Query 033311
Match_columns 122
No_of_seqs 106 out of 213
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 12:21:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033311.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033311hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3440 Ubiquinol cytochrome c 100.0 1.7E-49 3.6E-54 291.8 10.1 111 5-122 12-122 (122)
2 PF02271 UCR_14kD: Ubiquinol-c 100.0 2.1E-47 4.6E-52 275.5 10.2 100 4-110 6-105 (105)
3 KOG1673 Ras GTPases [General f 48.0 17 0.00036 29.3 2.5 37 13-53 108-150 (205)
4 COG0568 RpoD DNA-directed RNA 48.0 12 0.00026 32.3 1.8 34 24-58 118-151 (342)
5 PF00462 Glutaredoxin: Glutare 36.1 26 0.00056 21.2 1.5 32 22-54 13-44 (60)
6 TIGR03761 ICE_PFL4669 integrat 33.2 64 0.0014 26.1 3.7 40 16-59 158-200 (216)
7 PRK07122 RNA polymerase sigma 31.6 43 0.00093 26.8 2.5 55 26-82 58-121 (264)
8 PF08134 cIII: cIII protein fa 30.0 61 0.0013 20.3 2.4 18 55-72 18-35 (44)
9 TIGR00365 monothiol glutaredox 28.6 54 0.0012 22.4 2.3 31 23-54 32-62 (97)
10 PF07881 Fucose_iso_N1: L-fuco 25.5 62 0.0013 25.6 2.4 46 20-70 117-163 (171)
11 PF08707 PriCT_2: Primase C te 23.2 55 0.0012 21.5 1.5 24 46-69 1-24 (78)
12 PF12536 DUF3734: Patatin phos 22.6 84 0.0018 22.3 2.4 49 45-93 22-74 (108)
13 TIGR02606 antidote_CC2985 puta 21.7 77 0.0017 20.8 1.9 31 43-75 26-56 (69)
14 PRK05658 RNA polymerase sigma 21.1 62 0.0013 29.3 1.8 50 26-77 398-452 (619)
15 PF11387 DUF2795: Protein of u 20.8 47 0.001 20.2 0.7 16 44-59 23-38 (44)
16 TIGR02393 RpoD_Cterm RNA polym 20.5 76 0.0016 24.6 2.0 57 27-84 19-83 (238)
17 PF02809 UIM: Ubiquitin intera 20.2 52 0.0011 16.7 0.7 11 65-75 6-16 (18)
No 1
>KOG3440 consensus Ubiquinol cytochrome c reductase, subunit QCR7 [Energy production and conversion]
Probab=100.00 E-value=1.7e-49 Score=291.83 Aligned_cols=111 Identities=50% Similarity=0.693 Sum_probs=105.3
Q ss_pred HHHhhchhhHHHHHHHHHHhhhHHhhhccccccCCCCCCChHHHHHHhcCCHHHHHHHHHHHHHHHhhhccccCCChhhh
Q 033311 5 LQSLLDPKKNWLAAQHMKTISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPREIVDARNQRLKRAMDLSMKHEYLPEDLQ 84 (122)
Q Consensus 5 L~k~~~P~~~~~a~~y~~~~g~~yrk~GL~yDDl~~e~e~~~V~eALrRLP~~~~~~R~~Ri~RA~qlS~~h~~LPkeqw 84 (122)
+.++|.| +.+|++|++| ||||||+||||+.| +|++|+|||+|||++++|+|++||+||+||||+|++|||+||
T Consensus 12 ~~k~~~~----~~~~~~nl~g--~rkyGL~~DDl~~e-~n~dvkeAlrRLPr~~~d~R~~Ri~RA~~Lsm~h~~LPk~ew 84 (122)
T KOG3440|consen 12 LGKLFLP----LRKWAYNLSG--FRKYGLRYDDLYYE-ENEDVKEALRRLPRELYDARNYRIKRAMDLSMTHEILPKEEW 84 (122)
T ss_pred chHHHHH----HHHHHHHHhh--hhhhCccccccccc-cCHHHHHHHHHCcHHHHHHHHHHHHHHHHHhhhcccCCHHHh
