: Laminin 27.1 89 0.0019 24.3 3.5 63 27-93 22-87 (131)
23 PF02699 YajC: Preprotein tran 26.8 21 0.00046 26.9 0.0 47 27-84 34-80 (82)
24 smart00652 eIF1a eukaryotic tr 26.6 69 0.0015 24.4 2.7 35 52-87 8-54 (83)
25 PF09124 Endonuc-dimeris: T4 r 25.2 1E+02 0.0022 22.5 3.2 39 160-199 12-50 (54)
26 PF15008 DUF4518: Domain of un 25.1 1.1E+02 0.0023 28.5 4.2 40 163-203 60-99 (262)
27 PF14321 DUF4382: Domain of un 23.8 1.6E+02 0.0036 23.5 4.6 47 45-92 18-70 (139)
28 PRK01833 tatA twin arginine tr 23.7 8.1 0.00018 29.5 -2.8 9 60-68 3-11 (74)
29 PF12244 DUF3606: Protein of u 23.6 90 0.0019 22.2 2.7 25 170-201 23-48 (57)
30 cd01104 HTH_MlrA-CarA Helix-Tu 22.5 65 0.0014 22.0 1.8 20 160-179 8-27 (68)
31 PRK00720 tatA twin arginine tr 22.0 9 0.0002 29.6 -2.8 9 60-68 3-11 (78)
32 COG0155 CysI Sulfite reductase 21.6 93 0.002 31.1 3.3 45 23-68 161-209 (510)
33 PF03743 TrbI: Bacterial conju 21.4 1.3E+02 0.0028 24.8 3.6 44 26-78 38-82 (187)
34 TIGR00523 eIF-1A eukaryotic/ar 21.0 99 0.0021 24.5 2.7 25 51-76 21-45 (99)
35 COG2193 Bfr Bacterioferritin ( 20.9 65 0.0014 28.1 1.8 44 163-213 16-59 (157)
36 TIGR00988 hip integration host 20.6 1.3E+02 0.0028 22.4 3.2 33 185-217 1-34 (94)
37 PF13588 HSDR_N_2: Type I rest 20.5 74 0.0016 24.0 1.9 15 63-77 81-95 (112)
38 cd00561 CobA_CobO_BtuR ATP:cor 20.4 60 0.0013 27.4 1.5 20 26-45 121-140 (159)
39 PF13411 MerR_1: MerR HTH fami 20.1 59 0.0013 22.2 1.2 23 160-182 8-30 (69)
No 1
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=99.84 E-value=3.2e-21 Score=135.39 Aligned_cols=53 Identities=42% Similarity=0.658 Sum_probs=41.0
Q ss_pred cchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhhccccCChHHHHHHHHHHHh
Q 027380 164 LEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHFMSQQMDELQVIVGFVQAAK 217 (224)
Q Consensus 164 Le~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF~sq~VdE~eVI~~Fi~avK 217 (224)
|+++|||||++||+|+ ..|+.+|+||+.+|.+||++|+|||.+||++|||+||
T Consensus 1 L~~~tLrrY~~~~~l~-~~~~~sK~qLa~~V~kHF~s~~v~E~evI~~Fly~vk 53 (53)
T PF13867_consen 1 LQTPTLRRYKKHYKLP-ERPRSSKEQLANAVRKHFNSQPVDENEVIANFLYKVK 53 (53)
T ss_dssp S-HHHHHHHHHHTT-----SS--HHHHHHHHHHHHTT----HHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHhCCC-CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhC
Confidence 7899999999999994 4679999999999999999999999999999999997
No 2
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=95.77 E-value=0.022 Score=45.97 Aligned_cols=57 Identities=19% Similarity=0.185 Sum_probs=40.6
Q ss_pred ccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEeecCcEEEEeeceee-eecCCCCCCcC
Q 027380 27 LSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVLTNGIEVKLQRNALS-VIEAPTGNEED 94 (224)
Q Consensus 27 lsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL~NG~EVkLQRNALs-viE~PtG~Eed 94 (224)
++-|=+..+|+-+| |++|.|.+- + ..+==|.+..|.+++++|+|++ |+.|....||+
T Consensus 36 ~~~Lk~GD~VvT~g---------Gi~G~V~~I-~-d~~v~leia~gv~i~~~r~AI~~v~~p~~~~~e~ 93 (109)
T PRK05886 36 HESLQPGDRVHTTS---------GLQATIVGI-T-DDTVDLEIAPGVVTTWMKLAVRDRILPDDEDDEE 93 (109)
T ss_pred HHhcCCCCEEEECC---------CeEEEEEEE-e-CCEEEEEECCCeEEEEEhhheeeecCCCcccccc
Confidence 45667778888877 999999873 3 2333334458999999999999 66666644443
No 3
>PF04648 MF_alpha: Yeast mating factor alpha hormone; InterPro: IPR006742 This repeated sequence,WHWLQLKPGQPMY, characterises the mating factor alpha-1 or alpha-1 mating pheromone [contains: Mating factor alpha].The hormone is excreted into the culture medium by haploid cells of the alpha mating type and acts on cells of the opposite mating type (type A) by binding to a cognate G-protein coupled receptor which is coupled to a downstream signal transduction pathway. It inhibits DNA synthesis in type A cells synchronising them with type alpha, and so mediates the conjugation process.; GO: 0000772 mating pheromone activity, 0019953 sexual reproduction, 0005576 extracellular region
Probab=94.51 E-value=0.013 Score=31.75 Aligned_cols=11 Identities=55% Similarity=1.368 Sum_probs=9.9
Q ss_pred eEEEEeecCcE
Q 027380 64 WHWLVLTNGIE 74 (224)
Q Consensus 64 WHWLvL~NG~E 74 (224)
||||.|..|+.
