Query 033436
Match_columns 119
No_of_seqs 104 out of 213
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 13:51:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033436.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033436hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02271 UCR_14kD: Ubiquinol-c 100.0 1.5E-44 3.1E-49 260.5 9.0 93 10-105 8-100 (105)
2 KOG3440 Ubiquinol cytochrome c 100.0 1.7E-42 3.8E-47 255.0 8.8 102 1-105 2-105 (122)
3 COG0568 RpoD DNA-directed RNA 56.5 6 0.00013 34.0 1.3 35 22-57 116-150 (342)
4 TIGR03761 ICE_PFL4669 integrat 54.4 30 0.00065 27.9 4.9 49 8-60 150-201 (216)
5 KOG1673 Ras GTPases [General f 43.8 21 0.00045 28.8 2.4 37 13-53 108-150 (205)
6 PF09803 DUF2346: Uncharacteri 42.7 66 0.0014 22.2 4.5 37 35-72 39-75 (80)
7 PF00462 Glutaredoxin: Glutare 41.1 19 0.00041 21.7 1.5 33 21-54 12-44 (60)
8 PRK07122 RNA polymerase sigma 39.0 25 0.00053 28.1 2.2 52 24-77 56-112 (264)
9 PF08134 cIII: cIII protein fa 34.1 47 0.001 20.9 2.4 17 55-71 18-34 (44)
10 TIGR00365 monothiol glutaredox 30.8 47 0.001 22.7 2.3 33 21-54 30-62 (97)
11 PF08664 YcbB: YcbB domain; I 27.7 61 0.0013 24.4 2.6 22 56-77 61-82 (134)
12 PF12536 DUF3734: Patatin phos 27.4 62 0.0013 23.0 2.5 48 45-92 22-73 (108)
13 TIGR02393 RpoD_Cterm RNA polym 26.8 32 0.0007 26.6 1.0 56 27-83 19-82 (238)
14 PF08900 DUF1845: Domain of un 26.4 94 0.002 24.7 3.6 26 27-54 169-194 (217)
15 TIGR02606 antidote_CC2985 puta 26.3 54 0.0012 21.6 1.9 31 43-75 26-56 (69)
16 PF08707 PriCT_2: Primase C te 26.1 42 0.00091 22.1 1.3 28 46-73 1-30 (78)
17 PRK05658 RNA polymerase sigma 25.2 39 0.00084 30.5 1.3 52 24-77 396-452 (619)
18 PRK05901 RNA polymerase sigma 23.2 29 0.00063 31.2 0.2 50 25-75 288-341 (509)
19 PF11387 DUF2795: Protein of u 22.6 41 0.00088 20.5 0.7 16 44-59 23-38 (44)
20 PF07881 Fucose_iso_N1: L-fuco 20.7 88 0.0019 24.8 2.4 46 20-70 117-163 (171)
21 PF02809 UIM: Ubiquitin intera 20.6 42 0.00091 17.1 0.4 11 65-75 6-16 (18)
No 1
>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=1.5e-44 Score=260.47 Aligned_cols=93 Identities=39% Similarity=0.497 Sum_probs=73.4
Q ss_pred hhHHHHHHHHHHHHhhhHHhhhccccccCCCCCCChHHHHHHhcCCHHHHHHHHHHHHHHHhccccccCCChhhhcccCC
Q 033436 10 DPKKNWLAAQHMKTISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPREIVDARNQRLKRAMDLSMKHEYLPEDLQAMQTP 89 (119)
Q Consensus 10 ~p~~~~~a~wy~~~~g~g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~~~~~R~~Ri~RA~qlS~~h~~LPkeqwtk~ee 89 (119)
..+..|+++||+|++ ||||+||+||||++| +||+|+|||+|||+++.++|+|||+||+|||++|++||||||||+++
T Consensus 8 ~~~~~~~~~w~~n~~--gyrk~GL~~DDl~~e-~~~~v~eAl~RLp~~~~~~R~~Ri~RA~~ls~~~~~LPke~wtk~e~ 84 (105)
T PF02271_consen 8 SKFFKPLAKWYYNAS--GYRKYGLRYDDLLNE-EDPDVQEALRRLPPDEQYDRNFRIKRAMQLSLKHQYLPKEQWTKPEE 84 (105)
T ss_dssp HHHHHHHHHHHHHHH--GGGGGT--GGGGS----SHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHT----GGGS--GGG
T ss_pred HHHHHHHHHHHHHhc--chhhhcccHHhccCC-CCHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhcccCCHHHccCccc
Confidence 334556669999977 699999999999999 99999999999999999999999999999999999999999999999
Q ss_pred CCcChHHHHHHHHhhh
Q 033436 90 FRNYLQDMLALVSILE 105 (119)
Q Consensus 90 d~~YL~P~i~ev~~e~ 105 (119)
|++||+|||+||++|.