Confidence 4455555 8899999987 99999999999999 799999999999999999999999999999999999999999
Q ss_pred hcccCCcchhHHHHHHHHHHHHHHHHhCCCCcccccCC
Q 033311 85 AMQTPFRNYLQDMLALVKREKAEREALGALPLYQRTIP 122 (122)
Q Consensus 85 tk~eed~~YL~P~i~eV~~E~~Er~~~d~~~~~~r~~~ 122 (122)
||++||++||+|||.||++|++||++||+++||.|.+|
T Consensus 85 tk~eed~~YL~pyL~ev~~ErkERee~~~l~~~~~~~~ 122 (122)
T KOG3440|consen 85 TKYEEDVKYLEPYLAEVEAERKEREELDALIVYKRTKQ 122 (122)
T ss_pred hcccchhhHHHHHHHHHHHHHHHHHHhhCCCCCcccCC
Confidence 99999999999999999999999999999999999876
No 2
>PF02271 UCR_14kD: Ubiquinol-cytochrome C reductase complex 14kD subunit; InterPro: IPR003197 The cytochrome bd type terminal oxidases catalyse quinol dependent, Na+ independent oxygen uptake []. Members of this family are integral membrane proteins and contain a protoheame IX centre B558. Cytochrome bd may play an important role in microaerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae, where it is expressed under all conditions that permit diazotrophy []. The 14 kDa (or VI) subunit of the complex is not directly involved in electron transfer, but has a role in assembly of the complex [].; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006122 mitochondrial electron transport, ubiquinol to cytochrome c; PDB: 3L74_F 3H1K_F 3L72_F 3H1L_S 3L71_S 3L70_S 3L73_F 3L75_F 1P84_G 3CXH_G ....
Probab=100.00 E-value=2.1e-47 Score=275.53 Aligned_cols=100 Identities=42% Similarity=0.642 Sum_probs=81.9
Q ss_pred HHHHhhchhhHHHHHHHHHHhhhHHhhhccccccCCCCCCChHHHHHHhcCCHHHHHHHHHHHHHHHhhhccccCCChhh
Q 033311 4 LLQSLLDPKKNWLAAQHMKTISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPREIVDARNQRLKRAMDLSMKHEYLPEDL 83 (122)
Q Consensus 4 ~L~k~~~P~~~~~a~~y~~~~g~~yrk~GL~yDDl~~e~e~~~V~eALrRLP~~~~~~R~~Ri~RA~qlS~~h~~LPkeq 83 (122)
.|+++++| +++||+|++| ||||||+||||++| +||+|+|||+|||+++.++|+|||+||+|||++|++|||||
T Consensus 6 ~~~~~~~~----~~~w~~n~~g--yrk~GL~~DDl~~e-~~~~v~eAl~RLp~~~~~~R~~Ri~RA~~ls~~~~~LPke~ 78 (105)
T PF02271_consen 6 WLSKFFKP----LAKWYYNASG--YRKYGLRYDDLLNE-EDPDVQEALRRLPPDEQYDRNFRIKRAMQLSLKHQYLPKEQ 78 (105)
T ss_dssp HHHHHHHH----HHHHHHHHHG--GGGGT--GGGGS----SHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHT----GGG
T ss_pred HHHHHHHH----HHHHHHHhcc--hhhhcccHHhccCC-CCHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhcccCCHHH
Confidence 46777777 9999999876 99999999999999 89999999999999999999999999999999999999999
Q ss_pred hhcccCCcchhHHHHHHHHHHHHHHHH
Q 033311 84 QAMQTPFRNYLQDMLALVKREKAEREA 110 (122)
Q Consensus 84 wtk~eed~~YL~P~i~eV~~E~~Er~~ 110 (122)