T Consensus 1 WhWL~~~~GqP 11 (13)
T PF04648_consen 1 WHWLRLSPGQP 11 (13)
T ss_pred CcceeccCCCc
Confidence 99999999974
No 4
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=93.51 E-value=0.14 Score=33.14 Aligned_cols=35 Identities=26% Similarity=0.379 Sum_probs=30.4
Q ss_pred ccccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhh
Q 027380 161 LSKLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHF 198 (224)
Q Consensus 161 L~KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF 198 (224)
|.++.++-||.+.+.++| ..+.+|++|++-+..||
T Consensus 1 l~~l~v~eLk~~l~~~gL---~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 1 LSKLTVAELKEELKERGL---STSGKKAELIERLKEHL 35 (35)
T ss_dssp TTTSHHHHHHHHHHHTTS----STSSHHHHHHHHHHHH
T ss_pred CCcCcHHHHHHHHHHCCC---CCCCCHHHHHHHHHHhC
Confidence 467889999999999999 55678999999999986
No 5
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=92.25 E-value=0.33 Score=31.66 Aligned_cols=35 Identities=9% Similarity=0.322 Sum_probs=29.0
Q ss_pred ccchhHHHHHHHhcccccCCCCC-CHHHHHHHHHhhh
Q 027380 163 KLEMGALWRYWRHFNLVDAIPNP-SREQLIDVVQRHF 198 (224)
Q Consensus 163 KLe~~TLrRYkkhfkL~~~~P~~-sKeQLv~aV~rHF 198 (224)
.-...-|+.|-+.|++ .+.+.. +|++|++.|.+|+
T Consensus 3 tWs~~~L~~wL~~~gi-~~~~~~~~rd~Ll~~~k~~y 38 (38)
T PF10281_consen 3 TWSDSDLKSWLKSHGI-PVPKSAKTRDELLKLAKKNY 38 (38)
T ss_pred CCCHHHHHHHHHHcCC-CCCCCCCCHHHHHHHHHHhC
Confidence 3456789999999999 556666 9999999999875
No 6
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=88.14 E-value=1.1 Score=28.51 Aligned_cols=34 Identities=18% Similarity=0.275 Sum_probs=28.7
Q ss_pred cccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhh
Q 027380 162 SKLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHF 198 (224)
Q Consensus 162 ~KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF 198 (224)
.++.++.||.+.+.++| ....+|++|++-+..|.
T Consensus 2 ~~l~~~~Lk~~l~~~gl---~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKKRGL---STSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHHcCC---CCCCCHHHHHHHHHHhC
Confidence 56889999999999999 34568999999988763
No 7
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=77.45 E-value=7.5 Score=31.65 Aligned_cols=53 Identities=25% Similarity=0.425 Sum_probs=37.0
Q ss_pred cccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEee-cCcEEEEeeceeeeecCCC
Q 027380 26 ELSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVLT-NGIEVKLQRNALSVIEAPT 89 (224)
Q Consensus 26 elsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL~-NG~EVkLQRNALsviE~Pt 89 (224)
-++-|=+.++|+-+| |+.|+|.+ ++-- =-.++|. .|.+++++|+|++-+-++.
T Consensus 33 m~~sLk~GD~VvT~G---------Gi~G~V~~-I~~~-~~~v~le~~gv~i~v~r~AI~~Vv~~~ 86 (113)
T PRK06531 33 QLNAIQKGDEVVTIG---------GLYGTVDE-VDTE-AKTIVLDVDGVYLTFELAAIKRVVPKA 86 (113)
T ss_pred HHHhcCCCCEEEECC---------CcEEEEEE-EecC-CCEEEEEECCEEEEEEhhHhhhhcCCC
Confidence 455677888888877 99999964 3221 1245553 7999999999998554433
No 8
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=76.61 E-value=3.5 Score=27.71 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=29.1
Q ss_pred cccccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhh
Q 027380 160 DLSKLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHF 198 (224)
Q Consensus 160 DL~KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF 198 (224)
||.++.+.-|+.+.+.++|.. .....|++|+.+|.+.=
T Consensus 1 eL~~~~~~eL~~iAk~lgI~~-~~~~~K~eLI~~Il~~q 38 (43)
T PF07498_consen 1 ELKSMTLSELREIAKELGIEG-YSKMRKQELIFAILKAQ 38 (43)
T ss_dssp HHHCS-HHHHHHHHHCTT-TT-GCCS-HHHHHHHHHHHH
T ss_pred CcccCCHHHHHHHHHHcCCCC-CCcCCHHHHHHHHHHHH
Confidence 567788999999999999954 47789999999987753
No 9
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=76.36 E-value=2.9 Score=41.58 Aligned_cols=37 Identities=27% Similarity=0.577 Sum_probs=32.5
Q ss_pred cccccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhhc
Q 027380 160 DLSKLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHFM 199 (224)
Q Consensus 160 DL~KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF~ 199 (224)
.|.+|.++.||-|.+.|+| .....|++|++.|..||.