T Consensus 85 d~~YL~p~i~ev~~E~ 100 (105)
T PF02271_consen 85 DVPYLQPYIEEVEKER 100 (105)
T ss_dssp S--SSHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHH
Confidence 9999999999999986
No 2
>KOG3440 consensus Ubiquinol cytochrome c reductase, subunit QCR7 [Energy production and conversion]
Probab=100.00 E-value=1.7e-42 Score=254.95 Aligned_cols=102 Identities=45% Similarity=0.538 Sum_probs=90.9
Q ss_pred ChHHHHHHHh--hHHHHHHHHHHHHhhhHHhhhccccccCCCCCCChHHHHHHhcCCHHHHHHHHHHHHHHHhccccccC
Q 033436 1 MASLLQSLLD--PKKNWLAAQHMKTISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPREIVDARNQRLKRAMDLSMKHEY 78 (119)
Q Consensus 1 ~~~~L~~~~~--p~~~~~a~wy~~~~g~g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~~~~~R~~Ri~RA~qlS~~h~~ 78 (119)
|++.++++.. .++.++.+|++|++ |||||||+||||+.| +|++|+|||+|||++++|+|++||+|||||||+|++
T Consensus 2 ma~~~~~~~~~~k~~~~~~~~~~nl~--g~rkyGL~~DDl~~e-~n~dvkeAlrRLPr~~~d~R~~Ri~RA~~Lsm~h~~ 78 (122)
T KOG3440|consen 2 MASYIQKSPVLGKLFLPLRKWAYNLS--GFRKYGLRYDDLYYE-ENEDVKEALRRLPRELYDARNYRIKRAMDLSMTHEI 78 (122)
T ss_pred hhhhHHHcccchHHHHHHHHHHHHHh--hhhhhCccccccccc-cCHHHHHHHHHCcHHHHHHHHHHHHHHHHHhhhccc
Confidence 4444333332 35566778999998 699999999999999 799999999999999999999999999999999999
Q ss_pred CChhhhcccCCCCcChHHHHHHHHhhh
Q 033436 79 LPEDLQAMQTPFRNYLQDMLALVSILE 105 (119)
Q Consensus 79 LPkeqwtk~eed~~YL~P~i~ev~~e~ 105 (119)
|||+||||++||++||+|||.||++|.
T Consensus 79 LPk~ewtk~eed~~YL~pyL~ev~~Er 105 (122)
T KOG3440|consen 79 LPKEEWTKYEEDVKYLEPYLAEVEAER 105 (122)
T ss_pred CCHHHhhcccchhhHHHHHHHHHHHHH
Confidence 999999999999999999999999884
No 3
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=56.48 E-value=6 Score=34.02 Aligned_cols=35 Identities=23% Similarity=0.423 Sum_probs=31.0
Q ss_pred HHhhhHHhhhccccccCCCCCCChHHHHHHhcCCHH
Q 033436 22 KTISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPRE 57 (119)
Q Consensus 22 ~~~g~g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~ 57 (119)
-+++++|..+||-+-|||.| .|.-+.+|+.+..++
T Consensus 116 vsIAk~Y~~rGL~~~DLIQE-GniGLmkAVekFdp~ 150 (342)
T COG0568 116 VSIAKKYTGRGLPFLDLIQE-GNIGLMKAVEKFDPE 150 (342)
T ss_pred HHHHHHhhcCCCcHHHHHhc-ccHHHHHHHHhcCcc
Confidence 34556899999999999999 899999999999887
No 4
>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=54.38 E-value=30 Score=27.92 Aligned_cols=49 Identities=24% Similarity=0.425 Sum_probs=34.3
Q ss_pred HHhhHHHHHHHHHHHHhhhHHhhhccccccCCCCCCChHHHHHHhc---CCHHHHH
Q 033436 8 LLDPKKNWLAAQHMKTISKRLRNFGLRYDDLYDPYYDLDIKEALDR---LPREIVD 60 (119)
Q Consensus 8 ~~~p~~~~~a~wy~~~~g~g~rk~GL~yDDLl~e~e~~~V~eALrR---LP~~~~~ 60 (119)
+++-...++.+-|.-+. .||-.|+-+||.... |+..++|+.+ ||+++..
