Query psy6174
Match_columns 174
No_of_seqs 9 out of 11
Neff 1.6
Searched_HMMs 46136
Date Fri Aug 16 19:35:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6174.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6174hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00659 POLO_box: POLO box du 46.4 19 0.00041 23.8 2.2 23 24-47 4-26 (68)
2 PHA03257 Capsid triplex subuni 30.3 21 0.00046 32.1 0.6 8 164-171 265-272 (316)
3 PF12540 DUF3736: Protein of u 29.7 46 0.001 26.7 2.4 64 94-162 43-112 (147)
4 KOG4163|consensus 28.2 21 0.00046 34.4 0.3 25 109-134 195-221 (551)
5 KOG3950|consensus 26.6 61 0.0013 29.3 2.8 80 30-114 106-198 (292)
6 PF10628 CotE: Outer spore coa 25.5 1.5E+02 0.0032 25.1 4.7 44 35-92 102-147 (182)
7 PF00394 Cu-oxidase: Multicopp 23.3 93 0.002 23.2 2.9 32 85-117 69-100 (159)
8 COG4535 CorC Putative Mg2+ and 22.1 38 0.00083 30.5 0.7 43 119-173 68-110 (293)
9 PF05240 APOBEC_C: APOBEC-like 21.3 27 0.00059 24.2 -0.3 16 26-42 7-22 (55)
10 PF15029 DUF4526: Protein of u 20.8 71 0.0015 28.1 2.0 135 16-173 24-178 (232)
11 KOG2345|consensus 20.1 55 0.0012 29.7 1.2 24 135-158 268-291 (302)
12 PF09383 NIL: NIL domain; Int 20.1 78 0.0017 20.9 1.7 35 27-61 19-53 (76)
No 1
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=46.37 E-value=19 Score=23.76 Aligned_cols=23 Identities=30% Similarity=0.510 Sum_probs=18.0
Q ss_pred eecceeeeecCceEEEEecCcceE
Q psy6174 24 LLGLSTLRRDGDVTVNVMSAHTTV 47 (174)
Q Consensus 24 LyGLsSLkR~gdV~Vn~m~~hTTv 47 (174)
=||+.-.--+|.|-|| ..|||.|
T Consensus 4 k~gi~~~LSng~vqv~-FnD~tki 26 (68)
T PF00659_consen 4 KYGIGYQLSNGTVQVN-FNDHTKI 26 (68)
T ss_dssp CSEEEEEETTSEEEEE-ETTS-EE
T ss_pred ceEEEEEEeCCCEEEE-EeCCCEE
Confidence 3677777779999999 8999876
No 2
>PHA03257 Capsid triplex subunit 2; Provisional
Probab=30.31 E-value=21 Score=32.10 Aligned_cols=8 Identities=63% Similarity=1.331 Sum_probs=6.5
Q ss_pred CCCCcccc
Q psy6174 164 SRYPVYEE 171 (174)
Q Consensus 164 ~~~~~~~~ 171 (174)
-||||||.
T Consensus 265 rr~~~yea 272 (316)
T PHA03257 265 RRFPVYEA 272 (316)
T ss_pred ccccHHHH
Confidence 48999983
No 3
>PF12540 DUF3736: Protein of unknown function (DUF3736); InterPro: IPR022207 This domain family is found in eukaryotes, and is typically between 135 and 160 amino acids in length.