T Consensus 548 ~l~kltv~~Lk~~l~~~g~---~~~~kKadLi~~i~~~~~ 584 (584)
T TIGR00578 548 TLGKLTVSVLKDFCRAYGL---RSGSKKQELLDALTKHFK 584 (584)
T ss_pred ChhhccHHHHHHHHHHcCC---CccccHHHHHHHHHHHhC
Confidence 5788999999999999988 345678999999999984
No 10
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=71.37 E-value=5.2 Score=31.82 Aligned_cols=51 Identities=31% Similarity=0.505 Sum_probs=37.1
Q ss_pred ccccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEeecCcEEEEeeceee-eec
Q 027380 25 EELSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVLTNGIEVKLQRNALS-VIE 86 (224)
Q Consensus 25 eelsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL~NG~EVkLQRNALs-viE 86 (224)
+-|+-|=+..+|+-+| |++|.|.|--= .. ==+.|-.|.++++.|||.. ++|
T Consensus 39 ~ml~sL~kGD~VvT~g---------Gi~G~V~~v~d-~~-v~I~l~~~~~i~~~k~aI~~v~~ 90 (97)
T COG1862 39 ELLNSLKKGDEVVTIG---------GIVGTVTKVGD-DT-VEIELGDGTKIKFEKEAIATVLE 90 (97)
T ss_pred HHHHhccCCCEEEEcC---------CeEEEEEEEec-Cc-EEEEECCCeEEEEEHHHHHhhcc
Confidence 3456677888898887 89999988543 22 2235556899999999998 443
No 11
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=60.65 E-value=10 Score=25.17 Aligned_cols=33 Identities=15% Similarity=0.297 Sum_probs=21.7
Q ss_pred cccchhHHHHHHHhcccccCCCCCCHHHHHHHHH
Q 027380 162 SKLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQ 195 (224)
Q Consensus 162 ~KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~ 195 (224)
.+|.++-||+.-..+++ +...+..|++|++-+.
T Consensus 2 ~sltV~~Lk~iL~~~~I-~~ps~AkKaeLv~L~~ 34 (35)
T PF12949_consen 2 KSLTVAQLKRILDEHGI-EFPSNAKKAELVALFN 34 (35)
T ss_dssp TT--SHHHHHHHHHHT----SSS--SHHHHHH--
T ss_pred CcCcHHHHHHHHHHcCC-CCCCCCCHHHHHHHHc
Confidence 56899999999999999 7788999999998653
No 12
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=57.96 E-value=17 Score=27.80 Aligned_cols=46 Identities=26% Similarity=0.515 Sum_probs=33.7
Q ss_pred ccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEe--ecCcEEEEeeceeeee
Q 027380 27 LSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVL--TNGIEVKLQRNALSVI 85 (224)
Q Consensus 27 lsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL--~NG~EVkLQRNALsvi 85 (224)
++-|=+.++|+-+| |++|.|.+- + + .+++| ..|.+++++|+|++-+
T Consensus 35 ~~~L~~Gd~VvT~g---------Gi~G~V~~i-~--d-~~v~vei~~g~~i~~~r~aI~~v 82 (84)
T TIGR00739 35 IESLKKGDKVLTIG---------GIIGTVTKI-A--E-NTIVIELNDNTEITFSKNAIVEV 82 (84)
T ss_pred HHhCCCCCEEEECC---------CeEEEEEEE-e--C-CEEEEEECCCeEEEEEhHHhhhc
Confidence 45566677888776 999999843 3 2 45554 5789999999998744
No 13
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=53.74 E-value=18 Score=27.19 Aligned_cols=38 Identities=21% Similarity=0.380 Sum_probs=29.7
Q ss_pred eEeeccceeeeccccCceEEEEeecCcEE------EEeeceeeee
Q 027380 47 VLVGLQGVVKKAVGLGGWHWLVLTNGIEV------KLQRNALSVI 85 (224)
Q Consensus 47 vLVGL~GVVkKAVGLGGWHWLvL~NG~EV------kLQRNALsvi 85 (224)
-++=+.|+|.+++| +|.=++.|.||.++ |+.+|-.-++
T Consensus 3 ~~ie~~G~V~e~L~-~~~f~V~l~ng~~vla~i~GKmr~~rI~I~ 46 (68)
T TIGR00008 3 DKIEMEGKVTESLP-NAMFRVELENGHEVLAHISGKIRMHYIRIL 46 (68)
T ss_pred cEEEEEEEEEEECC-CCEEEEEECCCCEEEEEecCcchhccEEEC
Confidence 45678899999999 45777899999998 5666666655
No 14
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=53.69 E-value=22 Score=28.41 Aligned_cols=49 Identities=29% Similarity=0.559 Sum_probs=37.5
Q ss_pred ccccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEe--ecCcEEEEeeceeeeec
Q 027380 25 EELSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVL--TNGIEVKLQRNALSVIE 86 (224)
Q Consensus 25 eelsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL--~NG~EVkLQRNALsviE 86 (224)
+-++-|=+.++|+-+| |++|.|.+.-+ ..++| ..|..+++-|+|++-+.