T Consensus 150 ~l~~g~~~vR~vf~~~~--~yr~~gvtR~D~~~~--n~~a~~Aie~~G~lp~dIL~ 201 (216)
T TIGR03761 150 WLDKGAHLIRRLFGLAQ--RYRHSGVTRDDFAAN--NARARKAIERFGELPQDILE 201 (216)
T ss_pred HHHHHHHHHHHHHHHHH--hhhcCCCCHHHHHhC--CHHHHHHHHHcCCCCHHHHc
Confidence 33334444444455555 699999999999844 9999999988 5666543
No 5
>KOG1673 consensus Ras GTPases [General function prediction only]
Probab=43.78 E-value=21 Score=28.78 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhhhHHhh------hccccccCCCCCCChHHHHHHhc
Q 033436 13 KNWLAAQHMKTISKRLRN------FGLRYDDLYDPYYDLDIKEALDR 53 (119)
Q Consensus 13 ~~~~a~wy~~~~g~g~rk------~GL~yDDLl~e~e~~~V~eALrR 53 (119)
.|.+-.||..+- |+|| .|-+||+++.= .|+.|+-+.|
T Consensus 108 LnSi~~WY~QAr--~~NktAiPilvGTKyD~fi~l--p~e~Q~~I~~ 150 (205)
T KOG1673|consen 108 LNSIKEWYRQAR--GLNKTAIPILVGTKYDLFIDL--PPELQETISR 150 (205)
T ss_pred HHHHHHHHHHHh--ccCCccceEEeccchHhhhcC--CHHHHHHHHH
Confidence 455667888877 5988 58899999965 6888887765
No 6
>PF09803 DUF2346: Uncharacterized conserved protein (DUF2346); InterPro: IPR018625 Members of this family of proteins have no known function.
Probab=42.75 E-value=66 Score=22.18 Aligned_cols=37 Identities=32% Similarity=0.585 Sum_probs=30.0
Q ss_pred cccCCCCCCChHHHHHHhcCCHHHHHHHHHHHHHHHhc
Q 033436 35 YDDLYDPYYDLDIKEALDRLPREIVDARNQRLKRAMDL 72 (119)
Q Consensus 35 yDDLl~e~e~~~V~eALrRLP~~~~~~R~~Ri~RA~ql 72 (119)
.+-+... +++...+.|.++=++....|..||.|+++-
T Consensus 39 ~~~~~pp-e~~~~~~ele~~~~~~~~k~~~rl~~~~e~ 75 (80)
T PF09803_consen 39 KRELYPP-ENEEIREELEEFKEELRKKREERLLREMEE 75 (80)
T ss_pred hcccCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444 788899999999999999999999998864
No 7
>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=41.06 E-value=19 Score=21.73 Aligned_cols=33 Identities=24% Similarity=0.349 Sum_probs=24.3
Q ss_pred HHHhhhHHhhhccccccCCCCCCChHHHHHHhcC
Q 033436 21 MKTISKRLRNFGLRYDDLYDPYYDLDIKEALDRL 54 (119)
Q Consensus 21 ~~~~g~g~rk~GL~yDDLl~e~e~~~V~eALrRL 54 (119)
+..+-+.+++.|+.|+.+=.+ +++..+++|+.+
T Consensus 12 C~~~~~~L~~~~i~y~~~dv~-~~~~~~~~l~~~ 44 (60)
T PF00462_consen 12 CKKAKEFLDEKGIPYEEVDVD-EDEEAREELKEL 44 (60)
T ss_dssp HHHHHHHHHHTTBEEEEEEGG-GSHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCeeeEcccc-cchhHHHHHHHH
Confidence 344445789999999988777 677777777654
No 8
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=38.95 E-value=25 Score=28.15 Aligned_cols=52 Identities=19% Similarity=0.268 Sum_probs=39.7
Q ss_pred hhhHHhhhccccccCCCCCCChHHHHHHhcCCHH-----HHHHHHHHHHHHHhcccccc
Q 033436 24 ISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPRE-----IVDARNQRLKRAMDLSMKHE 77 (119)
Q Consensus 24 ~g~g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~-----~~~~R~~Ri~RA~qlS~~h~ 77 (119)
+++.|+..|+-.|||+.+ -+--+-+|+.+..++ ..|+ .++|+-++.-.+.+.
