Query 024808
Match_columns 262
No_of_seqs 190 out of 411
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:33:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024808.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024808hhsearch_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 7.1E-41 1.5E-45 304.2 15.5 212 40-251 5-231 (249)
2 PF03366 YEATS: YEATS family; 100.0 2.9E-35 6.3E-40 228.5 8.2 82 71-152 1-82 (84)
3 COG5033 TFG3 Transcription ini 100.0 2.3E-34 5.1E-39 255.5 11.9 184 41-247 4-202 (225)
4 PF09154 DUF1939: Domain of un 47.6 11 0.00023 27.6 1.2 14 113-126 36-49 (57)
5 PLN00172 ubiquitin conjugating 46.5 40 0.00087 28.4 4.8 35 68-102 27-61 (147)
6 smart00212 UBCc Ubiquitin-conj 28.9 1.5E+02 0.0033 24.3 5.4 35 69-103 26-60 (145)
7 PF15500 Toxin_39: Putative RN 20.3 1.5E+02 0.0032 24.1 3.6 29 232-260 68-96 (96)
8 cd00195 UBCc Ubiquitin-conjuga 18.4 2.9E+02 0.0062 22.5 5.1 33 70-102 27-59 (141)
9 PF14564 Membrane_bind: Membra 17.1 1.6E+02 0.0035 24.1 3.3 36 113-148 55-90 (110)
10 PTZ00390 ubiquitin-conjugating 17.0 3E+02 0.0064 23.4 5.0 34 69-102 29-62 (152)
No 1
>KOG3149 consensus Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=100.00 E-value=7.1e-41 Score=304.16 Aligned_cols=212 Identities=38% Similarity=0.575 Sum_probs=179.1
Q ss_pred ccceeeeeEEEEeEEEccceEEcCCCCCCCCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCCCcccccCCCcEEEeee
Q 024808 40 LNKKLKDVEISIPIVYGNVAFWLGKKASEYQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNNPTRAVESPPFELSESG 119 (262)
Q Consensus 40 ~~kr~k~~~I~~pIv~Gn~a~~l~kk~~e~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~G 119 (262)
..+|++.++|+++|+|||.|++++++.++.+||.|+||||+.+++|++.||+||+|+||+||+||+|+|++|||+|+|+|
T Consensus 5 ~~~~~~~~~~~~~iv~G~~a~~~~~~~~~~~th~w~v~v~~~~~ed~~~~V~KV~f~LH~sf~~P~Rvv~~pPf~i~EtG 84 (249)
T KOG3149|consen 5 SIKRTKECTISVPIVPGNRAAILGKRLPDGFTHIWEVYVRGPGKEDISAFVDKVVFKLHESFPNPRRVVESPPFEITETG 84 (249)
T ss_pred CcceeeeeeEEeeeecCccccccCCCCCcccceeeEEEecCcCccccceeeeeeeeecccccccccccccCCCceEEeec
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeEEEEEEEEEeecCCCCCEEEEEeeccCCCCC---CCC-----------CCCCCCeEEEeee-EEEecCCCHHHHHHH
Q 024808 120 WGEFEIAITLYFHADVCDKPLNLYHHLKLYPEDE---SGS-----------MSTKKPVVVESYD-EIVFPEPSDSFLARV 184 (262)
Q Consensus 120 WGEF~I~I~I~F~~d~~ekp~~i~H~L~L~~~~~---~~~-----------~~~~~pVv~E~yd-eIvF~nPse~f~~~L 184 (262)
||+|+|.|+|||.++.+++++.++|+|.|+.++. ..+ ...+.+|+.+.|+ +++|++|++.++..+
T Consensus 85 wgeF~i~i~i~f~d~~~~~~v~~~~~l~l~~~~~p~~~~~~~~~~~~~~~~~~~r~~v~~~~~~~e~~f~~~~~~~~~~~ 164 (249)
T KOG3149|consen 85 WGEFEIQIEIFFTDDANEKKVTLYHDLKLHSYGAPPVPHEESTKKTFVNPTISLRIPVVREGVDVEIVFPDPTESTSIEA 164 (249)
T ss_pred cccceEEEEEEeccCCCCceeeeeeeEEeeccCCCCccchhhhcccccccchhcccccccccccceeecCCCCccccccc
Confidence 9999999999999999999999999999998742 111 2457789999999 999999999999999
Q ss_pred hcCCCccCCCCCCCCCCCCCCCccccccccCCCCCCCcchhhhcccChHHHHHHHHHHHHHHHHcCc
Q 024808 185 QNHPAVTLPRLPVGFTLPPPVPIEDTSKRKRGDTKDHPLAQWFMNFSEADELLQLAAARQQVSKNGM 251 (262)
Q Consensus 185 ~~~p~~~~~~~p~~~~~p~~~~~~~~~~~~~~~t~~~~~~~~f~~~~E~~El~~l~~a~~~v~~~~~ 251 (262)