T Consensus 48 ~~~~~Lk~Gd~VvT~g---------Gi~G~Vv~i~~----~~v~lei~~g~~i~~~r~aI~~v~ 98 (106)
T PRK05585 48 KMLSSLAKGDEVVTNG---------GIIGKVTKVSE----DFVIIELNDDTEIKIQKSAIAAVL 98 (106)
T ss_pred HHHHhcCCCCEEEECC---------CeEEEEEEEeC----CEEEEEECCCeEEEEEhHHhhhhc
Confidence 4455677788888777 99999988643 46654 58899999999998653
No 15
>PLN02431 ferredoxin--nitrite reductase
Probab=52.46 E-value=12 Score=37.62 Aligned_cols=34 Identities=24% Similarity=0.371 Sum_probs=27.2
Q ss_pred ccccccccCcceEEEEecCC--ccceeE--eeccceee
Q 027380 23 SEEELSVLPRHTKVVVTGNN--RTKSVL--VGLQGVVK 56 (224)
Q Consensus 23 g~eelsvLPrhTkV~VTGNn--RTKsvL--VGL~GVVk 56 (224)
++.+++-|||+.|+-|+|.. .+.... ||+.++.+
T Consensus 245 ~~~~~~~LPrKfkiavsG~~~~~~~~~~nDigf~~~~~ 282 (587)
T PLN02431 245 GNPEITNLPRKWNVCVVGSHDLFEHPHINDLAYMPATK 282 (587)
T ss_pred CCcccccCCCCeEEEEecCccccccccccceEEEEEEE
Confidence 56788999999999999954 445444 89999877
No 16
>PF01077 NIR_SIR: Nitrite and sulphite reductase 4Fe-4S domain; InterPro: IPR006067 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP) (IPR005117 from INTERPRO), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a siroheme through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. In the E. coli SiR-HP enzyme (1.8.1.2 from EC), the iron is bound to cysteine residues at positions 433, 439, 478 and 482, the latter also forming the siroheme ligand.; GO: 0016491 oxidoreductase activity, 0020037 heme binding, 0051536 iron-sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 1ZJ8_B 1ZJ9_A 2AKJ_A 3VKT_A 3VKR_A 3VKS_A 3B0M_A 3B0N_A 3VKP_A 3B0J_A ....
Probab=40.25 E-value=32 Score=27.57 Aligned_cols=42 Identities=29% Similarity=0.439 Sum_probs=27.9
Q ss_pred ccccccCcceEEEEec--CCccceeE--eeccceeeeccccCceEEE
Q 027380 25 EELSVLPRHTKVVVTG--NNRTKSVL--VGLQGVVKKAVGLGGWHWL 67 (224)
Q Consensus 25 eelsvLPrhTkV~VTG--NnRTKsvL--VGL~GVVkKAVGLGGWHWL 67 (224)
.+..-||++-||-|+| |+.+...+ +|+.|+.++.-+- ||..+
T Consensus 39 ~~~~~lp~k~kI~isGCpn~C~~~~i~DIG~~g~~~~~~~~-g~~v~ 84 (157)
T PF01077_consen 39 FEDPNLPRKFKIAISGCPNSCARPQINDIGFIGVKKPNGEE-GFDVY 84 (157)
T ss_dssp HHCSCSSS-BEEEEESSTTSTTSGGGSSEEEEEEEESTCEE-EEEEE
T ss_pred ccccccccccccceeecccccccccccccccceeeeccccc-eeeee
Confidence 3455799999999998 45554443 8999988865443 34433
No 17
>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]
Probab=37.83 E-value=19 Score=32.17 Aligned_cols=17 Identities=41% Similarity=0.743 Sum_probs=13.6
Q ss_pred ccccCcceEEEEecCCc
Q 027380 27 LSVLPRHTKVVVTGNNR 43 (224)
Q Consensus 27 lsvLPrhTkV~VTGNnR 43 (224)
|.-=|.||.||+||++-
T Consensus 149 l~~kP~~~~vIiTGr~a 165 (198)
T COG2109 149 LKARPEHTHVIITGRGA 165 (198)
T ss_pred HhcCCCCcEEEEECCCC
Confidence 44558999999999764
No 18
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=36.76 E-value=44 Score=32.61 Aligned_cols=35 Identities=23% Similarity=0.451 Sum_probs=26.8
Q ss_pred ccccccccCcceEEEEecC--CccceeE--eeccceeee
Q 027380 23 SEEELSVLPRHTKVVVTGN--NRTKSVL--VGLQGVVKK 57 (224)
Q Consensus 23 g~eelsvLPrhTkV~VTGN--nRTKsvL--VGL~GVVkK 57 (224)
+..+.+-|||..||-|+|. +...... ||+.|+.+.
