Query psy3598
Match_columns 175
No_of_seqs 35 out of 37
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 20:41:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3598.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3598hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4336|consensus 100.0 4.2E-37 9E-42 270.2 7.2 162 9-175 129-293 (323)
2 cd08049 TAF8 TATA Binding Prot 99.6 2.1E-16 4.6E-21 107.0 5.2 48 9-56 7-54 (54)
3 PF10406 TAF8_C: Transcription 99.6 2E-16 4.4E-21 106.7 4.8 46 8-53 6-51 (51)
4 PF05670 DUF814: Domain of unk 28.4 46 0.00099 24.0 2.0 20 10-29 37-56 (90)
5 PF02724 CDC45: CDC45-like pro 25.6 19 0.00041 34.8 -0.6 61 25-91 32-99 (622)
6 PF04931 DNA_pol_phi: DNA poly 23.8 45 0.00097 32.7 1.6 8 87-94 640-647 (784)
7 KOG0718|consensus 22.6 1.4E+02 0.0031 29.4 4.6 47 29-77 94-150 (546)
8 smart00667 LisH Lissencephaly 22.4 94 0.002 17.2 2.2 21 41-61 2-22 (34)
9 PF14687 DUF4460: Domain of un 21.7 91 0.002 24.1 2.6 21 39-59 5-25 (112)
10 COG4829 CatC1 Muconolactone de 20.3 1E+02 0.0022 24.3 2.5 49 18-66 3-59 (98)
No 1
>KOG4336|consensus
Probab=100.00 E-value=4.2e-37 Score=270.21 Aligned_cols=162 Identities=22% Similarity=0.313 Sum_probs=147.9
Q ss_pred CCCCCCCchhcccccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhHhCCCccccCCCCCceeeeccCCCCCccc-cccC
Q psy3598 9 RSLLKSSVVALLAETHKQPVTEYEAIREKAATQKRDLARALNKFIIKTEPIEHIFDEADDRFTLIVPKPEMLPYL-CLIP 87 (175)
Q Consensus 9 ~~~fP~pHTYirTpt~k~PvteYeaIREkaA~QkRdvEkALtrFlaKT~pt~SLF~~d~~~FpLI~~kP~~~pYL-ALlP 87 (175)
-||||+|||||.||++++|+|+|++|||++|+|+|++|+||++|++||+|++|||+++.+.|++++|+|.++||. ||||
T Consensus 129 LPpfPdpHTYi~Tpi~~~p~tsyk~iRe~aaqe~r~~e~AL~~~~~r~~p~~slf~~~~~~~~e~a~~p~~~py~~almp 208 (323)
T KOG4336|consen 129 LPPFPDPHTYIKTPIYKVPDTSYKAIREKAAQESRNSEKALTNYLKRNSPTSSLFPTDPSLFPEDACKPFNLPYSNALMP 208 (323)
T ss_pred CCCCCCCcccccCCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhccCCCCCcCHHHhcCccccchHHhhCc
Confidence 489999999999999999999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred CCccccc-cchhhhccCCccCCCChhhhhccccccchhcccCcchhhH-hhhcCCCCCCCCCCCCCCCCCCCCCCCcCCC
Q psy3598 88 KDQVFEE-DEDNIQASPQKKKKPTPVKKKSKKKKVEEDEEDGEEDEAE-EEEGEGNEEPEDTSNMVPDSEAIDNPYLRPV 165 (175)
Q Consensus 88 ~dQVFD~-die~~~~~~~r~~d~~~~k~~~~~~~~~~e~~~g~~~~~e-~~~~~~~~~t~~~~~~~~~~~~IDNPyLR~~ 165 (175)
.+||||+ .+++++.+++|+.+..-..+|.. ++.++...+++....+ .|+-....+|+++ .+.+++. |+|.|+.