|||+++|++||+|||+||++|++||++
T Consensus 79 wtk~e~d~~YL~p~i~ev~~E~~Er~e 105 (105)
T PF02271_consen 79 WTKPEEDVPYLQPYIEEVEKERKEREE 105 (105)
T ss_dssp S--GGGS--SSHHHHHHHHHHHHHHHH
T ss_pred ccCcccchHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999986
No 3
>KOG1673 consensus Ras GTPases [General function prediction only]
Probab=48.02 E-value=17 Score=29.28 Aligned_cols=37 Identities=22% Similarity=0.325 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHhhhHHhh------hccccccCCCCCCChHHHHHHhc
Q 033311 13 KNWLAAQHMKTISKRLRN------FGLRYDDLYDPYYDLDIKEALDR 53 (122)
Q Consensus 13 ~~~~a~~y~~~~g~~yrk------~GL~yDDl~~e~e~~~V~eALrR 53 (122)
+|.+-.||..|-| +|| .|-+||+++.= .|+.|+-+.|
T Consensus 108 LnSi~~WY~QAr~--~NktAiPilvGTKyD~fi~l--p~e~Q~~I~~ 150 (205)
T KOG1673|consen 108 LNSIKEWYRQARG--LNKTAIPILVGTKYDLFIDL--PPELQETISR 150 (205)
T ss_pred HHHHHHHHHHHhc--cCCccceEEeccchHhhhcC--CHHHHHHHHH
Confidence 4667789988866 998 58999999964 6888887765
No 4
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=47.96 E-value=12 Score=32.27 Aligned_cols=34 Identities=24% Similarity=0.417 Sum_probs=29.6
Q ss_pred hhhHHhhhccccccCCCCCCChHHHHHHhcCCHHH
Q 033311 24 ISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPREI 58 (122)
Q Consensus 24 ~g~~yrk~GL~yDDl~~e~e~~~V~eALrRLP~~~ 58 (122)
++++|..+||-+-||+.| .|.-+.+|+.+..++-
T Consensus 118 IAk~Y~~rGL~~~DLIQE-GniGLmkAVekFdp~r 151 (342)
T COG0568 118 IAKKYTGRGLPFLDLIQE-GNIGLMKAVEKFDPEK 151 (342)
T ss_pred HHHHhhcCCCcHHHHHhc-ccHHHHHHHHhcCccc
Confidence 345799999999999999 7999999999988753
No 5
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=36.10 E-value=26 Score=21.18 Aligned_cols=32 Identities=25% Similarity=0.369 Sum_probs=23.6
Q ss_pred HHhhhHHhhhccccccCCCCCCChHHHHHHhcC
Q 033311 22 KTISKRLRNFGLRYDDLYDPYYDLDIKEALDRL 54 (122)
Q Consensus 22 ~~~g~~yrk~GL~yDDl~~e~e~~~V~eALrRL 54 (122)
..+-+.+++.|+.|+.+-.+ .++..+++|+.+
T Consensus 13 ~~~~~~L~~~~i~y~~~dv~-~~~~~~~~l~~~ 44 (60)
T PF00462_consen 13 KKAKEFLDEKGIPYEEVDVD-EDEEAREELKEL 44 (60)
T ss_dssp HHHHHHHHHTTBEEEEEEGG-GSHHHHHHHHHH
T ss_pred HHHHHHHHHcCCeeeEcccc-cchhHHHHHHHH
Confidence 34446689999999988777 577777777653
No 6
>TIGR03761 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=33.22 E-value=64 Score=26.09 Aligned_cols=40 Identities=25% Similarity=0.440 Sum_probs=29.3
Q ss_pred HHHHHHHHhhhHHhhhccccccCCCCCCChHHHHHHhc---CCHHHH
Q 033311 16 LAAQHMKTISKRLRNFGLRYDDLYDPYYDLDIKEALDR---LPREIV 59 (122)
Q Consensus 16 ~a~~y~~~~g~~yrk~GL~yDDl~~e~e~~~V~eALrR---LP~~~~ 59 (122)
+-+-|.-+. .||-.|+-.||... .|+..++|+.+ ||+++.