T Consensus 174 ~~~~~~~LPrKfki~vsGc~~~c~~~~i~DiG~~~~~~~ 212 (513)
T PRK09566 174 GNPEFSNLPRKFNIAIAGGRDNSVHAEINDIAFVPAYKD 212 (513)
T ss_pred CCCcccCCCCceEEEEECCCCCcccccccceEEEEEEEC
Confidence 4566788999999999994 5555544 899998763
No 19
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=35.67 E-value=48 Score=26.25 Aligned_cols=40 Identities=25% Similarity=0.550 Sum_probs=33.7
Q ss_pred ceeEeeccceeeeccccCceEEEEeecCcEE------EEeeceeeee
Q 027380 45 KSVLVGLQGVVKKAVGLGGWHWLVLTNGIEV------KLQRNALSVI 85 (224)
Q Consensus 45 KsvLVGL~GVVkKAVGLGGWHWLvL~NG~EV------kLQRNALsvi 85 (224)
|.-++=+.|+|.++++= +==++.|.||.+| |+.+|-+-++
T Consensus 3 ke~~ie~~G~V~e~Lp~-~~frV~LenG~~vla~isGKmR~~rIrIl 48 (87)
T PRK12442 3 KEELIELDGIVDEVLPD-SRFRVTLENGVEVGAYASGRMRKHRIRIL 48 (87)
T ss_pred ccceEEEEEEEEEECCC-CEEEEEeCCCCEEEEEeccceeeeeEEec
Confidence 44577889999999984 4667789999999 7899999988
No 20
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=31.87 E-value=38 Score=33.90 Aligned_cols=34 Identities=29% Similarity=0.361 Sum_probs=26.1
Q ss_pred ccccccccCcceEEEEecC--CccceeE--eeccceee
Q 027380 23 SEEELSVLPRHTKVVVTGN--NRTKSVL--VGLQGVVK 56 (224)
Q Consensus 23 g~eelsvLPrhTkV~VTGN--nRTKsvL--VGL~GVVk 56 (224)
++++++=|||+.||-|+|. +...... ||+.++.+
T Consensus 220 ~~~~~~~LPrKfkiaisg~~~~~~~~~~nDigf~a~~~ 257 (593)
T PRK09567 220 NDRSLYGLPRKFNVAFDGGGRIATLEDTNDIGFQAVRV 257 (593)
T ss_pred CCchhcCCCCCeEEEEECCCcccccccccceeeEEEEe
Confidence 3567788999999999985 4555544 79988875
No 21
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=28.93 E-value=45 Score=23.33 Aligned_cols=29 Identities=38% Similarity=0.674 Sum_probs=18.0
Q ss_pred cceeee-ccccCce--EEEEeecCcEEEEeeceeeeecCC
Q 027380 52 QGVVKK-AVGLGGW--HWLVLTNGIEVKLQRNALSVIEAP 88 (224)
Q Consensus 52 ~GVVkK-AVGLGGW--HWLvL~NG~EVkLQRNALsviE~P 88 (224)
.|.++| .=..++| +|+||.+ +.|..-..+
T Consensus 2 ~G~L~k~~~~~~~W~~r~~vl~~--------~~L~~~~~~ 33 (91)
T cd01246 2 EGWLLKWTNYLKGWQKRWFVLDN--------GLLSYYKNK 33 (91)
T ss_pred eEEEEEecccCCCceeeEEEEEC--------CEEEEEecC
Confidence 454443 4456999 7889864 456666443
No 22
>PF00054 Laminin_G_1: Laminin G domain; InterPro: IPR012679 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, which includes a large number of extracellular proteins. The C terminus of laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions has been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each has five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012680 from INTERPRO).; PDB: 1OKQ_A 1DYK_A 2C5D_A 1H30_A 1LHW_A 1KDK_A 1LHU_A 1KDM_A 1LHO_A 1D2S_A ....
Probab=27.05 E-value=89 Score=24.30 Aligned_cols=63 Identities=19% Similarity=0.276 Sum_probs=38.6
Q ss_pred ccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEe-ecCcEEEEeeceeee--ecCCCCCCc
Q 027380 27 LSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVL-TNGIEVKLQRNALSV--IEAPTGNEE 93 (224)
Q Consensus 27 lsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL-~NG~EVkLQRNALsv--iE~PtG~Ee 93 (224)
+++-=+.-+|.+.=|+-...+.+= .-. .+--|-||.+.+ .++..+.||=|...+ .+.|.|..-
T Consensus 22 ial~L~~G~l~~~~~~G~~~~~~~--~~~--~i~dg~wh~v~~~r~~~~~~L~Vd~~~~~~~~s~~~~~~ 87 (131)
T PF00054_consen 22 IALELRDGRLEFRYNLGSGPASLR--SPQ--KINDGKWHTVSVSRNGRNGSLSVDGEEVVTGESPSGATQ 87 (131)
T ss_dssp EEEEEETTEEEEEEESSSEEEEEE--ESS--ETTSSSEEEEEEEEETTEEEEEETTSEEEEEEECSSSSS
T ss_pred EEEEEECCEEEEEEeCCCccceec--CCC--ccCCCcceEEEEEEcCcEEEEEECCccceeeecCCcccc
Confidence 333334445555544443322221 111 277899999955 789999999888777 677765544
No 23
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=26.80 E-value=21 Score=26.90 Aligned_cols=47 Identities=26% Similarity=0.400 Sum_probs=0.8
Q ss_pred ccccCcceEEEEecCCccceeEeeccceeeeccccCceEEEEeecCcEEEEeeceeee
Q 027380 27 LSVLPRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVLTNGIEVKLQRNALSV 84 (224)
Q Consensus 27 lsvLPrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL~NG~EVkLQRNALsv 84 (224)
++-|=..++|+-+| |+.|.|.+- =+..==|.+.+|.++++.|+|+.-