Probab=29.71 E-value=46 Score=26.66 Aligned_cols=64 Identities=28% Similarity=0.391 Sum_probs=34.9
Q ss_pred CceeeEEEeeecCceeeeccCCCcchhhhhhhc---ccchhHHHHHHHHHHHhhhhc---CCCCCCCCCCCCCCC
Q psy6174 94 GQATLHSIRVLQPKQVRVDSQDDHDSTREFLWK---RSSHIAHLVTEKLTSAARSLL---QPIPSNTPHIPLPPP 162 (174)
Q Consensus 94 g~AtLhSIrVlQPkqvrV~S~DnHdrTREfvW~---RS~~IA~lVseKL~~Aarsml---~p~p~~t~~~~~~~~ 162 (174)
+.|++|+|= -||--++ |+.-+|.+|+|+ ++...|.-..+-...--+-|| .|.|..-++.|-.|+
T Consensus 43 v~a~~~~V~-~~pPl~~----~~~~~~~~fl~~~~~~~~~~~~~~~~~~~~~r~r~l~~~~p~~q~~~~~p~~Ps 112 (147)
T PF12540_consen 43 VPATLRRVP-EQPPLVL----DASTMKVEFLWRVGQTTPQQACRYYQGQRRKRRRMLREEPPSPQEKQGKPPVPS 112 (147)
T ss_pred ccCCCCccC-CCCCeee----cccccchhHHHHhhccccchhhHhhhccccccccccccCCCCccccccCCCCCC
Confidence 357777663 3555544 456799999998 444555544444333344455 344444444443333
No 4
>KOG4163|consensus
Probab=28.23 E-value=21 Score=34.36 Aligned_cols=25 Identities=40% Similarity=0.612 Sum_probs=16.9
Q ss_pred eeecc--CCCcchhhhhhhcccchhHHH
Q psy6174 109 VRVDS--QDDHDSTREFLWKRSSHIAHL 134 (174)
Q Consensus 109 vrV~S--~DnHdrTREfvW~RS~~IA~l 134 (174)
||-|- +--.-|||||+||- -|-||+
T Consensus 195 vRWEfk~p~PFlRtrEFLWQE-GHTAfa 221 (551)
T KOG4163|consen 195 VRWEFKHPQPFLRTREFLWQE-GHTAFA 221 (551)
T ss_pred eeeeccCCCcchhhhHHHHhc-CcchhC
Confidence 44443 34567999999996 466665
No 5
>KOG3950|consensus
Probab=26.60 E-value=61 Score=29.27 Aligned_cols=80 Identities=29% Similarity=0.479 Sum_probs=50.8
Q ss_pred eeecCceEEEEecCcceEEeeeeecceeEeeehhhcchhhhhhhhc------ccccce-eeeeeEEEEeeCC-ceeeEEE
Q psy6174 30 LRRDGDVTVNVMSAHTTVKAKFFVGPLMLKVEKEFGRGVKKELRSA------TATTAE-MMGKINLRVMHGG-QATLHSI 101 (174)
Q Consensus 30 LkR~gdV~Vn~m~~hTTvK~kF~~GPL~LkVEKefgrgakkelrSA------TAtT~E-M~Gkl~lrv~~gg-~AtLhSI 101 (174)
|+-.-+|+||.-.++..|-++|++||= +||-.-. +=|+++- +|.-.| -+|-=+|||+-.| +--=|||
T Consensus 106 ~~S~rnvtvnarn~~g~v~~~l~lgp~--~ve~~~~---~Fev~~~dgk~LFsad~dEv~vgae~LRv~g~~GavF~~sv 180 (292)
T KOG3950|consen 106 LQSARNVTVNARNPNGKVTGQLILGPK--KVEAQCK---RFEVNDVDGKLLFSADEDEVVVGAEKLRVLGAEGAVFEHSV 180 (292)
T ss_pred EEeccCeeEEccCCCCceeeeEEechH--HHhhhhc---eeEEecCCCcEEEEeccceeEeeeeeeEeccCCcccccccc
Confidence 566779999999999999999999997 6664322 2233221 233334 3677789998644 4444665
Q ss_pred ee----ecC-ceeeeccC
Q psy6174 102 RV----LQP-KQVRVDSQ 114 (174)
Q Consensus 102 rV----lQP-kqvrV~S~ 114 (174)
.- -|| +.+|.|||
T Consensus 181 eTp~VRa~P~~~LRLESP 198 (292)
T KOG3950|consen 181 ETPHVRADPFQELRLESP 198 (292)
T ss_pred cCCcccCCCCccccccCC
Confidence 32 133 34667764
No 6
>PF10628 CotE: Outer spore coat protein E (CotE); InterPro: IPR018901 CotE is a morphogenic protein that is required for the assembly of the outer coat of the endospore [] and spore resistance to lysozyme []. CotE also regulates the expression of cotA, cotB, cotC and other genes encoding spore outer coat proteins []. The timing of cotE expression has been shown in Bacillus subtilis to affect spore coat morphology but not lysozyme resistance [].
