Query 024443
Match_columns 267
No_of_seqs 184 out of 412
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:39:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024443.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024443hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3149 Transcription initiati 100.0 4.9E-41 1.1E-45 306.0 16.0 213 39-251 4-231 (249)
2 PF03366 YEATS: YEATS family; 100.0 3.3E-35 7.1E-40 228.8 8.2 82 71-152 1-82 (84)
3 COG5033 TFG3 Transcription ini 100.0 1.7E-34 3.7E-39 257.2 11.8 189 40-251 3-206 (225)
4 KOG1349 Gpi-anchor transamidas 52.1 24 0.00053 33.8 4.7 36 225-260 151-191 (309)
5 PLN00172 ubiquitin conjugating 47.4 45 0.00097 28.3 5.2 34 69-102 28-61 (147)
6 PF09154 DUF1939: Domain of un 44.2 13 0.00028 27.3 1.2 14 113-126 36-49 (57)
7 COG0031 CysK Cysteine synthase 40.6 20 0.00043 34.5 2.3 30 236-265 122-151 (300)
8 smart00212 UBCc Ubiquitin-conj 26.5 2.1E+02 0.0045 23.5 5.9 35 69-103 26-60 (145)
9 cd00195 UBCc Ubiquitin-conjuga 19.1 3.1E+02 0.0067 22.4 5.5 34 70-103 27-60 (141)
10 COG5206 GPI8 Glycosylphosphati 17.7 1.2E+02 0.0026 29.5 3.0 36 225-260 151-191 (382)
No 1
>KOG3149 consensus Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=100.00 E-value=4.9e-41 Score=305.97 Aligned_cols=213 Identities=37% Similarity=0.567 Sum_probs=182.9
Q ss_pred cccceeeeeEEEEeEEEccceEEcCCCCCCCCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCCCcceecCCCcEEEee
Q 024443 39 NLNKKLKDVEISIPIVYGNVAFWLGKKASEYQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNNPTRAVESPPFELSES 118 (267)
Q Consensus 39 ~~~kR~k~v~I~~pIv~Gn~A~~l~kk~~e~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~ 118 (267)
.+.+|++.++|+++|+|||.|++++++.++.+||.|+|||||.++||++.||+||+|+||+||+||+|+|++|||+|+|+
T Consensus 4 ~~~~~~~~~~~~~~iv~G~~a~~~~~~~~~~~th~w~v~v~~~~~ed~~~~V~KV~f~LH~sf~~P~Rvv~~pPf~i~Et 83 (249)
T KOG3149|consen 4 ASIKRTKECTISVPIVPGNRAAILGKRLPDGFTHIWEVYVRGPGKEDISAFVDKVVFKLHESFPNPRRVVESPPFEITET 83 (249)
T ss_pred cCcceeeeeeEEeeeecCccccccCCCCCcccceeeEEEecCcCccccceeeeeeeeecccccccccccccCCCceEEee
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeEEEEEEEEEeecCCCCCEEEEEEeecCCCCC---CCC-----------CCCCCCeEEEeee-EEEecCCCHHHHHH
Q 024443 119 GWGEFEIAITLYFHADVCDKPLNLYHHLKLYPEDE---SGS-----------MSTKKPVVVESYD-EIVFPEPSDSFLAR 183 (267)
Q Consensus 119 GWGEF~I~I~I~F~~d~~ekpi~i~H~L~L~~~~~---~~~-----------~~~~~pVv~E~yd-eIvF~nPse~f~~~ 183 (267)
|||||+|.|+|||.++.+++++.++|+|.|+.++. ..+ ...+.+|+.+.|+ +++|++|++.++..
T Consensus 84 GwgeF~i~i~i~f~d~~~~~~v~~~~~l~l~~~~~p~~~~~~~~~~~~~~~~~~~r~~v~~~~~~~e~~f~~~~~~~~~~ 163 (249)
T KOG3149|consen 84 GWGEFEIQIEIFFTDDANEKKVTLYHDLKLHSYGAPPVPHEESTKKTFVNPTISLRIPVVREGVDVEIVFPDPTESTSIE 163 (249)
T ss_pred ccccceEEEEEEeccCCCCceeeeeeeEEeeccCCCCccchhhhcccccccchhcccccccccccceeecCCCCcccccc
Confidence 99999999999999999999999999999998752 111 2457889999999 99999999999999
Q ss_pred HHcCCCccCCCCCCCCCCCCCCCccccccccCCCCCCCcchhhhcCcChHHHHHHHHHHHHHHHhcCC
Q 024443 184 VQNHPAVTLPRLPVGFTLPPPVPIEDTSKRKRGDTKDHPLAQWFMNFSEADELLQLAAARQQEHSNSP 251 (267)
Q Consensus 184 L~~~p~~~~~~~p~~~~~p~~~~~e~~~~~~~~~t~~~~~~~~f~~~~E~~El~~L~~ar~~V~~~~~ 251 (267)
+...+.....+.+.....++...........+..+++.-...+.....|.+|.++|..+.+.++++..