T Consensus 34 ~~~Lk~Gd~VvT~g---------Gi~G~V~~i--~~~~v~lei~~g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 34 LASLKPGDEVVTIG---------GIYGTVVEI--DDDTVVLEIAPGVEITVEKSAIAR 80 (82)
T ss_dssp GG--------------------------------------------------------
T ss_pred HHcCCCCCEEEECC---------cEEEEEEEE--eCCEEEEEECCCeEEEEEHHHhHh
Confidence 34455566777666 999999887 444555677889999999999863
No 24
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=26.56 E-value=69 Score=24.44 Aligned_cols=35 Identities=20% Similarity=0.335 Sum_probs=26.8
Q ss_pred cceeeeccccCceEEEEeecCcEE------------EEeeceeeeecC
Q 027380 52 QGVVKKAVGLGGWHWLVLTNGIEV------------KLQRNALSVIEA 87 (224)
Q Consensus 52 ~GVVkKAVGLGGWHWLvL~NG~EV------------kLQRNALsviE~ 87 (224)
-|+|.++.| ++.+-+.|.||.++ ++.|.-.-++|+
T Consensus 8 ~g~V~~~lG-~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 8 IAQVVKMLG-NGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred EEEEEEEcC-CCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 488999999 66999999999876 355666666653
No 25
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=25.16 E-value=1e+02 Score=22.50 Aligned_cols=39 Identities=10% Similarity=0.235 Sum_probs=27.3
Q ss_pred cccccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhhc
Q 027380 160 DLSKLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHFM 199 (224)
Q Consensus 160 DL~KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF~ 199 (224)
-|++|..+-...-..-+.+ +-.++.+|+||+..--+-|+
T Consensus 12 ~FSRl~k~eMiaem~~~G~-~y~~~~tK~~Lvk~fkKql~ 50 (54)
T PF09124_consen 12 WFSRLTKPEMIAEMDSYGF-EYNEKDTKAQLVKIFKKQLK 50 (54)
T ss_dssp HHHTS-HHHHHHHHHHTT-----TTS-HHHHHHHHHHHHH
T ss_pred HHHhcCHHHHHHHHHHhCC-cCCccccHHHHHHHHHHHHH
Confidence 5788888888888878777 77899999999998777664
No 26
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=25.11 E-value=1.1e+02 Score=28.46 Aligned_cols=40 Identities=23% Similarity=0.320 Sum_probs=34.2
Q ss_pred ccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhhccccC
Q 027380 163 KLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHFMSQQM 203 (224)
Q Consensus 163 KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF~sq~V 203 (224)
|..-.-|=+|-.-.++ .+.|+++|.+|+..+..+|.++..
T Consensus 60 kV~RelLFkYLa~kgv-~v~p~s~K~~LI~~~l~~W~~~~~ 99 (262)
T PF15008_consen 60 KVKRELLFKYLASKGV-IVPPDSEKADLIQRVLQYWSSQLQ 99 (262)
T ss_pred cccHHHHHHHHHHcCC-CCCCCccHHHHHHHHHHHHhcccc
Confidence 4566788999999988 778999999999999999987653
No 27
>PF14321 DUF4382: Domain of unknown function (DUF4382)
Probab=23.82 E-value=1.6e+02 Score=23.48 Aligned_cols=47 Identities=30% Similarity=0.356 Sum_probs=34.0
Q ss_pred ceeEeeccceeeeccccCceEEEEeecCcEEEE--eece----eeeecCCCCCC
Q 027380 45 KSVLVGLQGVVKKAVGLGGWHWLVLTNGIEVKL--QRNA----LSVIEAPTGNE 92 (224)
Q Consensus 45 KsvLVGL~GVVkKAVGLGGWHWLvL~NG~EVkL--QRNA----LsviE~PtG~E 92 (224)
.+|.|.+..|.=+-.+-++|+|+-+. ..+|-| +.|. |.-.|-|.|.=
T Consensus 18 ~~v~v~i~~v~~~~~~~~~~~~~~~~-~~~vdLl~l~~g~~~~l~~~~lpaG~Y 70 (139)
T PF14321_consen 18 DSVNVTISSVELHPSDGGDGGWVTLD-PQTVDLLDLQNGVSQLLADAELPAGTY 70 (139)
T ss_pred CEEEEEEEEEEEEECCCCCceEEEcC-CceEEeehccCCceEEEeccccCCCcE
Confidence 56778888888888888899999998 556665 3332 55667777753
No 28
>PRK01833 tatA twin arginine translocase protein A; Provisional
Probab=23.74 E-value=8.1 Score=29.53 Aligned_cols=9 Identities=33% Similarity=1.003 Sum_probs=5.5
Q ss_pred ccCceEEEE
Q 027380 60 GLGGWHWLV 68 (224)
Q Consensus 60 GLGGWHWLv 68 (224)
|+|.||||+
T Consensus 3 g~g~~elli 11 (74)
T PRK01833 3 GISIWQLLI 11 (74)
T ss_pred CccHHHHHH
Confidence 466666664
No 29
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=23.61 E-value=90 Score=22.21 Aligned_cols=25 Identities=36% Similarity=0.638 Sum_probs=19.6
Q ss_pred HHHH-HhcccccCCCCCCHHHHHHHHHhhhccc
Q 027380 170 WRYW-RHFNLVDAIPNPSREQLIDVVQRHFMSQ 201 (224)
Q Consensus 170 rRYk-khfkL~~~~P~~sKeQLv~aV~rHF~sq 201 (224)
.+|| +.|++ |.+||..||.++-.+.