T Consensus 158 vR~vf~~~~--~yr~~gvtR~D~~~--~n~~a~~Aie~~G~lp~dIL 200 (216)
T TIGR03761 158 IRRLFGLAQ--RYRHSGVTRDDFAA--NNARARKAIERFGELPQDIL 200 (216)
T ss_pred HHHHHHHHH--hhhcCCCCHHHHHh--CCHHHHHHHHHcCCCCHHHH
Confidence 334344443 49999999999984 49999999988 455554
No 7
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=31.56 E-value=43 Score=26.85 Aligned_cols=55 Identities=16% Similarity=0.228 Sum_probs=41.2
Q ss_pred hHHhhhccccccCCCCCCChHHHHHHhcCCHHH-----HHHHHHHHHHHHhhhccccC----CChh
Q 033311 26 KRLRNFGLRYDDLYDPYYDLDIKEALDRLPREI-----VDARNQRLKRAMDLSMKHEY----LPED 82 (122)
Q Consensus 26 ~~yrk~GL~yDDl~~e~e~~~V~eALrRLP~~~-----~~~R~~Ri~RA~qlS~~h~~----LPke 82 (122)
..|...|+-+|||+.+ -+--+-+|+.+..+.- .| =.++|+-++.-.+.+.. +|..
T Consensus 58 ~~y~~~g~~~~DLiQe-G~iGLi~AierFDp~~G~~FsTY-A~~~Irg~I~~~lr~~~~~ir~Pr~ 121 (264)
T PRK07122 58 RRFDGRGEPRDDLVQV-ARVGLVNAVNRFDVETGSDFVSF-AVPTIMGEVRRHFRDNSWSVKVPRR 121 (264)
T ss_pred HHHHhCCCCHHHHHHH-HHHHHHHHHHHcCCCCCCChHHH-HHHHHHHHHHHHHHHcCCccccCHH
Confidence 4566679999999998 6788899999998742 34 45688888877776543 5644
No 8
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=30.00 E-value=61 Score=20.28 Aligned_cols=18 Identities=28% Similarity=0.259 Sum_probs=13.6
Q ss_pred CHHHHHHHHHHHHHHHhh
Q 033311 55 PREIVDARNQRLKRAMDL 72 (122)
Q Consensus 55 P~~~~~~R~~Ri~RA~ql 72 (122)
++.|.--|++|++||...
T Consensus 18 ~ESELskr~rrLIRaa~k 35 (44)
T PF08134_consen 18 TESELSKRIRRLIRAARK 35 (44)
T ss_pred cHHHHHHHHHHHHHHHHH
Confidence 355677799999999743
No 9
>TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation.
Probab=28.62 E-value=54 Score=22.41 Aligned_cols=31 Identities=13% Similarity=0.243 Sum_probs=23.3
Q ss_pred HhhhHHhhhccccccCCCCCCChHHHHHHhcC
Q 033311 23 TISKRLRNFGLRYDDLYDPYYDLDIKEALDRL 54 (122)
Q Consensus 23 ~~g~~yrk~GL~yDDl~~e~e~~~V~eALrRL 54 (122)
.+-+-+++.|+.|..+=.+ +++.++++|..+
T Consensus 32 ~ak~lL~~~~i~~~~~di~-~~~~~~~~l~~~ 62 (97)
T TIGR00365 32 RAVQILKACGVPFAYVNVL-EDPEIRQGIKEY 62 (97)
T ss_pred HHHHHHHHcCCCEEEEECC-CCHHHHHHHHHH
Confidence 3445689999999987665 678888887754
No 10
>PF07881 Fucose_iso_N1: L-fucose isomerase, first N-terminal domain; InterPro: IPR012888 Proteins containing this domain are similar to L-fucose isomerase expressed by Escherichia coli (P11552 from SWISSPROT, 5.3.1.3 from EC). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta-sheets with surrounding alpha helices. Domain 1 demonstrates the beta-alpha-beta-alpha- beta Rossman fold. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues, and domain 1 from the adjacent subunit contributing some other residues []. ; GO: 0008736 L-fucose isomerase activity, 0006004 fucose metabolic process, 0005737 cytoplasm; PDB: 3A9R_A 3A9T_C 3A9S_C 1FUI_E.
