Query psy17879
Match_columns 154
No_of_seqs 129 out of 321
Neff 3.5
Searched_HMMs 46136
Date Sat Aug 17 01:20:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17879.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17879hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02209 VHP: Villin headpiece 99.8 2.8E-21 6.2E-26 121.6 4.0 36 119-154 1-36 (36)
2 smart00153 VHP Villin headpiec 99.8 8.2E-21 1.8E-25 119.3 4.0 36 119-154 1-36 (36)
3 KOG1044|consensus 99.8 1.1E-20 2.4E-25 174.9 5.3 91 59-154 566-670 (670)
4 KOG0443|consensus 99.8 1.9E-19 4.1E-24 170.5 5.8 63 91-154 764-827 (827)
5 KOG0445|consensus 99.8 1.2E-19 2.7E-24 170.7 2.0 106 46-154 814-919 (919)
6 TIGR01764 excise DNA binding d 53.0 14 0.0003 21.8 2.2 21 119-139 1-21 (49)
7 PF12728 HTH_17: Helix-turn-he 52.9 13 0.00028 23.1 2.1 21 119-139 1-21 (51)
8 COG2996 Predicted RNA-bindinin 49.5 12 0.00027 33.2 2.2 46 84-138 220-265 (287)
9 PF07467 BLIP: Beta-lactamase 42.9 14 0.0003 31.0 1.4 21 117-137 28-49 (183)
10 PF09286 Pro-kuma_activ: Pro-k 40.8 22 0.00047 26.7 2.0 29 117-145 45-73 (143)
11 PF05391 Lsm_interact: Lsm int 34.4 27 0.00059 20.0 1.3 12 118-129 8-19 (21)
12 PF05930 Phage_AlpA: Prophage 30.7 29 0.00063 22.1 1.1 23 118-140 2-24 (51)
13 PF10256 Erf4: Golgin subfamil 29.1 35 0.00075 25.0 1.5 14 116-129 26-39 (118)
14 PF08447 PAS_3: PAS fold; Int 25.7 49 0.0011 21.4 1.6 15 122-136 5-19 (91)
15 PF00165 HTH_AraC: Bacterial r 25.2 53 0.0011 19.7 1.6 20 118-137 18-41 (42)
16 COG3735 Uncharacterized protei 25.0 62 0.0013 29.0 2.5 32 112-143 100-137 (299)
17 PRK09391 fixK transcriptional 24.6 67 0.0015 25.6 2.5 33 115-147 175-208 (230)
18 PRK11753 DNA-binding transcrip 24.0 74 0.0016 24.2 2.5 31 117-147 166-197 (211)
19 PF12833 HTH_18: Helix-turn-he 23.2 71 0.0015 21.1 2.0 16 123-138 65-80 (81)
20 PRK11161 fumarate/nitrate redu 22.5 84 0.0018 24.6 2.6 33 115-147 180-213 (235)
21 PF02201 SWIB: SWIB/MDM2 domai 21.5 9.6 0.00021 26.5 -2.6 33 111-143 39-71 (76)
22 PF07022 Phage_CI_repr: Bacter 21.2 39 0.00085 22.6 0.4 23 121-145 14-36 (66)
23 PF02809 UIM: Ubiquitin intera 20.8 30 0.00065 18.7 -0.2 14 122-135 4-17 (18)
24 PRK13918 CRP/FNR family transc 20.6 92 0.002 23.6 2.4 33 115-147 145-178 (202)
25 PRK15070 propanediol utilizati 20.4 49 0.0011 28.3 1.0 22 109-130 25-46 (211)
26 KOG3591|consensus 20.1 38 0.00082 27.5 0.2 19 105-123 121-139 (173)
No 1
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=99.83 E-value=2.8e-21 Score=121.62 Aligned_cols=36 Identities=56% Similarity=1.041 Sum_probs=31.8
Q ss_pred CCChHHHHHHhCCCHHHHhhChhHHHHHHhHhcCCC
Q psy17879 119 HLSDVEFETLFLCTRAEFYRLPTWRRNDLKKRARLF 154 (154)
Q Consensus 119 YLSDeDF~~VFGMsr~EF~~LP~WKQ~~LKK~~gLF 154 (154)
||||+||++||||+|+||++||+|||+++||++|||
T Consensus 1 YLsd~dF~~vFgm~~~eF~~lP~WKq~~lKK~~~LF 36 (36)
T PF02209_consen 1 YLSDEDFEKVFGMSREEFYKLPKWKQNNLKKKAGLF 36 (36)
T ss_dssp GS-HHHHHHHHSS-HHHHHHS-HHHHHHHHHHTTT-
T ss_pred CcCHHHHHHHHCCCHHHHHHChHHHHHHHHHHhCCC
Confidence 899999999999999999999999999999999998
No 2
>smart00153 VHP Villin headpiece domain.