T Consensus 209 ~~~v~~~d~~~~~~i~~~~~~~~~l~d~g~~-~~~enq~m~~d~~~l~~pe~~~~~~~~ts~--~iee~~r--ks~~~~~ 283 (323)
T KOG4336|consen 209 RKQVFDEDELEENNIEQYAKYRVELADEGVT-KFEENQLMLKDSETLEKPESRHQSSRTTSK--TIEEQDR--KSMTRAM 283 (323)
T ss_pred cccchhhhhhhhhhHHHhhhcchhhhhcccc-hhhHHHHHhhchhhhhCccccccccccchh--hhHhccc--chhhhcc
Confidence 9999999 78999999999999999999975 6777777777777666 7777778888887 7777776 9999999
Q ss_pred CCCccccCCC
Q psy3598 166 KYPQRIKSVK 175 (175)
Q Consensus 166 k~Pk~~k~~~ 175 (175)
+.+.++++.+
T Consensus 284 ~~~~~~~~l~ 293 (323)
T KOG4336|consen 284 TCLPGVQKLK 293 (323)
T ss_pred ccCcccccCC
Confidence 9999988653
No 2
>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8. The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo
Probab=99.64 E-value=2.1e-16 Score=106.97 Aligned_cols=48 Identities=23% Similarity=0.173 Sum_probs=46.2
Q ss_pred CCCCCCCchhcccccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhHh
Q psy3598 9 RSLLKSSVVALLAETHKQPVTEYEAIREKAATQKRDLARALNKFIIKT 56 (175)
Q Consensus 9 ~~~fP~pHTYirTpt~k~PvteYeaIREkaA~QkRdvEkALtrFlaKT 56 (175)
-|+||++|||++||++..+++||.++|+++|+|+|++|+||.+|++++
T Consensus 7 LP~FP~~HTY~~Tp~~~~~~~d~~~~r~~~~~~~r~~e~aL~~l~~~~ 54 (54)
T cd08049 7 LPPFPDPHTYKRTPTYSERETDPKKLREELASQRRLAEKALLRLQQKT 54 (54)
T ss_pred CCCCCCchhhccCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 489999999999999999999999999999999999999999999874
No 3
>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []. The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].
Probab=99.64 E-value=2e-16 Score=106.66 Aligned_cols=46 Identities=26% Similarity=0.189 Sum_probs=44.3
Q ss_pred CCCCCCCCchhcccccCCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy3598 8 NRSLLKSSVVALLAETHKQPVTEYEAIREKAATQKRDLARALNKFI 53 (175)
Q Consensus 8 ~~~~fP~pHTYirTpt~k~PvteYeaIREkaA~QkRdvEkALtrFl 53 (175)
.-|.||++|||++||++..+++||.+||+++|+|+|++|+||.+||
T Consensus 6 ~lP~fP~~HTY~~Tp~~~~~~~d~~~~r~~~~~~~r~~e~aL~~l~ 51 (51)
T PF10406_consen 6 WLPPFPPPHTYKRTPIYNERETDPKKIREKAAEQSRLAEKALRKLL 51 (51)
T ss_pred cCCCCCCCcccccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4589999999999999999999999999999999999999999986
No 4
>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 from SWISSPROT where the N-terminal region is involved in this activity []. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Probab=28.36 E-value=46 Score=23.99 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=16.3
Q ss_pred CCCCCCchhcccccCCCCcc
Q psy3598 10 SLLKSSVVALLAETHKQPVT 29 (175)
Q Consensus 10 ~~fP~pHTYirTpt~k~Pvt 29 (175)
..+||||+.|+..-...+..
T Consensus 37 ~~~pg~hvil~~~~~~~~~~ 56 (90)
T PF05670_consen 37 DDFPGPHVILRNNPGDEPPP 56 (90)
T ss_pred cCCCCCEEEEECCCCccchH
Confidence 46899999999987777654
No 5
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=25.58 E-value=19 Score=34.82 Aligned_cols=61 Identities=18% Similarity=0.296 Sum_probs=40.3
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHhHhCCCccc---cCC-CCCceeeeccCCCCCccc--cccC-CCcc
Q psy3598 25 KQPVTEYEAIREKAATQKRDLARALNKFIIKTEPIEHI---FDE-ADDRFTLIVPKPEMLPYL--CLIP-KDQV 91 (175)
Q Consensus 25 k~PvteYeaIREkaA~QkRdvEkALtrFlaKT~pt~SL---F~~-d~~~FpLI~~kP~~~pYL--ALlP-~dQV 91 (175)
-.||..|..|+.-..+...++.. =+|.-||-+..| |.- .+-.|.+|+. ++||- -|.. .+||
