Query psy6561
Match_columns 223
No_of_seqs 19 out of 21
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 21:16:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6561.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6561hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13567 DUF4131: Domain of un 47.5 68 0.0015 23.5 5.5 50 15-66 96-150 (176)
2 PRK03348 DNA polymerase IV; Pr 36.6 26 0.00057 33.0 2.3 42 28-72 408-449 (454)
3 PF14913 DPCD: DPCD protein fa 26.6 35 0.00076 30.4 1.3 36 148-183 124-160 (194)
4 cd02859 AMPKbeta_GBD_like AMP- 25.6 2.6E+02 0.0057 20.1 7.1 19 34-56 2-20 (79)
5 PF01064 Activin_recp: Activin 19.5 1.4E+02 0.003 21.0 2.9 34 97-130 20-53 (83)
6 PF11639 HapK: REDY-like prote 16.1 1E+02 0.0023 25.1 1.9 36 39-79 27-62 (104)
7 PF12658 Ten1: Telomere cappin 15.9 1E+02 0.0022 25.0 1.8 18 39-58 18-35 (124)
8 KOG1047|consensus 15.2 80 0.0017 32.5 1.2 22 19-40 137-158 (613)
9 KOG0863|consensus 15.0 91 0.002 29.1 1.4 25 13-37 51-75 (264)
10 PF06268 Fascin: Fascin domain 14.1 97 0.0021 23.3 1.2 15 145-159 36-50 (111)
No 1
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=47.49 E-value=68 Score=23.50 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=36.2
Q ss_pred eeeEEee----cceeeecCCCCCeEEEEeccccc-CCCCCeEEEeeeecCCCCCCCC
Q psy6561 15 QYEFNVH----ARSIFPCFAHGGITVLFQYPKCI-LPISDKIRLFGKVPADVSSPRS 66 (223)
Q Consensus 15 qyvlnVh----arSIFPC~~~gGV~VlfqyPsC~-l~~~DRVRVyg~~~a~v~s~~~ 66 (223)
+|.+.|+ ...-.|+. +-+.+..+-++.. +..+|++++-|+++.-..+.+|
T Consensus 96 ~~~~~~~~~~~~~~~~~~~--~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~~~~~~Np 150 (176)
T PF13567_consen 96 RFTLRVERVLAGGNWIPVS--GKILLYLPKDSQPRLQPGDRIRVRGKLKPPSGPTNP 150 (176)
T ss_pred EEEEEEEEeeccccccccc--eeeEEEeccccccccCCCCEEEEEEEEecCCCCCCC
Confidence 5666654 34555664 7888888888888 7789999999999955444444
No 2
>PRK03348 DNA polymerase IV; Provisional
Probab=36.65 E-value=26 Score=33.01 Aligned_cols=42 Identities=21% Similarity=0.224 Sum_probs=34.8
Q ss_pred cCCCCCeEEEEecccccCCCCCeEEEeeeecCCCCCCCCCCceeE
Q psy6561 28 CFAHGGITVLFQYPKCILPISDKIRLFGKVPADVSSPRSPSSQIY 72 (223)
Q Consensus 28 C~~~gGV~VlfqyPsC~l~~~DRVRVyg~~~a~v~s~~~P~sL~Y 72 (223)
=.|||-|+|.|+++..- -.+||-|...+.+-.+.+|+++|.+
T Consensus 408 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~ 449 (454)
T PRK03348 408 GAGHGVVTVRFETRTTG---PGPVRTFPVDDPDLTPADPLDSLDW 449 (454)
T ss_pred cCCCeEEEEEeccCCCC---CCCccccCCCCcccCcCCCCCcccc
Confidence 45788999999999655 5799999999988888888877754
No 3
>PF14913 DPCD: DPCD protein family
Probab=26.63 E-value=35 Score=30.41 Aligned_cols=36 Identities=28% Similarity=0.481 Sum_probs=27.2
Q ss_pred EEEecCcccccc-cccccccccccccccceeeeeccc
Q psy6561 148 KIRTSNNKYLKS-TIPAITKGASKRRSNKISVSNFHN 183 (223)
Q Consensus 148 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 183 (223)
-|||+|.||.|. .||-+-.-.-+-..+.+|+.--||
T Consensus 124 vvRTtNKKYyKk~~IPDl~R~~l~l~~~~ls~~h~nN 160 (194)
T PF14913_consen 124 VVRTTNKKYYKKFSIPDLDRCGLPLEQSALSFAHQNN 160 (194)
T ss_pred EEECcCccceeEecCCcHHhhCCCcchhhceeeeecC