Probab=99.82 E-value=8.2e-21 Score=119.31 Aligned_cols=36 Identities=56% Similarity=0.991 Sum_probs=35.7
Q ss_pred CCChHHHHHHhCCCHHHHhhChhHHHHHHhHhcCCC
Q psy17879 119 HLSDVEFETLFLCTRAEFYRLPTWRRNDLKKRARLF 154 (154)
Q Consensus 119 YLSDeDF~~VFGMsr~EF~~LP~WKQ~~LKK~~gLF 154 (154)
||||+||++||||+|+||++||+|||+++||++|||
T Consensus 1 yLsdeeF~~vfgmsr~eF~~LP~WKq~~lKk~~~LF 36 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFYKLPLWKQNQLKKKLGLF 36 (36)
T ss_pred CCCHHHHHHHHCCCHHHHHhCcHhhHHHHHhhcCCC
Confidence 899999999999999999999999999999999998
No 3
>KOG1044|consensus
Probab=99.81 E-value=1.1e-20 Score=174.86 Aligned_cols=91 Identities=52% Similarity=0.872 Sum_probs=78.2
Q ss_pred ccccCCCcc----------cccccCc-cccccCCCCCCCCCCCCCCcCCHHHHHhhc---CCCCCCCCccccccCCChHH
Q psy17879 59 SSTYAGSLG----------YAASYSN-HIQRSLPNMSQPMSLEPPKIYPYHLLIITN---YRLPPDVDRKNLERHLSDVE 124 (154)
Q Consensus 59 s~t~~g~l~----------~~~~~~~-~~Rrslp~~s~~l~~~~~k~Ypye~L~~~~---~~LP~gVDptklE~YLSDeD 124 (154)
|++|+|++| +...+|- -.+.+||+|.. ..++|||+.|+.++ .+||++||+++||+||+.||
T Consensus 566 stS~sgs~G~~r~~~~~~~g~~p~g~~~~~~SlP~~~~-----e~KiypYe~L~vTnrgr~klp~dVDRtrLERHL~~e~ 640 (670)
T KOG1044|consen 566 STSYSGSSGGYRDYQTLRDGPMPAGRMDRGVSLPNMML-----EPKIYPYEMLMVTNRGRNKLPRDVDRTRLERHLSPED 640 (670)
T ss_pred cccccCCCccccccccccCCCccccccccccccccccc-----cccccChHHheecccccccCcccchhhHHhhccCHHH
Confidence 577888887 2211122 36778999643 68999999999877 78999999999999999999
Q ss_pred HHHHhCCCHHHHhhChhHHHHHHhHhcCCC
Q psy17879 125 FETLFLCTRAEFYRLPTWRRNDLKKRARLF 154 (154)
Q Consensus 125 F~~VFGMsr~EF~~LP~WKQ~~LKK~~gLF 154 (154)
|.+||||+.+||++||.|||+||||++.||
T Consensus 641 F~eiF~MSi~EF~rL~LWkRnnlKkkAkLF 670 (670)
T KOG1044|consen 641 FSEIFGMSISEFDRLPLWKRNNLKKKAKLF 670 (670)
T ss_pred HHHHhccCHhhhchhhhhhhhhhhhhhccC
Confidence 999999999999999999999999999999
No 4
>KOG0443|consensus
Probab=99.77 E-value=1.9e-19 Score=170.48 Aligned_cols=63 Identities=40% Similarity=0.742 Sum_probs=57.8
Q ss_pred CCCcCCHHHHHhhc-CCCCCCCCccccccCCChHHHHHHhCCCHHHHhhChhHHHHHHhHhcCCC
Q psy17879 91 PPKIYPYHLLIITN-YRLPPDVDRKNLERHLSDVEFETLFLCTRAEFYRLPTWRRNDLKKRARLF 154 (154)
Q Consensus 91 ~~k~Ypye~L~~~~-~~LP~gVDptklE~YLSDeDF~~VFGMsr~EF~~LP~WKQ~~LKK~~gLF 154 (154)
+...|||++|+.+. .++|+ |||+|+|.|||++||+.+|||+|+||++||+|||++|||+.+||
T Consensus 764 p~~~~~~e~l~~~~~~~~~~-id~~rrE~yLs~~dF~~~Fgmtk~eF~~LPkWKq~~lKk~~~LF 827 (827)