T Consensus 56 iA~~y~~~g~~~~DLiQe-G~iGLi~AierFDp~~G~~FsTYA-~~~Irg~I~~~lr~~ 112 (264)
T PRK07122 56 IARRFDGRGEPRDDLVQV-ARVGLVNAVNRFDVETGSDFVSFA-VPTIMGEVRRHFRDN 112 (264)
T ss_pred HHHHHHhCCCCHHHHHHH-HHHHHHHHHHHcCCCCCCChHHHH-HHHHHHHHHHHHHHc
Confidence 344677779999999999 688899999999886 2443 568888887777554
No 9
>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=34.11 E-value=47 Score=20.88 Aligned_cols=17 Identities=29% Similarity=0.315 Sum_probs=13.5
Q ss_pred CHHHHHHHHHHHHHHHh
Q 033436 55 PREIVDARNQRLKRAMD 71 (119)
Q Consensus 55 P~~~~~~R~~Ri~RA~q 71 (119)
++.|.-.|++|++||..
T Consensus 18 ~ESELskr~rrLIRaa~ 34 (44)
T PF08134_consen 18 TESELSKRIRRLIRAAR 34 (44)
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 45577889999999964
No 10
>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=30.80 E-value=47 Score=22.67 Aligned_cols=33 Identities=12% Similarity=0.210 Sum_probs=24.4
Q ss_pred HHHhhhHHhhhccccccCCCCCCChHHHHHHhcC
Q 033436 21 MKTISKRLRNFGLRYDDLYDPYYDLDIKEALDRL 54 (119)
Q Consensus 21 ~~~~g~g~rk~GL~yDDLl~e~e~~~V~eALrRL 54 (119)
++.+-+-++++|+.|+.+=.+ +++.++++|..+
T Consensus 30 C~~ak~lL~~~~i~~~~~di~-~~~~~~~~l~~~ 62 (97)
T TIGR00365 30 SARAVQILKACGVPFAYVNVL-EDPEIRQGIKEY 62 (97)
T ss_pred HHHHHHHHHHcCCCEEEEECC-CCHHHHHHHHHH
Confidence 344445689999999987666 688888888754
No 11
>PF08664 YcbB: YcbB domain; InterPro: IPR013972 YcbB is a DNA-binding protein [].
Probab=27.73 E-value=61 Score=24.42 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHhcccccc
Q 033436 56 REIVDARNQRLKRAMDLSMKHE 77 (119)
Q Consensus 56 ~~~~~~R~~Ri~RA~qlS~~h~ 77 (119)
.++..+=-+|||||+.-++.|-
T Consensus 61 ~~e~Ka~EQRIRRai~~al~nl 82 (134)
T PF08664_consen 61 EKEKKAIEQRIRRAIKQALTNL 82 (134)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 6677778899999999998875
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=27.36 E-value=62 Score=22.96 Aligned_cols=48 Identities=21% Similarity=0.227 Sum_probs=33.7
Q ss_pred hHHHHHHhcCCHHHHHHHHHHHHHHHhcc----ccccCCChhhhcccCCCCc
Q 033436 45 LDIKEALDRLPREIVDARNQRLKRAMDLS----MKHEYLPEDLQAMQTPFRN 92 (119)
Q Consensus 45 ~~V~eALrRLP~~~~~~R~~Ri~RA~qlS----~~h~~LPkeqwtk~eed~~ 92 (119)
-.|.+.+.+||+++..+...+..+.+.|. +-|-+-+...+.-...|..