Confidence 589999999985 688887666666667777766555
No 4
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=25.59 E-value=2.6e+02 Score=20.14 Aligned_cols=19 Identities=16% Similarity=0.408 Sum_probs=15.3
Q ss_pred eEEEEecccccCCCCCeEEEeee
Q psy6561 34 ITVLFQYPKCILPISDKIRLFGK 56 (223)
Q Consensus 34 V~VlfqyPsC~l~~~DRVRVyg~ 56 (223)
++|.|+++. ..++|.|-|-
T Consensus 2 ~~v~f~~~~----~a~~V~v~G~ 20 (79)
T cd02859 2 VPTTFVWPG----GGKEVYVTGS 20 (79)
T ss_pred eEEEEEEcC----CCcEEEEEEE
Confidence 578888887 4689999984
No 5
>PF01064 Activin_recp: Activin types I and II receptor domain; InterPro: IPR000472 Transforming growth factor-beta (TGF-beta) forms a family with other growth factors described in PDOC00223 from PROSITEDOC. The receptors for most of the members of this growth factor family are related. These proteins are receptor-type kinases of Ser/Thr type PDOC00100 from PROSITEDOC), which have a single transmembrane domain and a specific hydrophilic Cys-rich ligand-binding domain [, , ]. The C-terminal part of the extracellular domain is conserved. Some of the receptors of this family contain subclass-specific N-terminal extensions of this homology domain. The type I receptors also possess 7 extracellular residues preceding the cysteine box.; GO: 0004675 transmembrane receptor protein serine/threonine kinase activity, 0005024 transforming growth factor beta-activated receptor activity, 0016020 membrane; PDB: 3EVS_C 1BTE_A 1LX5_B 2GOO_C 2HLR_A 4FAO_W 2H64_C 2H62_D 1S4Y_C 1NYU_C ....
Probab=19.52 E-value=1.4e+02 Score=20.97 Aligned_cols=34 Identities=26% Similarity=0.333 Sum_probs=26.3
Q ss_pred cceeEEEEEeccCcceeeeccccccceeccCCCC
Q psy6561 97 VEYCFVYVSQDSTGAVSDVKSDCVPTYPVSGQGP 130 (223)
Q Consensus 97 ~eYCFvYVSqA~tGAV~dv~~~CVPTlPv~~~~~ 130 (223)
..+||+.+.+..+|.+..+.+-|++.......+.
T Consensus 20 ~~~Cf~~~~~~~~~~~~~~~~GC~~~~~~~~~~~ 53 (83)
T PF01064_consen 20 GGFCFTSWEQDNGGGVEIVKKGCWSNEEDCPLCR 53 (83)
T ss_dssp SCEEEEEEEEETTESEEEEEEEEEESTGGGTTTS
T ss_pred CCEEEEEEEEeeccceeEEEcCccCCccCcceec
Confidence 6899999999988656667779998776655443
No 6
>PF11639 HapK: REDY-like protein HapK; InterPro: IPR021667 This family of proteins represents HapK, a protein of unknown function, with two homologues PigK and RedY. The monomer structure of the protein contains a four-stranded anti parallel beta-sheet, three alpha-helices and a short C-terminal tail which it uses for dimer formation []. The surface of HapK has a deep cavity with consists of a kinked helix and a beta-four strand. HapK could be involved in prodigiosin biosynthesis, specifically the binding of a bipyrrole intermediate such as HBM or MBM []. ; PDB: 2JDJ_B.
Probab=16.10 E-value=1e+02 Score=25.14 Aligned_cols=36 Identities=31% Similarity=0.438 Sum_probs=22.9
Q ss_pred ecccccCCCCCeEEEeeeecCCCCCCCCCCceeEEEEeeec
Q psy6561 39 QYPKCILPISDKIRLFGKVPADVSSPRSPSSQIYITEKKVI 79 (223)
Q Consensus 39 qyPsC~l~~~DRVRVyg~~~a~v~s~~~P~sL~YI~ErRI~ 79 (223)
+||.|- .-..||=|.+.+++ +...+| .|||+=..|.