T KOG0443|consen 764 PRPAFPYEQLLTQSEDPVPD-IDPTRREAYLSEEEFVSVFGMTKEEFYALPKWKQNKLKKQFGLF 827 (827)
T ss_pred cccCCCHHHHhccccCcCCC-CChhHhhhhccHHHHHHHhCcCHHHHhhcchhHHHHHhhhhccC
Confidence 33599999999544 56777 99999999999999999999999999999999999999999999
No 5
>KOG0445|consensus
Probab=99.76 E-value=1.2e-19 Score=170.73 Aligned_cols=106 Identities=27% Similarity=0.400 Sum_probs=81.0
Q ss_pred CcCCCCCCCCcccccccCCCcccccccCccccccCCCCCCCCCCCCCCcCCHHHHHhhcCCCCCCCCccccccCCChHHH
Q psy17879 46 HHVPNGGAPELPVSSTYAGSLGYAASYSNHIQRSLPNMSQPMSLEPPKIYPYHLLIITNYRLPPDVDRKNLERHLSDVEF 125 (154)
Q Consensus 46 ~~~~~~~~~~~~~s~t~~g~l~~~~~~~~~~Rrslp~~s~~l~~~~~k~Ypye~L~~~~~~LP~gVDptklE~YLSDeDF 125 (154)
++++--|++++.|.+-|..-- -+...-+.+-.+...+.++|...-.++||+++|.. ++||+||||.+||.||+||||
T Consensus 814 ~~vV~aGlEPl~Fk~lFp~We-~red~D~~~s~~i~~v~d~La~~c~T~yple~l~a--rpLPeGvdp~rLE~YLtdeDF 890 (919)
T KOG0445|consen 814 SYVVHAGLEPLTFKNLFPSWE-HREDIDTEVSNQITLVEDVLAKLCKTIYPLEDLLA--RPLPEGVDPLRLEIYLTDEDF 890 (919)
T ss_pred ceEEEcCcChhhhhhhCCCce-eccccCCCcCCchhHHHHHHHHHhhhcChHHHHhc--CCCCCCCCchhheeeechHHH
Confidence 455555777777776664331 11111122333333344467777778999999974 599999999999999999999
Q ss_pred HHHhCCCHHHHhhChhHHHHHHhHhcCCC
Q psy17879 126 ETLFLCTRAEFYRLPTWRRNDLKKRARLF 154 (154)
Q Consensus 126 ~~VFGMsr~EF~~LP~WKQ~~LKK~~gLF 154 (154)
+.+|||+|+||++||.|||+++||+.|||
T Consensus 891 ~~al~~~R~Ef~alp~WKQ~~lkK~~GLF 919 (919)
T KOG0445|consen 891 EFALDMTRDEFNALPAWKQVNLKKAKGLF 919 (919)
T ss_pred HHHhccCHHHhhcchhhhhhhhhhhccCC
Confidence 99999999999999999999999999999
No 6
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=52.96 E-value=14 Score=21.80 Aligned_cols=21 Identities=24% Similarity=0.282 Sum_probs=18.8
Q ss_pred CCChHHHHHHhCCCHHHHhhC
Q psy17879 119 HLSDVEFETLFLCTRAEFYRL 139 (154)
Q Consensus 119 YLSDeDF~~VFGMsr~EF~~L 139 (154)
||+-+|..+.+|+++..++.+
T Consensus 1 ~lt~~e~a~~lgis~~ti~~~ 21 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDTVYRL 21 (49)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
Confidence 789999999999999988764
No 7
>PF12728 HTH_17: Helix-turn-helix domain
Probab=52.93 E-value=13 Score=23.10 Aligned_cols=21 Identities=29% Similarity=0.311 Sum_probs=18.9
Q ss_pred CCChHHHHHHhCCCHHHHhhC
Q psy17879 119 HLSDVEFETLFLCTRAEFYRL 139 (154)
Q Consensus 119 YLSDeDF~~VFGMsr~EF~~L 139 (154)
|||-+|..+.+|+++..++.+
T Consensus 1 ~lt~~e~a~~l~is~~tv~~~ 21 (51)
T PF12728_consen 1 YLTVKEAAELLGISRSTVYRW 21 (51)