T Consensus 23 v~ywa~~~gv-------t~~~L~~AV~~vG~~~ 48 (57)
T PF12244_consen 23 VRYWAKRFGV-------TEEQLREAVRAVGNSR 48 (57)
T ss_pred HHHHHHHHCc-------CHHHHHHHHHHHCcCH
Confidence 4566 88866 7799999999998664
No 30
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=22.46 E-value=65 Score=21.97 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=15.4
Q ss_pred cccccchhHHHHHHHhcccc
Q 027380 160 DLSKLEMGALWRYWRHFNLV 179 (224)
Q Consensus 160 DL~KLe~~TLrRYkkhfkL~ 179 (224)
....+...|||+|.+.+.+.
T Consensus 8 ~~~gvs~~tlr~w~~~~g~~ 27 (68)
T cd01104 8 RLTGVSPDTLRAWERRYGLP 27 (68)
T ss_pred HHHCcCHHHHHHHHHhCCCC
Confidence 34557889999999877664
No 31
>PRK00720 tatA twin arginine translocase protein A; Provisional
Probab=21.96 E-value=9 Score=29.62 Aligned_cols=9 Identities=44% Similarity=1.472 Sum_probs=5.4
Q ss_pred ccCceEEEE
Q 027380 60 GLGGWHWLV 68 (224)
Q Consensus 60 GLGGWHWLv 68 (224)
|+|.||||+
T Consensus 3 g~g~~ellI 11 (78)
T PRK00720 3 SFSIWHWLI 11 (78)
T ss_pred CCcHHHHHH
Confidence 466666663
No 32
>COG0155 CysI Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]
Probab=21.61 E-value=93 Score=31.15 Aligned_cols=45 Identities=29% Similarity=0.462 Sum_probs=31.5
Q ss_pred ccccccccCcceEEEEecCCccc----eeEeeccceeeeccccCceEEEE
Q 027380 23 SEEELSVLPRHTKVVVTGNNRTK----SVLVGLQGVVKKAVGLGGWHWLV 68 (224)
Q Consensus 23 g~eelsvLPrhTkV~VTGNnRTK----svLVGL~GVVkKAVGLGGWHWLv 68 (224)
++.|.+-|||..||.|+|.-+-- +-=|||..+.+ --|+-||.-+|
T Consensus 161 ~~~~~~~LPRKFkiav~g~~~~~v~~~~~Di~~~a~~~-~~~~~Gf~v~V 209 (510)
T COG0155 161 GEKGFAYLPRKFKIAVDGGPDNDVDVLINDIGFVAIKE-NDGLLGFNVLV 209 (510)
T ss_pred CccchhcCCcceEEEEecCcccchhhhccceeEEEecc-cCCccceEEEE
Confidence 34579999999999999974321 12267777766 56777777664
No 33
>PF03743 TrbI: Bacterial conjugation TrbI-like protein ; InterPro: IPR005498 This entry represents type IV secretion system proteins VirB10, TraB and TrbI. Type IV secretion systems are found in plant and animal pathogens, as well as in symbiotic bacteria. The tumour-inducing (Ti) plasmid of Rhizobium radiobacter (Agrobacterium tumefaciens) encodes various DNA transfer systems: VirB, Tra and Trb, where the virB operon is required for the transfer DNA to the plant host and the tra/trb systems are required for the conjugal transfer of the Ti plasmid between cells of Agrobacterium [, ]. Of the two unlinked regions of octopine-type Ti plasmids that contain genes required for conjugal transfer, the tra gene cluster is probably required for conjugal DNA processing, whilst the other gene cluster, trb, probably directs the synthesis of a conjugal pilus and mating pore []. It has been suggested that TraB extends into the periplasmic space and is anchored in the inner membrane via a single transmembrane segment near the N terminus. It is also thought that TraB may interact with TraP, in order to stabilise the proposed transmembrane complex formed by the tra operon products []. The trbI gene encodes a 128-amino-acid polypeptide that is an intrinsic inner-membrane protein. TrbI may influence the kinetics of pilus outgrowth and/or retraction []. Although not essential for conjugation, the TrbI protein greatly increases conjugational efficiency []. In Plasmid pTiC58, all of the trb genes except trbI and trbK are essential for conjugal transfer [].; PDB: 2BHV_E 3JQO_b.
Probab=21.43 E-value=1.3e+02 Score=24.76 Aligned_cols=44 Identities=16% Similarity=0.319 Sum_probs=24.8
Q ss_pred ccccc-CcceEEEEecCCccceeEeeccceeeeccccCceEEEEeecCcEEEEe
Q 027380 26 ELSVL-PRHTKVVVTGNNRTKSVLVGLQGVVKKAVGLGGWHWLVLTNGIEVKLQ 78 (224)
Q Consensus 26 elsvL-PrhTkV~VTGNnRTKsvLVGL~GVVkKAVGLGGWHWLvL~NG~EVkLQ 78 (224)
.--+| |+.|+|+-+.+.--. .|.+ --.--|.+++++||..+.+.