...+.......+....++............+..+++.-...+.....|.+|.+++..+.+.+++.-|
T Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~e~~~~d~~~~~~~~~~~~~~ 231 (249)
T KOG3149|consen 165 SSRPVGPGSNLAAVTDLKQVKSKTLPSLLSKESSKDVKTEKSSERPNEIDEVDRLEKKIKELKKEIN 231 (249)
T ss_pred CCCCCcCCccccccccccccccccCcccccccccccccccccccccccchhhhhhhhhhhhhhhHHH
Confidence 9998766555554444444433333333344556666666777788899999998888777766544
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=2.9e-35 Score=228.45 Aligned_cols=82 Identities=54% Similarity=1.007 Sum_probs=70.5
Q ss_pred eeeEEEEEeCCCCCCcccceeeeEEEeCCCCCCCcccccCCCcEEEeeeEEeEEEEEEEEEeecCCCCCEEEEEeeccCC
Q 024808 71 SHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNNPTRAVESPPFELSESGWGEFEIAITLYFHADVCDKPLNLYHHLKLYP 150 (262)
Q Consensus 71 tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~GWGEF~I~I~I~F~~d~~ekp~~i~H~L~L~~ 150 (262)
||+|+||||+.+++|++++|+||+|+|||||+||+|++++|||+|+|+|||||+|.|+|+|++++++++++|.|+|+|++
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 024808 151 ED 152 (262)
Q Consensus 151 ~~ 152 (262)
++
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=2.3e-34 Score=255.51 Aligned_cols=184 Identities=28% Similarity=0.481 Sum_probs=143.9
Q ss_pred cceeeeeEEEEeEEEccceEEcCCC--CCCCCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCCCcccccCCCcEEEee
Q 024808 41 NKKLKDVEISIPIVYGNVAFWLGKK--ASEYQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNNPTRAVESPPFELSES 118 (262)
Q Consensus 41 ~kr~k~~~I~~pIv~Gn~a~~l~kk--~~e~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~ 118 (262)
.+|+.++.++++|++| .|..++.. .+-.+||-|.||||++++||+++||+||+|+|||||+||+|++++|||+|.|+
T Consensus 4 ~krt~r~~t~r~Iipg-ea~~~~~e~~~P~r~th~w~v~v~~~g~E~~~~iv~KVifkLH~Tf~NP~Rti~~pPFeI~Et 82 (225)
T COG5033 4 VKRTERLKTQRVIIPG-EAKPLGNEERFPVRHTHIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPPFEIKET 82 (225)
T ss_pred ceeeEeeeeeceeccC-ccccCCccccCCchhhEEEEEEEeCCCCcchhhhhheeeEEeccccCCCcccccCCCcEEEec
Confidence 6899999999999999 99999864 77789999999999999999999999999999999999999999999999999
Q ss_pred eEEeEEEEEEEEEeecCCCCCEEEEEeeccCCCCCCCC-------------CCCCCCeEEEeeeEEEecCCCHHHHHHHh
Q 024808 119 GWGEFEIAITLYFHADVCDKPLNLYHHLKLYPEDESGS-------------MSTKKPVVVESYDEIVFPEPSDSFLARVQ 185 (262)
Q Consensus 119 GWGEF~I~I~I~F~~d~~ekp~~i~H~L~L~~~~~~~~-------------~~~~~pVv~E~ydeIvF~nPse~f~~~L~ 185 (262)
|||||+|.|+|||.++++++.+..+|++..+++....+ .+....|-+..+++++|++|-..++.+|.
T Consensus 83 GWGEF~i~I~iff~~~age~~~~fyl~f~~~~Y~v~~~v~~~~~~~~l~~elsk~geve~~~~~~~~~nep~i~~~k~~~ 162 (225)
T COG5033 83 GWGEFDIQIKIFFAEKAGEKTIHFYLHFGDEPYAVDEPVDIPVNRPDLTSELSKSGEVESVYKREKRFNEPNIQALKLLN 162 (225)
T ss_pred ccccceEEEEEEEecCCCceEeehhhhcccccccccccccccccccchhhhhhhcCcccceeeeeecccCchhHHHHhhh
Confidence 99999999999999998887755555555555431111 12233455666999999999999999999
Q ss_pred cCCCccCCCCCCCCCCCCCCCccccccccCCCCCCCcchhhhcccChHHHHHHHHHHHHHHH
Q 024808 186 NHPAVTLPRLPVGFTLPPPVPIEDTSKRKRGDTKDHPLAQWFMNFSEADELLQLAAARQQVS 247 (262)
Q Consensus 186 ~~p~~~~~~~p~~~~~p~~~~~~~~~~~~~~~t~~~~~~~~f~~~~E~~El~~l~~a~~~v~ 247 (262)
..+.. .+.+|++ ..+.|++ |..+.+.|+.+++.-+.+.+.