Probab=25.45 E-value=62 Score=25.62 Aligned_cols=46 Identities=20% Similarity=0.319 Sum_probs=22.6
Q ss_pred HHHHhhhHHhhhccccccCCCCCCChHHHHHHh-cCCHHHHHHHHHHHHHHH
Q 033311 20 HMKTISKRLRNFGLRYDDLYDPYYDLDIKEALD-RLPREIVDARNQRLKRAM 70 (122)
Q Consensus 20 y~~~~g~~yrk~GL~yDDl~~e~e~~~V~eALr-RLP~~~~~~R~~Ri~RA~ 70 (122)
|..+++..++|.||..-=++- .+||.+=. .+|+++. +++-|..||.
T Consensus 117 yLaAa~aa~~Q~Gip~f~IyG----~~vqD~~D~~ip~dV~-eKll~farAa 163 (171)
T PF07881_consen 117 YLAAALAAHNQKGIPAFRIYG----HDVQDADDTSIPEDVQ-EKLLRFARAA 163 (171)
T ss_dssp HHHHHHHHHHHCT---EEEE-----SS---TT--S--HHHH-HHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCcceeecc----ccccCCCCCcCcHHHH-HHHHHHHHHH
Confidence 566777789999998765553 23444333 4555533 3666676664
No 11
>PF08707 PriCT_2: Primase C terminal 2 (PriCT-2) ; InterPro: IPR014819 This alpha helical domain is found at the C-terminal of primases. ; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=23.22 E-value=55 Score=21.51 Aligned_cols=24 Identities=38% Similarity=0.710 Sum_probs=17.3
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHH
Q 033311 46 DIKEALDRLPREIVDARNQRLKRA 69 (122)
Q Consensus 46 ~V~eALrRLP~~~~~~R~~Ri~RA 69 (122)
+|++||+-||++...+|.-=++.+
T Consensus 1 ~~~~~L~~i~~~~~~~y~~W~~vg 24 (78)
T PF08707_consen 1 DIREALDHIPPDIADDYDDWIRVG 24 (78)
T ss_pred CHHHHHhcCCcccccCHHHHHHHH
Confidence 478999999998655555555544
No 12
>PF12536 DUF3734: Patatin phospholipase ; InterPro: IPR021095 This entry represents bacterial proteins of approximately 110 amino acids in length. These proteins are found in association with PF01734 from PFAM. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.
Probab=22.63 E-value=84 Score=22.29 Aligned_cols=49 Identities=20% Similarity=0.260 Sum_probs=34.9
Q ss_pred hHHHHHHhcCCHHHHHHHHHHHHHHHhh----hccccCCChhhhhcccCCcch
Q 033311 45 LDIKEALDRLPREIVDARNQRLKRAMDL----SMKHEYLPEDLQAMQTPFRNY 93 (122)
Q Consensus 45 ~~V~eALrRLP~~~~~~R~~Ri~RA~ql----S~~h~~LPkeqwtk~eed~~Y 93 (122)
-.|.+.+.+||+++..+-..+..+.+.| ++-|-+-+...+--...|..+
T Consensus 22 ~~i~~Ll~~lP~~~r~dp~~~~l~~~~~~~~~~IvhLiy~~~~~e~~sKDyeF 74 (108)
T PF12536_consen 22 HAIRELLERLPEELRDDPDVRELAELGCGKRVNIVHLIYRRKPYEGHSKDYEF 74 (108)
T ss_pred HHHHHHHHcCCHHHhCCHHHHHHHHhcCCCceEEEEeecCCCCccccccCccC
Confidence 5688999999999988888888887766 455555566666544444443
No 13
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=21.66 E-value=77 Score=20.84 Aligned_cols=31 Identities=19% Similarity=0.189 Sum_probs=23.0
Q ss_pred CChHHHHHHhcCCHHHHHHHHHHHHHHHhhhcc
Q 033311 43 YDLDIKEALDRLPREIVDARNQRLKRAMDLSMK 75 (122)
Q Consensus 43 e~~~V~eALrRLP~~~~~~R~~Ri~RA~qlS~~ 75 (122)
-+.+|.+|||.|-.++ ++.-.|+.+++-.+.