T Consensus 32 l~PV~gy~el~~~~~~~~~~~~~---vilIncGa~~dl~~~l~~~~~~~iyViDs---hRP~~L~Nv~~~~~~v 99 (622)
T PF02724_consen 32 LVPVSGYSELERAYEELDEDIKS---VILINCGATVDLEEFLELDEDVTIYVIDS---HRPWNLDNVFSDNDQV 99 (622)
T ss_pred EEEeCCHHHHHHHHHHHhhhhce---EEEEecCchhhHHHHhCCCCceEEEEEeC---CCCccHhhccCCCCcE
Confidence 47999999998887777444333 457788888865 544 3667777775 44444 5555 5654
No 6
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.77 E-value=45 Score=32.69 Aligned_cols=8 Identities=25% Similarity=0.588 Sum_probs=4.2
Q ss_pred CCCccccc
Q psy3598 87 PKDQVFEE 94 (175)
Q Consensus 87 P~dQVFD~ 94 (175)
+..+.||+
T Consensus 640 ~~~~~~~~ 647 (784)
T PF04931_consen 640 GQQELFEG 647 (784)
T ss_pred chhccccc
Confidence 34455665
No 7
>KOG0718|consensus
Probab=22.59 E-value=1.4e+02 Score=29.43 Aligned_cols=47 Identities=26% Similarity=0.431 Sum_probs=34.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhHhCCCcc---------cc-CCCCCceeeeccCC
Q psy3598 29 TEYEAIREKAATQKRDLARALNKFIIKTEPIEH---------IF-DEADDRFTLIVPKP 77 (175)
Q Consensus 29 teYeaIREkaA~QkRdvEkALtrFlaKT~pt~S---------LF-~~d~~~FpLI~~kP 77 (175)
...+-|||....++|- +.-.+-++|++|+.+ || .+|.++||+|..-.
T Consensus 94 ~tpeEIreE~Erl~r~--~de~~l~qr~~P~g~i~i~v~~t~lF~~~d~~~~p~i~~gs 150 (546)
T KOG0718|consen 94 KTPEEIREEYERLQRE--RDERRLQQRVQPTGEITINVNATPLFARNDESRFPLIEIGS 150 (546)
T ss_pred CCHHHHHHHHHHHHHH--HHHHHHHhhcCCCceEEEEecchhhhccCccccCCceeeee
Confidence 4567899998888774 444566889999865 47 45578999987743
No 8
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=22.39 E-value=94 Score=17.16 Aligned_cols=21 Identities=14% Similarity=0.385 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHhHhCCCcc
Q psy3598 41 QKRDLARALNKFIIKTEPIEH 61 (175)
Q Consensus 41 QkRdvEkALtrFlaKT~pt~S 61 (175)
+++++.+.+.+||.+.|-..+
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~t 22 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEET 22 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHHH
Confidence 578899999999999886655
No 9
>PF14687 DUF4460: Domain of unknown function (DUF4460)
Probab=21.66 E-value=91 Score=24.11 Aligned_cols=21 Identities=29% Similarity=0.365 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHhHhCCC
Q psy3598 39 ATQKRDLARALNKFIIKTEPI 59 (175)
Q Consensus 39 A~QkRdvEkALtrFlaKT~pt 59 (175)
.....++..||..|+.+.+|-
T Consensus 5 ~~~~~~l~~aLr~Fy~~VHPD 25 (112)
T PF14687_consen 5 NLSSPDLRSALRPFYFAVHPD 25 (112)
T ss_pred hhhhHHHHHHHHHHHHHhCCc
Confidence 456678999999999999995
No 10
>COG4829 CatC1 Muconolactone delta-isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.30 E-value=1e+02 Score=24.25 Aligned_cols=49 Identities=22% Similarity=0.229 Sum_probs=35.0
Q ss_pred hcccccCCCCcc------hHHHHHHHHHHHHHHHHHHHHHHHhHhCC--CccccCCC
Q psy3598 18 ALLAETHKQPVT------EYEAIREKAATQKRDLARALNKFIIKTEP--IEHIFDEA 66 (175)
Q Consensus 18 YirTpt~k~Pvt------eYeaIREkaA~QkRdvEkALtrFlaKT~p--t~SLF~~d 66 (175)
|+-|+|-+.|+. +=...|||+-+|+...|-.|.+.--+.|+ +-|||+-+
T Consensus 3 Flv~Mtv~~PdsMdad~~er~~A~Eka~s~~Lq~~G~~~~lWR~~GeyanyslFd~d 59 (98)
T COG4829 3 FLVTMTVRVPDSMDADAVERVRAREKARSRELQAQGKLLRLWRRPGEYANYSLFDAD 59 (98)
T ss_pred EEEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHHhcchHHHHHhccccccceeeecCC
Confidence 456788888885 33445788888877777777776666665 66799877
Done!