T Consensus 163 ~~~~~------~a~gl~~------------~~edd~~----~v~Ql~~d~~~~v~~~ie~~~ 202 (225)
T COG5033 163 GAKMK------LAIGLHK------------LREDDLV----FVVQLVQDPIMAVLNLIEKGE 202 (225)
T ss_pred cCccc------ccccCcc------------cccccce----eeEecCcCHHHHHHhccccCc
Confidence 87641 1233333 1245655 446666667776665554443
No 4
>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=47.56 E-value=11 Score=27.59 Aligned_cols=14 Identities=43% Similarity=1.149 Sum_probs=10.2
Q ss_pred cEEEeeeEEeEEEE
Q 024808 113 FELSESGWGEFEIA 126 (262)
Q Consensus 113 FeVtE~GWGEF~I~ 126 (262)
-.+.|.|||+|.++
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 35789999999986
No 5
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=46.49 E-value=40 Score=28.44 Aligned_cols=35 Identities=9% Similarity=0.198 Sum_probs=25.9
Q ss_pred CCCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCC
Q 024808 68 EYQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFN 102 (262)
Q Consensus 68 e~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 102 (262)
++..+.|.+.+.|+.+.....-+=++.+.+.+.|+
T Consensus 27 ~~nl~~w~~~i~GP~~tpyegg~f~~~i~fp~~YP 61 (147)
T PLN00172 27 DENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYP 61 (147)
T ss_pred CCChheEEEEEECCCCCCCCCCEEEEEEECCcccC
Confidence 35799999999998765543334467778888886
No 6
>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=28.86 E-value=1.5e+02 Score=24.29 Aligned_cols=35 Identities=11% Similarity=0.142 Sum_probs=24.7
Q ss_pred CCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCCC
Q 024808 69 YQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFNN 103 (262)
Q Consensus 69 ~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~n 103 (262)
+....|.+.+.|+.+.....-+=++++.|.+.|+.
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 37889999999876544322233788888888873
No 7
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=20.29 E-value=1.5e+02 Score=24.08 Aligned_cols=29 Identities=34% Similarity=0.373 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHHHHHHHcCccccCCcccc
Q 024808 232 EADELLQLAAARQQVSKNGMHAISSPLVQ 260 (262)
Q Consensus 232 E~~El~~l~~a~~~v~~~~~~~~~~~~~~ 260 (262)
++||-.+|.+|-..+..+|+.+...|+++
T Consensus 68 aAdeaakLi~alE~ar~ngg~ap~e~~v~ 96 (96)
T PF15500_consen 68 AADEAAKLIQALETARNNGGTAPKEPPVK 96 (96)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 78888999999999999999999988875
No 8
>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=18.36 E-value=2.9e+02 Score=22.50 Aligned_cols=33 Identities=12% Similarity=0.236 Sum_probs=22.8
Q ss_pred CeeeEEEEEeCCCCCCcccceeeeEEEeCCCCC
Q 024808 70 QSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFN 102 (262)
Q Consensus 70 ~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 102 (262)
....|.+-+.|+.+.....=+=++.+.+++.|+
T Consensus 27 ~~~~w~~~i~g~~~t~y~g~~~~~~~~~p~~yP 59 (141)
T cd00195 27 NLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYP 59 (141)
T ss_pred ChhEEEEEEecCCCCCccCCEEEEEEECCCccC
Confidence 678899999998544333334456777788876
No 9
>PF14564 Membrane_bind: Membrane binding; PDB: 1YHP_A 2B1O_A.
Probab=17.06 E-value=1.6e+02 Score=24.15 Aligned_cols=36 Identities=11% Similarity=0.433 Sum_probs=28.2
Q ss_pred cEEEeeeEEeEEEEEEEEEeecCCCCCEEEEEeecc
Q 024808 113 FELSESGWGEFEIAITLYFHADVCDKPLNLYHHLKL 148 (262)
Q Consensus 113 FeVtE~GWGEF~I~I~I~F~~d~~ekp~~i~H~L~L 148 (262)
.-|.+.+||.+...=.|||+.++....+.+.+...|
T Consensus 55 I~Vr~~~~g~~v~nGsvYFkY~~s~g~V~~~~~~~f 90 (110)
T PF14564_consen 55 ISVRDTDWGQYVANGSVYFKYNPSTGEVSIRKTENF 90 (110)
T ss_dssp EEEEESST-SEEEEEEEEEEEETTTTEEEEE-TTTS
T ss_pred EEEEeccCCceEecceEEEEECCCCCeEEEeecCCC
Confidence 358899999999999999999887888888874433
No 10
>PTZ00390 ubiquitin-conjugating enzyme; Provisional
Probab=17.05 E-value=3e+02 Score=23.39 Aligned_cols=34 Identities=6% Similarity=0.077 Sum_probs=24.0
Q ss_pred CCeeeEEEEEeCCCCCCcccceeeeEEEeCCCCC
Q 024808 69 YQSHKWTVYVRGATNEDLGVVIKRAVFQLHSSFN 102 (262)
Q Consensus 69 ~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 102 (262)
+..+.|.+.+.|+.+..-..=+=++.+.+-+.|+
T Consensus 29 ~d~~~w~~~i~GP~~tpY~gg~f~~~i~~p~~YP 62 (152)
T PTZ00390 29 GNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYP 62 (152)
T ss_pred CCccEEEEEEEcCCCCCCcCcEEEEEEECccccC
Confidence 4689999999998765543334456666667775
Done!