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 789999999999999998854
No 8
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=49.47 E-value=12 Score=33.18 Aligned_cols=46 Identities=15% Similarity=0.214 Sum_probs=30.2
Q ss_pred CCCCCCCCCCcCCHHHHHhhcCCCCCCCCccccccCCChHHHHHHhCCCHHHHhh
Q psy17879 84 SQPMSLEPPKIYPYHLLIITNYRLPPDVDRKNLERHLSDVEFETLFLCTRAEFYR 138 (154)
Q Consensus 84 s~~l~~~~~k~Ypye~L~~~~~~LP~gVDptklE~YLSDeDF~~VFGMsr~EF~~ 138 (154)
.+++......++.|-+.. ..-+| +-.--|+||..+.|||||..|.+
T Consensus 220 ~E~l~~daq~Il~yL~~~--gG~mp-------f~DKSsPEdIk~~FgiSKg~FKr 265 (287)
T COG2996 220 HEMLDEDAQMILTYLESN--GGFMP-------FNDKSSPEDIKATFGISKGQFKR 265 (287)
T ss_pred HHhhhhhHHHHHHHHHHc--CCccc-------cCCCCCHHHHHHHhCcCHHHHHH
Confidence 335555555566554333 33455 23456899999999999999953
No 9
>PF07467 BLIP: Beta-lactamase inhibitor (BLIP); InterPro: IPR009099 The beta-lactamase-inhibitor protein (BLIP) is produced by Streptomyces species. BLIP acts as a potent inhibitor of beta-lactamases such as TEM-1, which is the most widespread resistance enzyme to penicillin antibiotics. BLIP binds competitively to TEM-1 and makes direct contacts with TEM-1 active site residues. BLIP is able to inhibit a variety of class A beta-lactamases, possibly through flexibility of its two domains. The two tandemly repeated domains of BLIP have an alpha(2)-beta(4) structure, the beta-hairpin loop from domain 1 inserting into the active site of beta-lactamase []. BLIP shows no sequence similarity with BLIP-II, even though both bind to and inhibit TEM-1 [].; PDB: 3GMY_B 3GMX_B 3C4O_B 1XXM_C 1S0W_D 3N4I_B 3C7U_B 2G2W_B 3C7V_D 3E2K_C ....
Probab=42.87 E-value=14 Score=31.01 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=14.8
Q ss_pred ccCCChHHHHHH-hCCCHHHHh
Q psy17879 117 ERHLSDVEFETL-FLCTRAEFY 137 (154)
Q Consensus 117 E~YLSDeDF~~V-FGMsr~EF~ 137 (154)
+.+|++|-|++| |||+++|=.
T Consensus 28 ~s~lT~EkY~kIqfGMt~~EV~ 49 (183)
T PF07467_consen 28 CSKLTAEKYEKIQFGMTYDEVW 49 (183)
T ss_dssp --SS-HHHHHHS-TT-BHHHHH
T ss_pred ccccCHHHhhhHhcCCCHHHHH
Confidence 578999999887 899999854
No 10
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=40.76 E-value=22 Score=26.69 Aligned_cols=29 Identities=21% Similarity=0.454 Sum_probs=20.8
Q ss_pred ccCCChHHHHHHhCCCHHHHhhChhHHHH
Q psy17879 117 ERHLSDVEFETLFLCTRAEFYRLPTWRRN 145 (154)
Q Consensus 117 E~YLSDeDF~~VFGMsr~EF~~LP~WKQ~ 145 (154)
-+|||.+||.+.|+-+.+...+.-.|=+.