T Consensus 164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~e~~~~d~~~~~~~~~~~~~~ 231 (249)
T KOG3149|consen 164 ASSRPVGPGSNLAAVTDLKQVKSKTLPSLLSKESSKDVKTEKSSERPNEIDEVDRLEKKIKELKKEIN 231 (249)
T ss_pred cCCCCCcCCccccccccccccccccCcccccccccccccccccccccccchhhhhhhhhhhhhhhHHH
Confidence 99998776655555555555443444444455667777777888889999999999888777766543
No 2
>PF03366 YEATS: YEATS family; InterPro: IPR005033 Named the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit', this family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3QRL_A 2L7E_A 3FK3_C 3RLS_A.
Probab=100.00 E-value=3.3e-35 Score=228.76 Aligned_cols=82 Identities=54% Similarity=1.007 Sum_probs=70.5
Q ss_pred eeeEEEEEeCCCCCCcccceeeeEEEeCCCCCCCcceecCCCcEEEeeeEEeEEEEEEEEEeecCCCCCEEEEEEeecCC
Q 024443 71 SHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNNPTRAVESPPFELSESGWGEFEIAITLYFHADVCDKPLNLYHHLKLYP 150 (267)
Q Consensus 71 tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~GWGEF~I~I~I~F~~d~~ekpi~i~H~L~L~~ 150 (267)
||+|+||||+++++|++++|+||+|+|||||+||+|++++|||+|+|+|||||+|.|+|+|+++++++++++.|+|+|++
T Consensus 1 th~W~v~Vr~~~~~d~~~~i~kV~f~LHpsF~~p~r~v~~pPFevte~GWGeF~i~I~i~f~~~~~~~~~~~~h~L~l~~ 80 (84)
T PF03366_consen 1 THKWTVYVRGLDNEDLSYFIKKVTFKLHPSFPNPVRVVTKPPFEVTETGWGEFEIPIKIHFKDPSNEKPVTIQHDLKLHQ 80 (84)
T ss_dssp -EEEEEEEEECCCT--TTTEEEEEEES-TTSSS-EEECSSTTEEEEEEESS--EEEEEEECCCGGCTCEEEEEEE--SSS
T ss_pred CcEEEEEEEeCCCCCccceEEEEEEECCCCCCCCceEecCCCCEEEEeEeccEEEEEEEEEeCCCCCCcEEEEEEEEcCC
Confidence 79999999999999999999999999999999999999999999999999999999999999877899999999999998
Q ss_pred CC
Q 024443 151 ED 152 (267)
Q Consensus 151 ~~ 152 (267)
++
T Consensus 81 ~~ 82 (84)
T PF03366_consen 81 DG 82 (84)
T ss_dssp CE
T ss_pred CC
Confidence 64
No 3
>COG5033 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=100.00 E-value=1.7e-34 Score=257.17 Aligned_cols=189 Identities=28% Similarity=0.462 Sum_probs=148.9
Q ss_pred ccceeeeeEEEEeEEEccceEEcCCC--CCCCCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCCCcceecCCCcEEEe
Q 024443 40 LNKKLKDVEISIPIVYGNVAFWLGKK--ASEYQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNNPTRAVESPPFELSE 117 (267)
Q Consensus 40 ~~kR~k~v~I~~pIv~Gn~A~~l~kk--~~e~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE 117 (267)
..+|+.++.++++|++| .|..++.. .+-.+||-|.|||+++++||+++||+||+|+|||||+||+|++++|||+|.|
T Consensus 3 p~krt~r~~t~r~Iipg-ea~~~~~e~~~P~r~th~w~v~v~~~g~E~~~~iv~KVifkLH~Tf~NP~Rti~~pPFeI~E 81 (225)
T COG5033 3 PVKRTERLKTQRVIIPG-EAKPLGNEERFPVRHTHIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPPFEIKE 81 (225)
T ss_pred cceeeEeeeeeceeccC-ccccCCccccCCchhhEEEEEEEeCCCCcchhhhhheeeEEeccccCCCcccccCCCcEEEe
Confidence 36899999999999999 99999864 6778999999999999999999999999999999999999999999999999
Q ss_pred eeEEeEEEEEEEEEeecCCCCCEEEEEEeecCCCCCCCCC-------------CCCCCeEEEeeeEEEecCCCHHHHHHH
Q 024443 118 SGWGEFEIAITLYFHADVCDKPLNLYHHLKLYPEDESGSM-------------STKKPVVVESYDEIVFPEPSDSFLARV 184 (267)