Probab=25.47 E-value=1.5e+02 Score=25.09 Aligned_cols=44 Identities=25% Similarity=0.490 Sum_probs=30.6
Q ss_pred ceEEEEecCcceEEeeeee-c-ceeEeeehhhcchhhhhhhhcccccceeeeeeEEEEee
Q psy6174 35 DVTVNVMSAHTTVKAKFFV-G-PLMLKVEKEFGRGVKKELRSATATTAEMMGKINLRVMH 92 (174)
Q Consensus 35 dV~Vn~m~~hTTvK~kF~~-G-PL~LkVEKefgrgakkelrSATAtT~EM~Gkl~lrv~~ 92 (174)
+|.+.+...=..+.|...= | =++++||+||. .||+|.-+++|.-
T Consensus 102 eV~a~~~q~P~C~eA~Is~~G~~I~V~VErE~~--------------vEVIGETKv~V~v 147 (182)
T PF10628_consen 102 EVIARVIQQPNCLEASISSNGNKIIVEVEREFA--------------VEVIGETKVCVAV 147 (182)
T ss_pred eEEEEEccCCceEEEEEcCCCCEEEEEEEeeee--------------eeeeeceEEEEEE
Confidence 3444455555566666543 3 48899999994 7999999998853
No 7
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=23.35 E-value=93 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=21.4
Q ss_pred eeEEEEeeCCceeeEEEeeecCceeeeccCCCc
Q psy6174 85 KINLRVMHGGQATLHSIRVLQPKQVRVDSQDDH 117 (174)
Q Consensus 85 kl~lrv~~gg~AtLhSIrVlQPkqvrV~S~DnH 117 (174)
+..||++++|..+.+.+.+-.- .+.|-..|-+
T Consensus 69 ~~rlRliNa~~~~~~~~~i~gh-~~~Via~DG~ 100 (159)
T PF00394_consen 69 RYRLRLINAGASTSFNFSIDGH-PMTVIAADGV 100 (159)
T ss_dssp EEEEEEEEESSS-BEEEEETTB-CEEEEEETTE
T ss_pred EEEEEEEeccCCeeEEEEeecc-ceeEeeeccc
Confidence 5889999999999888887543 3444444433
No 8
>COG4535 CorC Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]
Probab=22.11 E-value=38 Score=30.50 Aligned_cols=43 Identities=28% Similarity=0.499 Sum_probs=27.4
Q ss_pred hhhhhhhcccchhHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCcccccC
Q psy6174 119 STREFLWKRSSHIAHLVTEKLTSAARSLLQPIPSNTPHIPLPPPPSRYPVYEEDN 173 (174)
Q Consensus 119 rTREfvW~RS~~IA~lVseKL~~Aarsml~p~p~~t~~~~~~~~~~~~~~~~~~~ 173 (174)
+-|+.|--||.+++--..|-|..-..-|.. ++| |||||+.||.
T Consensus 68 ~vrDiMIPRSQM~~l~~~~~l~~~l~~iie-----saH-------SRfPVi~edk 110 (293)
T COG4535 68 RVRDIMIPRSQMITLKRNQTLDECLDVIIE-----SAH-------SRFPVISEDK 110 (293)
T ss_pred hHhhhcccHHHheeccccCCHHHHHHHHHH-----hcc-------ccCCcccCCc
Confidence 456777777777765555555444433332 234 8999999985
No 9
>PF05240 APOBEC_C: APOBEC-like C-terminal domain; InterPro: IPR007904 This domain is found at the C terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. C to U RNA editing of mammalian apolipoprotein B (apoB) RNA is a site-specific posttranscriptional modification in which a single cytidine is enzymatically deaminated to uridine, thereby generating a UAA stop codon in the edited mRNA. The function of this domain is currently unknown.; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 2NYT_D.
Probab=21.27 E-value=27 Score=24.17 Aligned_cols=16 Identities=38% Similarity=0.690 Sum_probs=10.9
Q ss_pred cceeeeecCceEEEEec
Q psy6174 26 GLSTLRRDGDVTVNVMS 42 (174)
Q Consensus 26 GLsSLkR~gdV~Vn~m~ 42 (174)
||-.|.+.| |+|.||+
T Consensus 7 gLr~L~~aG-~~v~iM~ 22 (55)
T PF05240_consen 7 GLRRLCQAG-AQVSIMT 22 (55)
T ss_dssp HHHHHHHTT--EEEE--
T ss_pred HHHHHHHCC-CeEEecC
Confidence 777888888 8888885
No 10
>PF15029 DUF4526: Protein of unknown function (DUF4526)