T Consensus 45 gk~Lt~~e~~~~~~p~~~~v~~V~~wL~~ 73 (143)
T PF09286_consen 45 GKYLTPEEFAALFAPSPEDVAAVKSWLKS 73 (143)
T ss_dssp T----HHHHHHHHS--HHHHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58999999999999999999999999664
No 11
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=34.43 E-value=27 Score=19.99 Aligned_cols=12 Identities=25% Similarity=0.584 Sum_probs=9.9
Q ss_pred cCCChHHHHHHh
Q psy17879 118 RHLSDVEFETLF 129 (154)
Q Consensus 118 ~YLSDeDF~~VF 129 (154)
.-+|.+||.+.|
T Consensus 8 ~p~SNddFrkmf 19 (21)
T PF05391_consen 8 KPKSNDDFRKMF 19 (21)
T ss_pred CccchHHHHHHH
Confidence 457999999887
No 12
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=30.66 E-value=29 Score=22.13 Aligned_cols=23 Identities=35% Similarity=0.413 Sum_probs=17.5
Q ss_pred cCCChHHHHHHhCCCHHHHhhCh
Q psy17879 118 RHLSDVEFETLFLCTRAEFYRLP 140 (154)
Q Consensus 118 ~YLSDeDF~~VFGMsr~EF~~LP 140 (154)
+.|+-.|..+.+|+++..++.|=
T Consensus 2 rll~~~ev~~~~g~s~~ti~~~~ 24 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTIYRLI 24 (51)
T ss_dssp -EE-HHHHHHHHSS-HHHHHHHH
T ss_pred ccccHHHHHHHHCCCHHHHHHHH
Confidence 56788999999999999998763
No 13
>PF10256 Erf4: Golgin subfamily A member 7/ERF4 family; InterPro: IPR019383 Proteins in this entry include Golgin subfamily A member 7 and the Ras modification protein ERF4.
Probab=29.10 E-value=35 Score=25.01 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=12.5
Q ss_pred cccCCChHHHHHHh
Q psy17879 116 LERHLSDVEFETLF 129 (154)
Q Consensus 116 lE~YLSDeDF~~VF 129 (154)
|+.|||.+||+++-
T Consensus 26 L~~~is~~ef~~iI 39 (118)
T PF10256_consen 26 LSGYISPEEFEEII 39 (118)
T ss_pred hcCCCCHHHHHHHH
Confidence 78999999998775
No 14
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=25.74 E-value=49 Score=21.36 Aligned_cols=15 Identities=20% Similarity=0.286 Sum_probs=12.2
Q ss_pred hHHHHHHhCCCHHHH
Q psy17879 122 DVEFETLFLCTRAEF 136 (154)
Q Consensus 122 DeDF~~VFGMsr~EF 136 (154)
++.|.++||++.+++
T Consensus 5 s~~~~~i~G~~~~~~ 19 (91)
T PF08447_consen 5 SDNFYEIFGYSPEEI 19 (91)
T ss_dssp -THHHHHHTS-HHHH
T ss_pred eHHHHHHhCCCHHHh
Confidence 468999999999999
No 15
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=25.17 E-value=53 Score=19.71 Aligned_cols=20 Identities=15% Similarity=0.036 Sum_probs=11.4
Q ss_pred cCCChHH----HHHHhCCCHHHHh
Q psy17879 118 RHLSDVE----FETLFLCTRAEFY 137 (154)
Q Consensus 118 ~YLSDeD----F~~VFGMsr~EF~ 137 (154)
..+|..- |++.+||+..+|.