T Consensus 22 ~~i~~Ll~~lP~~~r~dp~~~~l~~~~~~~~~~IvhLiy~~~~~e~~sKDye 73 (108)
T PF12536_consen 22 HAIRELLERLPEELRDDPDVRELAELGCGKRVNIVHLIYRRKPYEGHSKDYE 73 (108)
T ss_pred HHHHHHHHcCCHHHhCCHHHHHHHHhcCCCceEEEEeecCCCCccccccCcc
Confidence 56789999999999888888888777663 4455556655554444443
No 13
>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=26.81 E-value=32 Score=26.62 Aligned_cols=56 Identities=14% Similarity=0.305 Sum_probs=39.7
Q ss_pred HHhhhccccccCCCCCCChHHHHHHhcCCHHH----HHHHHHHHHHHHhccccccC----CChhh
Q 033436 27 RLRNFGLRYDDLYDPYYDLDIKEALDRLPREI----VDARNQRLKRAMDLSMKHEY----LPEDL 83 (119)
Q Consensus 27 g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~~----~~~R~~Ri~RA~qlS~~h~~----LPkeq 83 (119)
.|...|+-.+||+.| -+--+-+|+.+..++- ..-=.++|+.|+.-.+..+. +|...
T Consensus 19 ~~~~~~~~~eDLiQe-G~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~~~ 82 (238)
T TIGR02393 19 KYTNRGLSFLDLIQE-GNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHM 82 (238)
T ss_pred HHhcCCCCHHHHHHH-HHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCHHH
Confidence 466669999999999 6888999999997742 22224788888765554443 66554
No 14
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 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=26.37 E-value=94 Score=24.67 Aligned_cols=26 Identities=27% Similarity=0.491 Sum_probs=22.4
Q ss_pred HHhhhccccccCCCCCCChHHHHHHhcC
Q 033436 27 RLRNFGLRYDDLYDPYYDLDIKEALDRL 54 (119)
Q Consensus 27 g~rk~GL~yDDLl~e~e~~~V~eALrRL 54 (119)
+|+-.|+.++|+... |+..++|+.++
T Consensus 169 ~yr~~gvtR~D~~~~--n~~~~~A~~~~ 194 (217)
T PF08900_consen 169 RYRHSGVTRDDFAAN--NARAQAAIERF 194 (217)
T ss_pred HHhccCCCHHHHHhc--CHHHHHHHHHc
Confidence 589999999999944 99999998775
No 15
>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=26.28 E-value=54 Score=21.57 Aligned_cols=31 Identities=19% Similarity=0.189 Sum_probs=23.2
Q ss_pred CChHHHHHHhcCCHHHHHHHHHHHHHHHhcccc
Q 033436 43 YDLDIKEALDRLPREIVDARNQRLKRAMDLSMK 75 (119)
Q Consensus 43 e~~~V~eALrRLP~~~~~~R~~Ri~RA~qlS~~ 75 (119)
-+.+|.+|||.|-.++ ++.-.|+.+++-...
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 467777777765544
No 16
>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=26.07 E-value=42 Score=22.06 Aligned_cols=28 Identities=39% Similarity=0.639 Sum_probs=18.7
Q ss_pred HHHHHHhcCCHHHHHHHH--HHHHHHHhcc
Q 033436 46 DIKEALDRLPREIVDARN--QRLKRAMDLS 73 (119)
Q Consensus 46 ~V~eALrRLP~~~~~~R~--~Ri~RA~qlS 73 (119)
+|++||+-||++...+|. .||-.|+.-.