T Consensus 38 g~~~lip~Gs~l~G~~~~~~s------~~~~---r~~~~~~~~i~p~G~~i~~~ 82 (187)
T PF03743_consen 38 GRRVLIPKGSRLIGEYTGDLS------SGQV---RVRVVWTRIIFPDGRSIDIP 82 (187)
T ss_dssp SSBEEE-TT-EEEEEEECEES------TTSE---EEEEEEEEEE-TT-EEEECS
T ss_pred CCEecccCCCEEEEEEeeccc------cccc---eEEEEEEEEEeCCCCEEEEC
Confidence 34556 999999887644211 0111 11234999999999999998
No 34
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=21.02 E-value=99 Score=24.50 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=20.7
Q ss_pred ccceeeeccccCceEEEEeecCcEEE
Q 027380 51 LQGVVKKAVGLGGWHWLVLTNGIEVK 76 (224)
Q Consensus 51 L~GVVkKAVGLGGWHWLvL~NG~EVk 76 (224)
+-|+|.++.| ++.+...|.||.++-
T Consensus 21 ~~g~V~~~lG-~~~~~V~~~dG~~~l 45 (99)
T TIGR00523 21 ILGVIEQMLG-AGRVKVRCLDGKTRL 45 (99)
T ss_pred EEEEEEEEcC-CCEEEEEeCCCCEEE
Confidence 3578999999 569999999998863
No 35
>COG2193 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]
Probab=20.89 E-value=65 Score=28.06 Aligned_cols=44 Identities=16% Similarity=0.273 Sum_probs=33.8
Q ss_pred ccchhHHHHHHHhcccccCCCCCCHHHHHHHHHhhhccccCChHHHHHHHH
Q 027380 163 KLEMGALWRYWRHFNLVDAIPNPSREQLIDVVQRHFMSQQMDELQVIVGFV 213 (224)
Q Consensus 163 KLe~~TLrRYkkhfkL~~~~P~~sKeQLv~aV~rHF~sq~VdE~eVI~~Fi 213 (224)
.++..++-+|+.|+.+ -.+++.++ +..||..+-++|-.=-..++
T Consensus 16 ~~EL~ainQYflHsrM-~~~WG~~~------L~~~~~~esi~Em~HAd~li 59 (157)
T COG2193 16 GLELAAINQYFLHSRM-YKNWGLTK------LAAHEYHESIEEMKHADQLI 59 (157)
T ss_pred HHHHHHHHHHHHHHHH-HhCcChHH------HHHHHHHHHHHHHHHHHHHH
Confidence 3678899999999999 55899998 88899887777754433333
No 36
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=20.57 E-value=1.3e+02 Score=22.44 Aligned_cols=33 Identities=9% Similarity=0.152 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHhhhcc-ccCChHHHHHHHHHHHh
Q 027380 185 PSREQLIDVVQRHFMS-QQMDELQVIVGFVQAAK 217 (224)
Q Consensus 185 ~sKeQLv~aV~rHF~s-q~VdE~eVI~~Fi~avK 217 (224)
++|.+|++.|.++... -+-+=.++|..|+..+.
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~~~i~ 34 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLEHMA 34 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence 4799999999987543 22344567888877653
No 37
>PF13588 HSDR_N_2: Type I restriction enzyme R protein N terminus (HSDR_N); PDB: 3H1T_A.
Probab=20.53 E-value=74 Score=24.01 Aligned_cols=15 Identities=40% Similarity=0.620 Sum_probs=10.7
Q ss_pred ceEEEEeecCcEEEE
Q 027380 63 GWHWLVLTNGIEVKL 77 (224)
Q Consensus 63 GWHWLvL~NG~EVkL 77 (224)
+=.|.+||||.+.++
T Consensus 81 ~~~~~i~tNG~~~~~ 95 (112)
T PF13588_consen 81 GAPYGILTNGKEFRF 95 (112)
T ss_dssp T-SEEEEE-SS-EEE
T ss_pred CCCEEEEECCCeEEE
Confidence 678999999999876
No 38
>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=20.44 E-value=60 Score=27.43 Aligned_cols=20 Identities=35% Similarity=0.509 Sum_probs=16.1
Q ss_pred cccccCcceEEEEecCCccc
Q 027380 26 ELSVLPRHTKVVVTGNNRTK 45 (224)
Q Consensus 26 elsvLPrhTkV~VTGNnRTK 45 (224)
-|.--|.++.||+||.|=.+
T Consensus 121 ll~~rp~~~evIlTGr~~p~ 140 (159)
T cd00561 121 LLKAKPEDLELVLTGRNAPK 140 (159)
T ss_pred HHHcCCCCCEEEEECCCCCH
Confidence 35567999999999998554
No 39
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.14 E-value=59 Score=22.25 Aligned_cols=23 Identities=22% Similarity=0.036 Sum_probs=18.4
Q ss_pred cccccchhHHHHHHHhcccccCC
Q 027380 160 DLSKLEMGALWRYWRHFNLVDAI 182 (224)
Q Consensus 160 DL~KLe~~TLrRYkkhfkL~~~~ 182 (224)
.+..+...|||.|.+.+-|+...
T Consensus 8 ~~~gvs~~tlr~y~~~gll~~~~ 30 (69)
T PF13411_consen 8 KLLGVSPSTLRYYEREGLLPPPR 30 (69)
T ss_dssp HHTTTTHHHHHHHHHTTSSTTBE
T ss_pred HHHCcCHHHHHHHHHhcCccccc
Confidence 45567889999999999986554
Done!