T Consensus 18 ~g~S~~~f~r~Fk~~~g~tp~~y~ 41 (42)
T PF00165_consen 18 AGFSPSYFSRLFKKETGMTPKQYR 41 (42)
T ss_dssp HTS-HHHHHHHHHHHTSS-HHHHH
T ss_pred HCCCHHHHHHHHHHHHCcCHHHHh
Confidence 3445554 4566689988874
No 16
>COG3735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.03 E-value=62 Score=28.97 Aligned_cols=32 Identities=25% Similarity=0.460 Sum_probs=27.8
Q ss_pred CccccccCCChHHHHH------HhCCCHHHHhhChhHH
Q psy17879 112 DRKNLERHLSDVEFET------LFLCTRAEFYRLPTWR 143 (154)
Q Consensus 112 DptklE~YLSDeDF~~------VFGMsr~EF~~LP~WK 143 (154)
+-..+|..||+|+++. -.||+-..+.++|.|-
T Consensus 100 ~~~~l~~~Ls~e~~~~le~~~~~lGi~~~~~~~~~pW~ 137 (299)
T COG3735 100 DGENLEDRLSPEQLARLEMILQELGIPLQALSKMPPWQ 137 (299)
T ss_pred CCcchhhhcCHHHHHHHHHHHHHcCCCHHHHhcCCcHH
Confidence 4567999999999974 4799999999999995
No 17
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=24.63 E-value=67 Score=25.63 Aligned_cols=33 Identities=15% Similarity=0.123 Sum_probs=29.2
Q ss_pred ccccCCChHHHHHHhCCCHHHHhh-ChhHHHHHH
Q psy17879 115 NLERHLSDVEFETLFLCTRAEFYR-LPTWRRNDL 147 (154)
Q Consensus 115 klE~YLSDeDF~~VFGMsr~EF~~-LP~WKQ~~L 147 (154)
..+..++-+|....+||+|+...+ |-+|+++.+
T Consensus 175 ~i~i~lt~~~IA~~lGisretlsR~L~~L~~~Gl 208 (230)
T PRK09391 175 MMALPMSRRDIADYLGLTIETVSRALSQLQDRGL 208 (230)
T ss_pred EEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCc
Confidence 457889999999999999999988 889998863
No 18
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=24.00 E-value=74 Score=24.22 Aligned_cols=31 Identities=19% Similarity=0.303 Sum_probs=27.6
Q ss_pred ccCCChHHHHHHhCCCHHHHhh-ChhHHHHHH
Q psy17879 117 ERHLSDVEFETLFLCTRAEFYR-LPTWRRNDL 147 (154)
Q Consensus 117 E~YLSDeDF~~VFGMsr~EF~~-LP~WKQ~~L 147 (154)
...++-+|....+|++|+..++ |-+||+.++
T Consensus 166 ~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gi 197 (211)
T PRK11753 166 QIKITRQEIGRIVGCSREMVGRVLKMLEDQGL 197 (211)
T ss_pred ecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCC
Confidence 4579999999999999999998 889998874
No 19
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=23.23 E-value=71 Score=21.08 Aligned_cols=16 Identities=25% Similarity=0.418 Sum_probs=11.7
Q ss_pred HHHHHHhCCCHHHHhh
Q psy17879 123 VEFETLFLCTRAEFYR 138 (154)
Q Consensus 123 eDF~~VFGMsr~EF~~ 138 (154)
..|++.|||+..+|.+
T Consensus 65 ~~fk~~~g~tP~~~r~ 80 (81)
T PF12833_consen 65 RAFKRYFGMTPSEYRK 80 (81)
T ss_dssp HHHHHHHSS-HHHHHH
T ss_pred HHHHHHHCcCHHHHHc
Confidence 4678888999999853
No 20
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=22.53 E-value=84 Score=24.58 Aligned_cols=33 Identities=9% Similarity=0.194 Sum_probs=28.0
Q ss_pred ccccCCChHHHHHHhCCCHHHHhh-ChhHHHHHH
Q psy17879 115 NLERHLSDVEFETLFLCTRAEFYR-LPTWRRNDL 147 (154)
Q Consensus 115 klE~YLSDeDF~~VFGMsr~EF~~-LP~WKQ~~L 147 (154)
....-++.+|....+||+|+...+ |-+|+++.+
T Consensus 180 ~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~ 213 (235)
T PRK11161 180 EFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGM 213 (235)
T ss_pred eeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCC
Confidence 345678999999999999999998 778888765
No 21
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=21.48 E-value=9.6 Score=26.48 Aligned_cols=33 Identities=21% Similarity=0.368 Sum_probs=26.6
Q ss_pred CCccccccCCChHHHHHHhCCCHHHHhhChhHH
Q psy17879 111 VDRKNLERHLSDVEFETLFLCTRAEFYRLPTWR 143 (154)
Q Consensus 111 VDptklE~YLSDeDF~~VFGMsr~EF~~LP~WK 143 (154)
.||.++..-+.|+.++++||..+-.|..|+..=
T Consensus 39 ~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l 71 (76)
T PF02201_consen 39 QDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLL 71 (76)
T ss_dssp BESSSTTEEE-TTSHHHHHHTSECSEEETTHHH
T ss_pred CCcccCceEecCHHHHHHhCCCeecHhhHHHHH
Confidence 577777788899999999999888888887754
No 22
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=21.16 E-value=39 Score=22.59 Aligned_cols=23 Identities=17% Similarity=0.450 Sum_probs=16.3
Q ss_pred ChHHHHHHhCCCHHHHhhChhHHHH
Q psy17879 121 SDVEFETLFLCTRAEFYRLPTWRRN 145 (154)
Q Consensus 121 SDeDF~~VFGMsr~EF~~LP~WKQ~ 145 (154)
++.||.+.+||++.-+.. .|++.