T Consensus 1 ~~~~~L~~i~~~~~~~y~~W~~vg~Al~~~ 30 (78)
T PF08707_consen 1 DIREALDHIPPDIADDYDDWIRVGMALKHE 30 (78)
T ss_pred CHHHHHhcCCcccccCHHHHHHHHHHHHHh
Confidence 478999999998644444 4555554433
No 17
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=25.20 E-value=39 Score=30.48 Aligned_cols=52 Identities=23% Similarity=0.376 Sum_probs=38.5
Q ss_pred hhhHHhhhccccccCCCCCCChHHHHHHhcCCHH-----HHHHHHHHHHHHHhcccccc
Q 033436 24 ISKRLRNFGLRYDDLYDPYYDLDIKEALDRLPRE-----IVDARNQRLKRAMDLSMKHE 77 (119)
Q Consensus 24 ~g~g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~-----~~~~R~~Ri~RA~qlS~~h~ 77 (119)
+++.|+..|+-++||+.| -|--.-+|+.+..+. ..|+ .++|+.|+.-++..+
T Consensus 396 iA~ky~~~gl~~~DLiQe-G~iGL~~Av~kfd~~~G~~FstYA-~~wIr~aI~~~i~~~ 452 (619)
T PRK05658 396 IAKKYTNRGLQFLDLIQE-GNIGLMKAVDKFEYRRGYKFSTYA-TWWIRQAITRSIADQ 452 (619)
T ss_pred HHHHHhhCCCCHHHHHHH-HHHHHHHHHHhcCccCCCchHHHh-HHHHHHHHHHHHHHc
Confidence 344677789999999999 688899999998765 3344 467777776655444
No 18
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=23.16 E-value=29 Score=31.21 Aligned_cols=50 Identities=22% Similarity=0.318 Sum_probs=36.2
Q ss_pred hhHHhhhccccccCCCCCCChHHHHHHhcCCHHH----HHHHHHHHHHHHhcccc
Q 033436 25 SKRLRNFGLRYDDLYDPYYDLDIKEALDRLPREI----VDARNQRLKRAMDLSMK 75 (119)
Q Consensus 25 g~g~rk~GL~yDDLl~e~e~~~V~eALrRLP~~~----~~~R~~Ri~RA~qlS~~ 75 (119)
++.|...|+-++||+.| -+--+-+|+.|..++- ..-=.++|+.|+.-.+.
T Consensus 288 AkrY~~~Gl~~eDLIQE-GnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~ 341 (509)
T PRK05901 288 AKRYTNRGLSFLDLIQE-GNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMA 341 (509)
T ss_pred HHHHhcCCCCHHHHHHH-HHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHH
Confidence 34677779999999999 6888999999998762 22235667777654443
No 19
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=22.60 E-value=41 Score=20.46 Aligned_cols=16 Identities=38% Similarity=0.530 Sum_probs=12.9
Q ss_pred ChHHHHHHhcCCHHHH
Q 033436 44 DLDIKEALDRLPREIV 59 (119)
Q Consensus 44 ~~~V~eALrRLP~~~~ 59 (119)
+.+|-++|++||++++
T Consensus 23 ~~~vl~~L~~lP~~~Y 38 (44)
T PF11387_consen 23 PDDVLDALERLPDREY 38 (44)
T ss_pred CHHHHHHHHHCCccCC
Confidence 4688999999997653
No 20
>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=20.69 E-value=88 Score=24.80 Aligned_cols=46 Identities=22% Similarity=0.338 Sum_probs=21.2
Q ss_pred HHHHhhhHHhhhccccccCCCCCCChHHHHHHh-cCCHHHHHHHHHHHHHHH
Q 033436 20 HMKTISKRLRNFGLRYDDLYDPYYDLDIKEALD-RLPREIVDARNQRLKRAM 70 (119)
Q Consensus 20 y~~~~g~g~rk~GL~yDDLl~e~e~~~V~eALr-RLP~~~~~~R~~Ri~RA~ 70 (119)
|..+++..++|.||..-=++- .+||.|=. .+|++ +.+++-|..||.
T Consensus 117 yLaAa~aa~~Q~Gip~f~IyG----~~vqD~~D~~ip~d-V~eKll~farAa 163 (171)
T PF07881_consen 117 YLAAALAAHNQKGIPAFRIYG----HDVQDADDTSIPED-VQEKLLRFARAA 163 (171)
T ss_dssp HHHHHHHHHHHCT---EEEE-----SS---TT--S--HH-HHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCcceeecc----ccccCCCCCcCcHH-HHHHHHHHHHHH
Confidence 566777789999998544432 23333332 34444 345566666653
No 21
>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=20.56 E-value=42 Score=17.15 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=6.6
Q ss_pred HHHHHHhcccc
Q 033436 65 RLKRAMDLSMK 75 (119)
Q Consensus 65 Ri~RA~qlS~~ 75 (119)
-|.||+.+|+.
T Consensus 6 ~L~~Al~~S~~ 16 (18)
T PF02809_consen 6 DLQRALEMSLE 16 (18)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHhhhc
Confidence 35666666653
Done!