Q Consensus 118 ~GWGEF~I~I~I~F~~d~~ekpi~i~H~L~L~~~~~~~~~-------------~~~~pVv~E~ydeIvF~nPse~f~~~L 184 (267)
+|||||+|.|+|||.++++++.+..+|++..+++....+. +....|-+..+++++|++|...++++|
T Consensus 82 tGWGEF~i~I~iff~~~age~~~~fyl~f~~~~Y~v~~~v~~~~~~~~l~~elsk~geve~~~~~~~~~nep~i~~~k~~ 161 (225)
T COG5033 82 TGWGEFDIQIKIFFAEKAGEKTIHFYLHFGDEPYAVDEPVDIPVNRPDLTSELSKSGEVESVYKREKRFNEPNIQALKLL 161 (225)
T ss_pred cccccceEEEEEEEecCCCceEeehhhhcccccccccccccccccccchhhhhhhcCcccceeeeeecccCchhHHHHhh
Confidence 9999999999999999998877555555555554311110 123345566799999999999999999
Q ss_pred HcCCCccCCCCCCCCCCCCCCCccccccccCCCCCCCcchhhhcCcChHHHHHHHHHHHHHHHhcCC
Q 024443 185 QNHPAVTLPRLPVGFTLPPPVPIEDTSKRKRGDTKDHPLAQWFMNFSEADELLQLAAARQQEHSNSP 251 (267)
Q Consensus 185 ~~~p~~~~~~~p~~~~~p~~~~~e~~~~~~~~~t~~~~~~~~f~~~~E~~El~~L~~ar~~V~~~~~ 251 (267)
...+.. -+..++.- .+.|.+ |..+.++|+.+++.-+.+.+..+.+
T Consensus 162 ~~~~~~------~a~gl~~~------------~edd~~----~v~Ql~~d~~~~v~~~ie~~~~~id 206 (225)
T COG5033 162 NGAKMK------LAIGLHKL------------REDDLV----FVVQLVQDPIMAVLNLIEKGEFKID 206 (225)
T ss_pred hcCccc------ccccCccc------------ccccce----eeEecCcCHHHHHHhccccCceEee
Confidence 887641 11222221 123433 6688888888888877776665543
No 4
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=52.11 E-value=24 Score=33.80 Aligned_cols=36 Identities=33% Similarity=0.595 Sum_probs=29.2
Q ss_pred hhhcCcChHHHHH--HHHHHHHHHHhcCCe---eEEEeccc
Q 024443 225 QWFMNFSEADELL--QLAAARQQEHSNSPF---FFLVDQFE 260 (267)
Q Consensus 225 ~~f~~~~E~~El~--~L~~ar~~V~~~~~~---~~~~~~~~ 260 (267)
.-|.+|-+++||. .|+-|.||.-+.++| ||++|--.
T Consensus 151 d~FlKFqd~eelts~dLadai~qm~e~~Ryneil~miDTCQ 191 (309)
T KOG1349|consen 151 DGFLKFQDAEELTSDDLADAIQQMWEKKRYNEILFMIDTCQ 191 (309)
T ss_pred ccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccc
Confidence 3599999999987 899999999777766 77787543
No 5
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=47.42 E-value=45 Score=28.25 Aligned_cols=34 Identities=9% Similarity=0.177 Sum_probs=25.7
Q ss_pred CCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCC
Q 024443 69 YQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFN 102 (267)
Q Consensus 69 ~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 102 (267)
+..++|.+.+.|+.+.....-+=++.+.+.+.|+
T Consensus 28 ~nl~~w~~~i~GP~~tpyegg~f~~~i~fp~~YP 61 (147)
T PLN00172 28 ENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYP 61 (147)
T ss_pred CChheEEEEEECCCCCCCCCCEEEEEEECCcccC
Confidence 5799999999998765553334477788888886
No 6
>PF09154 DUF1939: Domain of unknown function (DUF1939); InterPro: IPR015237 This entry represents a C-terminal domain associated with prokaryotic alpha-amylases. It adopts a secondary structure consisting of an eight-stranded antiparallel beta-sheet containing a Greek key motif. Its exact function has not, as yet, been determined []. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 1MXD_A 1MWO_A 1MXG_A 1W9X_A 2DIE_A 1VJS_A 1BPL_B 1BLI_A 1OB0_A 1E3Z_A ....