T Consensus 26 ~SEVir~aLR~le~~e--~~~~~Lr~~i~~g~~ 56 (69)
T TIGR02606 26 ASEVVRAALRLLEERE--TKLQALRDAIEEGEQ 56 (69)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHh
Confidence 3689999999887776 466777777765544
No 14
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=21.10 E-value=62 Score=29.28 Aligned_cols=50 Identities=20% Similarity=0.337 Sum_probs=36.8
Q ss_pred hHHhhhccccccCCCCCCChHHHHHHhcCCHH-----HHHHHHHHHHHHHhhhcccc
Q 033311 26 KRLRNFGLRYDDLYDPYYDLDIKEALDRLPRE-----IVDARNQRLKRAMDLSMKHE 77 (122)
Q Consensus 26 ~~yrk~GL~yDDl~~e~e~~~V~eALrRLP~~-----~~~~R~~Ri~RA~qlS~~h~ 77 (122)
+.|+..|+-++||+.| -|--.-+|+.+..+. ..| =.++|+.|+.-++..+
T Consensus 398 ~ky~~~gl~~~DLiQe-G~iGL~~Av~kfd~~~G~~FstY-A~~wIr~aI~~~i~~~ 452 (619)
T PRK05658 398 KKYTNRGLQFLDLIQE-GNIGLMKAVDKFEYRRGYKFSTY-ATWWIRQAITRSIADQ 452 (619)
T ss_pred HHHhhCCCCHHHHHHH-HHHHHHHHHHhcCccCCCchHHH-hHHHHHHHHHHHHHHc
Confidence 4577779999999999 688888999988663 233 3567777777666554
No 15
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=20.80 E-value=47 Score=20.16 Aligned_cols=16 Identities=38% Similarity=0.530 Sum_probs=12.9
Q ss_pred ChHHHHHHhcCCHHHH
Q 033311 44 DLDIKEALDRLPREIV 59 (122)
Q Consensus 44 ~~~V~eALrRLP~~~~ 59 (122)
+.+|-++|++||..++
T Consensus 23 ~~~vl~~L~~lP~~~Y 38 (44)
T PF11387_consen 23 PDDVLDALERLPDREY 38 (44)
T ss_pred CHHHHHHHHHCCccCC
Confidence 4689999999997653
No 16
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=20.45 E-value=76 Score=24.63 Aligned_cols=57 Identities=14% Similarity=0.291 Sum_probs=40.6
Q ss_pred HHhhhccccccCCCCCCChHHHHHHhcCCHHH----HHHHHHHHHHHHhhhccccC----CChhhh
Q 033311 27 RLRNFGLRYDDLYDPYYDLDIKEALDRLPREI----VDARNQRLKRAMDLSMKHEY----LPEDLQ 84 (122)
Q Consensus 27 ~yrk~GL~yDDl~~e~e~~~V~eALrRLP~~~----~~~R~~Ri~RA~qlS~~h~~----LPkeqw 84 (122)
.|...|+-.+||+.| -+--+-+|+.+..++- ..-=.++|+.|+.-.+..+. +|....
T Consensus 19 ~~~~~~~~~eDLiQe-G~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~~~~ 83 (238)
T TIGR02393 19 KYTNRGLSFLDLIQE-GNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMV 83 (238)
T ss_pred HHhcCCCCHHHHHHH-HHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCHHHH
Confidence 466669999999998 5788999999997632 22234788888876665553 676543
No 17
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=20.23 E-value=52 Score=16.71 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=7.3
Q ss_pred HHHHHHhhhcc
Q 033311 65 RLKRAMDLSMK 75 (122)
Q Consensus 65 Ri~RA~qlS~~ 75 (122)
-|.+|+.+|+.
T Consensus 6 ~L~~Al~~S~~ 16 (18)
T PF02809_consen 6 DLQRALEMSLE 16 (18)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHhhhc
Confidence 46677777764
Done!