T Consensus 14 ~~~~lA~~lgis~st~s~--~~~~r 36 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSN--NWKKR 36 (66)
T ss_dssp SCHHHHCCTT--HHHHH---HHHHS
T ss_pred CHHHHHHHhCcCHHHhhH--HHHhC
Confidence 567999999999999885 56654
No 23
>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=20.79 E-value=30 Score=18.69 Aligned_cols=14 Identities=14% Similarity=0.216 Sum_probs=11.8
Q ss_pred hHHHHHHhCCCHHH
Q psy17879 122 DVEFETLFLCTRAE 135 (154)
Q Consensus 122 DeDF~~VFGMsr~E 135 (154)
|++++.++.||+++
T Consensus 4 d~~L~~Al~~S~~e 17 (18)
T PF02809_consen 4 DEDLQRALEMSLEE 17 (18)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhhcc
Confidence 67889999998876
No 24
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=20.59 E-value=92 Score=23.62 Aligned_cols=33 Identities=9% Similarity=0.033 Sum_probs=28.5
Q ss_pred ccccCCChHHHHHHhCCCHHHHhh-ChhHHHHHH
Q psy17879 115 NLERHLSDVEFETLFLCTRAEFYR-LPTWRRNDL 147 (154)
Q Consensus 115 klE~YLSDeDF~~VFGMsr~EF~~-LP~WKQ~~L 147 (154)
..+..++-+|.....|++|+...+ |-+|++..+
T Consensus 145 ~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~ 178 (202)
T PRK13918 145 ETMIYATHDELAAAVGSVRETVTKVIGELSREGY 178 (202)
T ss_pred eEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCC
Confidence 567889999999999999999998 788887654
No 25
>PRK15070 propanediol utilization phosphotransacylase; Provisional
Probab=20.42 E-value=49 Score=28.33 Aligned_cols=22 Identities=36% Similarity=0.362 Sum_probs=19.2
Q ss_pred CCCCccccccCCChHHHHHHhC
Q psy17879 109 PDVDRKNLERHLSDVEFETLFL 130 (154)
Q Consensus 109 ~gVDptklE~YLSDeDF~~VFG 130 (154)
--|..+.+.-|||.+|++.+||
T Consensus 25 ipvgvS~RHvHLs~ed~e~LFG 46 (211)
T PRK15070 25 IPVGVSNRHVHLSQEDLEILFG 46 (211)
T ss_pred eEEEEecceeeCCHHHHHHhcC
Confidence 3366788999999999999998
No 26
>KOG3591|consensus
Probab=20.14 E-value=38 Score=27.46 Aligned_cols=19 Identities=42% Similarity=0.607 Sum_probs=16.5
Q ss_pred CCCCCCCCccccccCCChH
Q psy17879 105 YRLPPDVDRKNLERHLSDV 123 (154)
Q Consensus 105 ~~LP~gVDptklE~YLSDe 123 (154)
..||+|||++..-..||.+
T Consensus 121 y~LP~~vdp~~V~S~LS~d 139 (173)
T KOG3591|consen 121 YLLPEDVDPTSVTSTLSSD 139 (173)
T ss_pred ecCCCCCChhheEEeeCCC
Confidence 4799999999999988864
Done!