Probab=20.83 E-value=71 Score=28.05 Aligned_cols=135 Identities=27% Similarity=0.339 Sum_probs=70.1
Q ss_pred CCcccceeee--cceeeeecCceEEEEecCcceE-Eeee----eecceeEeeehhhcchh-----------hhhhhhccc
Q psy6174 16 SHPRAKATLL--GLSTLRRDGDVTVNVMSAHTTV-KAKF----FVGPLMLKVEKEFGRGV-----------KKELRSATA 77 (174)
Q Consensus 16 s~prAkaTLy--GLsSLkR~gdV~Vn~m~~hTTv-K~kF----~~GPL~LkVEKefgrga-----------kkelrSATA 77 (174)
..-||-|||. |+= |--. -+|..+|+=+-.= -+.| +|||+.|-|---|--=| -||-.-..-
T Consensus 24 D~dKaGaTLLFSGiF-LglV-GiTFTVmGWik~~g~shfeWTQLLGPILLsVGvtFiLIaVcKFkmlsC~~Cke~EE~~~ 101 (232)
T PF15029_consen 24 DDDKAGATLLFSGIF-LGLV-GITFTVMGWIKYQGVSHFEWTQLLGPILLSVGVTFILIAVCKFKMLSCQPCKESEERVL 101 (232)
T ss_pred cCcccceeeehhhHH-Hhhh-eeeEEEEeeeecceecceehhhhhcceeeeecceeeeeeeeeeeEEeeeeccccccccc
Confidence 4567888873 110 1111 2567777632211 1223 69999998854432111 133333334
Q ss_pred ccceeeeeeEEEEeeC--CceeeEEEeeecCceeeeccCCCcchhhhhhhcccchhHHHHHHHHHHHhhhhcCCCCCCCC
Q psy6174 78 TTAEMMGKINLRVMHG--GQATLHSIRVLQPKQVRVDSQDDHDSTREFLWKRSSHIAHLVTEKLTSAARSLLQPIPSNTP 155 (174)
Q Consensus 78 tT~EM~Gkl~lrv~~g--g~AtLhSIrVlQPkqvrV~S~DnHdrTREfvW~RS~~IA~lVseKL~~Aarsml~p~p~~t~ 155 (174)
-+..+.|.=+|- .+| ---|+|--.|.|=--=--.|+|.-- ++- -.-+-.+..|+.-+
T Consensus 102 d~eq~~gGqSfV-FTGINQPITFhGatVVqYIPPpY~sqe~~g------------~~~--------p~~~~~~~~~s~~~ 160 (232)
T PF15029_consen 102 DTEQTSGGQSFV-FTGINQPITFHGATVVQYIPPPYGSQEPMG------------MNT--------PVVSNCGLLPSGGA 160 (232)
T ss_pred ccccCCCCceEE-EecCCCCeEecceeEEEEcCCCCCCcCccc------------ccC--------cccCCcccCCCCCc
Confidence 556666665552 222 1346777777762111122332210 000 01122445667777
Q ss_pred CCCCCCCCCCCCcccccC
Q psy6174 156 HIPLPPPPSRYPVYEEDN 173 (174)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~ 173 (174)
-+..|.||.-|.||--||
T Consensus 161 ~~~~~spPqYy~iYp~DN 178 (232)
T PF15029_consen 161 AGTMPSPPQYYTIYPMDN 178 (232)
T ss_pred cccCCCCCcceEeccCCC
Confidence 788999999999999988
No 11
>KOG2345|consensus
Probab=20.09 E-value=55 Score=29.68 Aligned_cols=24 Identities=38% Similarity=0.587 Sum_probs=22.4
Q ss_pred HHHHHHHHhhhhcCCCCCCCCCCC
Q psy6174 135 VTEKLTSAARSLLQPIPSNTPHIP 158 (174)
Q Consensus 135 VseKL~~Aarsml~p~p~~t~~~~ 158 (174)
.||+|-+--++|++++|..-|+|+
T Consensus 268 yse~l~~lik~mlqvdP~qRP~i~ 291 (302)
T KOG2345|consen 268 YSEALHQLIKSMLQVDPNQRPTIP 291 (302)
T ss_pred ccHHHHHHHHHHhcCCcccCCCHH
Confidence 689999999999999999999986
No 12
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=20.08 E-value=78 Score=20.90 Aligned_cols=35 Identities=26% Similarity=0.306 Sum_probs=26.8
Q ss_pred ceeeeecCceEEEEecCcceEEeeeeecceeEeee
Q psy6174 27 LSTLRRDGDVTVNVMSAHTTVKAKFFVGPLMLKVE 61 (174)
Q Consensus 27 LsSLkR~gdV~Vn~m~~hTTvK~kF~~GPL~LkVE 61 (174)
||.|-|.-++.+|+..-+.+-=..=.+|=|+|.+.
T Consensus 19 is~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~ 53 (76)
T PF09383_consen 19 ISQLIREFGVDVNILHGNIEEIQGTPFGILILELP 53 (76)
T ss_dssp HHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred HHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEE
Confidence 56778888999999877666555667899999993
Done!