Probab=44.20 E-value=13 Score=27.27 Aligned_cols=14 Identities=43% Similarity=1.149 Sum_probs=10.1
Q ss_pred cEEEeeeEEeEEEE
Q 024443 113 FELSESGWGEFEIA 126 (267)
Q Consensus 113 FeVtE~GWGEF~I~ 126 (267)
-.+.|.|||+|.++
T Consensus 36 vtid~dG~~~f~v~ 49 (57)
T PF09154_consen 36 VTIDEDGWGEFPVP 49 (57)
T ss_dssp EEE-TTSEEEEEE-
T ss_pred EEECCCeEEEEEEC
Confidence 35789999999886
No 7
>COG0031 CysK Cysteine synthase [Amino acid transport and metabolism]
Probab=40.62 E-value=20 Score=34.45 Aligned_cols=30 Identities=20% Similarity=0.231 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhcCCeeEEEecccCCcCc
Q 024443 236 LLQLAAARQQEHSNSPFFFLVDQFENPKMF 265 (267)
Q Consensus 236 l~~L~~ar~~V~~~~~~~~~~~~~~~~~~~ 265 (267)
...+..|++-+..++.|++..+||+||.-+
T Consensus 122 ~~a~~~a~el~~~~p~~~~~~~Qf~NpaN~ 151 (300)
T COG0031 122 KGAIERAKELAAEIPGYAVWLNQFENPANP 151 (300)
T ss_pred HHHHHHHHHHHHhCCCceEchhhcCCCccH
Confidence 347778888888999999999999999643
No 8
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=26.54 E-value=2.1e+02 Score=23.55 Aligned_cols=35 Identities=11% Similarity=0.142 Sum_probs=24.9
Q ss_pred CCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCC
Q 024443 69 YQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNN 103 (267)
Q Consensus 69 ~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~n 103 (267)
+....|.+.+.|+.+.....-+=++++.|.+.|+.
T Consensus 26 ~~~~~w~~~i~gp~~~~y~g~~f~~~l~~p~~yP~ 60 (145)
T smart00212 26 DNLLEWTGTIVGPPGTPYEGGIFKLTIEFPPDYPF 60 (145)
T ss_pred CChheEEEEEEcCCCCCcCCcEEEEEEECCcccCC
Confidence 36889999999876544322233788888998874
No 9
>cd00195 UBCc Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
Probab=19.13 E-value=3.1e+02 Score=22.36 Aligned_cols=34 Identities=12% Similarity=0.199 Sum_probs=23.4
Q ss_pred CeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCC
Q 024443 70 QSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNN 103 (267)
Q Consensus 70 ~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~n 103 (267)
...+|.+-+.|+.+.....=+=++.+.+++.|+.
T Consensus 27 ~~~~w~~~i~g~~~t~y~g~~~~~~~~~p~~yP~ 60 (141)
T cd00195 27 NLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPF 60 (141)
T ss_pred ChhEEEEEEecCCCCCccCCEEEEEEECCCccCC
Confidence 6788999999985443333344567778888863
No 10
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=17.71 E-value=1.2e+02 Score=29.53 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=29.9
Q ss_pred hhhcCcChHHHHH--HHHHHHHHHHhcCCe---eEEEeccc
Q 024443 225 QWFMNFSEADELL--QLAAARQQEHSNSPF---FFLVDQFE 260 (267)
Q Consensus 225 ~~f~~~~E~~El~--~L~~ar~~V~~~~~~---~~~~~~~~ 260 (267)
.-|.+|-+++|+. .|+-|.+|+.++++| ||++|--.
T Consensus 151 d~FlKFqdaeemtseDladai~ql~~~kRyNeIlfmiDTCQ 191 (382)
T COG5206 151 DAFLKFQDAEEMTSEDLADAISQLAAKKRYNEILFMIDTCQ 191 (382)
T ss_pred ccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccc
Confidence 3489999999976 899999999999887 77777543
Done!