T Consensus 27 Dy~tc~--~L~sV~sF~V~r~s-~~~~aP--y~YiEiI~V~ 62 (104)
T PF11639_consen 27 DYPTCP--SLPSVRSFEVHRAS-SEADAP--YHYIEIIDVS 62 (104)
T ss_dssp HHHHGG--G-TTEEEEEEEE-----TT-S---SEEEEEEES
T ss_pred chhccc--CCCceeeEEEEEcc-CCCCCC--ccEEEEEecC
Confidence 588897 57889999999986 455566 8899866553
No 7
>PF12658 Ten1: Telomere capping, CST complex subunit; InterPro: IPR024222 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF8_D 3KF6_B 3K0X_A.
Probab=15.90 E-value=1e+02 Score=25.00 Aligned_cols=18 Identities=44% Similarity=0.837 Sum_probs=13.6
Q ss_pred ecccccCCCCCeEEEeeeec
Q psy6561 39 QYPKCILPISDKIRLFGKVP 58 (223)
Q Consensus 39 qyPsC~l~~~DRVRVyg~~~ 58 (223)
+-|+|. .++|||++|+-.
T Consensus 18 ~l~s~~--~g~KVRfLgcV~ 35 (124)
T PF12658_consen 18 QLPSCS--PGDKVRFLGCVS 35 (124)
T ss_dssp GGGCTT--CTEEEEEEEEEE
T ss_pred ccccCC--CCCEEEEEEEEe
Confidence 346776 699999999554
No 8
>KOG1047|consensus
Probab=15.18 E-value=80 Score=32.46 Aligned_cols=22 Identities=36% Similarity=0.723 Sum_probs=15.0
Q ss_pred EeecceeeecCCCCCeEEEEec
Q psy6561 19 NVHARSIFPCFAHGGITVLFQY 40 (223)
Q Consensus 19 nVharSIFPC~~~gGV~Vlfqy 40 (223)
.+|+||||||--.-.+.+-|..
T Consensus 137 AIhaRsi~PC~DTPavK~ty~a 158 (613)
T KOG1047|consen 137 AIHARSIFPCQDTPAVKSTYTA 158 (613)
T ss_pred HhHHheeccccCCCcceeEEEE
Confidence 4799999999744455544443
No 9
>KOG0863|consensus
Probab=15.04 E-value=91 Score=29.07 Aligned_cols=25 Identities=32% Similarity=0.460 Sum_probs=20.4
Q ss_pred cceeeEEeecceeeecCCCCCeEEE
Q psy6561 13 NHQYEFNVHARSIFPCFAHGGITVL 37 (223)
Q Consensus 13 S~qyvlnVharSIFPC~~~gGV~Vl 37 (223)
-.+-.|+-|+|-|||||.|-||.+-
T Consensus 51 r~~seLss~QkKi~~iD~h~g~siA 75 (264)
T KOG0863|consen 51 RAQSELSSHQKKIFKIDDHIGISIA 75 (264)
T ss_pred cchhHHHHhhheeEecccccceEEe
Confidence 3444788899999999999999853
No 10
>PF06268 Fascin: Fascin domain; InterPro: IPR022768 This family consists of several eukaryotic fascin or singed proteins. The fascins are a structurally unique and evolutionarily conserved group of actin cross-linking proteins. Fascins function in the organisation of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles. The cortical structures, which include filopodia, spikes, lamellipodial ribs, oocyte microvilli and the dendrites of dendritic cells, have roles in cell-matrix adhesion, cell interactions and cell migration, whereas the cytoplasmic actin bundles appear to participate in cell architecture []. Dictyostelium hisactophilin, another actin-binding protein, is a submembranous pH sensor that signals slight changes of the H+ concentration to actin by inducing actin polymerisation and binding to microfilaments only at pH values below seven []. Members of this family are histidine rich, typically contain the repeated motif of HHXH []. ; GO: 0030674 protein binding, bridging, 0051015 actin filament binding; PDB: 1DFC_B 3P53_B 3LLP_A 1HCE_A 1HCD_A.
Probab=14.15 E-value=97 Score=23.28 Aligned_cols=15 Identities=33% Similarity=0.414 Sum_probs=11.9
Q ss_pred eeeEEEecCcccccc
Q psy6561 145 AFWKIRTSNNKYLKS 159 (223)
Q Consensus 145 ~~~~~~~~~~~~~~~ 159 (223)
..|.||++|+|||..
T Consensus 36 ~~v~lrs~~GkYls~ 50 (111)
T PF06268_consen 36 YKVALRSHNGKYLSV 50 (111)
T ss_dssp EEEEEECTTSEEEEE
T ss_pred CEEEEEcCCCCEEEE
Confidence 345699999999983
Done!