Query 027120
Match_columns 228
No_of_seqs 155 out of 410
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 05:14:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027120.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027120hhsearch_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 2.4E-38 5.3E-43 281.9 14.1 166 33-198 5-185 (249)
2 PF03366 YEATS: YEATS family; 100.0 1.1E-35 2.4E-40 226.5 7.8 82 64-145 1-82 (84)
3 COG5033 TFG3 Transcription ini 100.0 2.1E-33 4.5E-38 245.0 11.1 148 34-182 4-166 (225)
4 PF09154 DUF1939: Domain of un 48.7 9.2 0.0002 27.3 1.0 14 106-119 36-49 (57)
5 PLN00172 ubiquitin conjugating 46.3 61 0.0013 26.7 5.7 45 62-106 28-74 (147)
6 smart00212 UBCc Ubiquitin-conj 26.6 2.6E+02 0.0057 22.3 6.4 45 62-106 26-72 (145)
7 cd00195 UBCc Ubiquitin-conjuga 18.5 4.1E+02 0.0088 21.1 5.9 34 63-96 27-60 (141)
8 KOG0417 Ubiquitin-protein liga 16.9 4.4E+02 0.0094 22.6 5.9 35 61-95 27-61 (148)
9 PTZ00390 ubiquitin-conjugating 16.3 4.6E+02 0.0099 21.7 5.9 42 62-103 29-72 (152)
10 COG3055 Uncharacterized protei 13.8 1.6E+02 0.0035 28.7 2.8 41 177-221 22-64 (381)
No 1
>KOG3149 consensus Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=100.00 E-value=2.4e-38 Score=281.92 Aligned_cols=166 Identities=46% Similarity=0.732 Sum_probs=149.4
Q ss_pred ccceeeceEEEEeEEEccceEEcCCCCCCCCceeEEEEEeCCCCCCcccceeeEEEEeCCCCCCCceeeecCCcEEEEee
Q 027120 33 AIKRLKDVEICVPIVYGTMAFHLGRKASESQSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFNNPTRVVESPPFELQECG 112 (228)
Q Consensus 33 ~~~R~k~~~I~~pIV~Gn~A~~l~k~~~e~~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~nP~Rvv~~PPFeVtE~G 112 (228)
+.+|++.++|+++|++||.|++++++.++.+||.|+||||+.+++|++.||+||+|+||+||++|+|++++|||+|+|+|
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 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeEEeeEEEEEccCCCCCCEEEEEEeeeCCCCC---CCC-----------CCCCCCeEEEeee-EEEecCCCHHHHHHH
Q 027120 113 WGEFEIAISLFFHSDVCDKPLDLYHHLKLYPEAE---SGP-----------KSTKKPVVMESYN-EIVFPEPAEGFFARV 177 (228)
Q Consensus 113 WGEF~I~I~I~F~~d~~ekpi~i~H~L~L~~~~~---~~~-----------~~~~~pVv~E~yd-eIVF~nPse~f~~~L 177 (228)
||||+|+|+|||.++.+++++.++|+|+|+.++. ..+ ...+.+++++.|| +++|++|+++++..+
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 9999999999999999999999999999988742 111 2346789999999 999999999999999
Q ss_pred HcCCCccCCCCCCCCCcCCCC
Q 027120 178 LNHPAVVVPRLPAGFVLPTPG 198 (228)
Q Consensus 178 ~~~~~~~~p~~~~~~~~p~p~ 198 (228)
...+..+..+.+.....+...
T Consensus 165 ~~~~~~~~~~~~~~~~~~~~~ 185 (249)
T KOG3149|consen 165 SSRPVGPGSNLAAVTDLKQVK 185 (249)
T ss_pred CCCCCcCCccccccccccccc
Confidence 999987777666655554443
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=1.1e-35 Score=226.45 Aligned_cols=82 Identities=55% Similarity=1.053 Sum_probs=70.3
Q ss_pred ceeEEEEEeCCCCCCcccceeeEEEEeCCCCCCCceeeecCCcEEEEeeEeeEEeeEEEEEccCCCCCCEEEEEEeeeCC
Q 027120 64 SHRWTVYVRGATNEDIGVVIKRVVFQLHPSFNNPTRVVESPPFELQECGWGEFEIAISLFFHSDVCDKPLDLYHHLKLYP 143 (228)
Q Consensus 64 tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~nP~Rvv~~PPFeVtE~GWGEF~I~I~I~F~~d~~ekpi~i~H~L~L~~ 143 (228)
||+|+||||+.+++|++++|+||+|+|||||+||+|++++|||+|+|+|||||+|.|+|+|+++++++++++.|+|+|++
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 79999999999999999999999999999999999999999999999999999999999999877899999999999987
Q ss_pred CC
Q 027120 144 EA 145 (228)
Q Consensus 144 ~~ 145 (228)
++
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=2.1e-33 Score=245.01 Aligned_cols=148 Identities=36% Similarity=0.630 Sum_probs=126.8
Q ss_pred cceeeceEEEEeEEEccceEEcCCC--CCCCCceeEEEEEeCCCCCCcccceeeEEEEeCCCCCCCceeeecCCcEEEEe
Q 027120 34 IKRLKDVEICVPIVYGTMAFHLGRK--ASESQSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFNNPTRVVESPPFELQEC 111 (228)
Q Consensus 34 ~~R~k~~~I~~pIV~Gn~A~~l~k~--~~e~~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~nP~Rvv~~PPFeVtE~ 111 (228)
.+|+.++.++++|++| .|..++.. .+-.+||-|.+|||++++||+++||+||+|+|||||+||+|++++|||+|.|+
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 67789999999999999999999999999999999999999999999999999
Q ss_pred eEeeEEeeEEEEEccCCCCCCEEEEEEeeeCCCCCCCCC-------------CCCCCeEEEeeeEEEecCCCHHHHHHHH
Q 027120 112 GWGEFEIAISLFFHSDVCDKPLDLYHHLKLYPEAESGPK-------------STKKPVVMESYNEIVFPEPAEGFFARVL 178 (228)
Q Consensus 112 GWGEF~I~I~I~F~~d~~ekpi~i~H~L~L~~~~~~~~~-------------~~~~pVv~E~ydeIVF~nPse~f~~~L~ 178 (228)
|||||+|.|+|||.+.++++.+..+|++.++++....+. +....|-+.++++++|+.|-..++++|.
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 999999999999999888886666555555554311110 1223455677999999999999999999
Q ss_pred cCCC
Q 027120 179 NHPA 182 (228)
Q Consensus 179 ~~~~ 182 (228)
+.+.
T Consensus 163 ~~~~ 166 (225)
T COG5033 163 GAKM 166 (225)
T ss_pred cCcc
Confidence 9883
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=48.71 E-value=9.2 Score=27.31 Aligned_cols=14 Identities=43% Similarity=1.070 Sum_probs=10.2
Q ss_pred cEEEEeeEeeEEee
Q 027120 106 FELQECGWGEFEIA 119 (228)
Q Consensus 106 FeVtE~GWGEF~I~ 119 (228)
-.+.|.|||+|.++
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 35779999999986
No 5
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=46.30 E-value=61 Score=26.72 Aligned_cols=45 Identities=13% Similarity=0.290 Sum_probs=31.2
Q ss_pred CCceeEEEEEeCCCCCCcccceeeEEEEeCCCCC--CCceeeecCCc
Q 027120 62 SQSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFN--NPTRVVESPPF 106 (228)
Q Consensus 62 ~~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~--nP~Rvv~~PPF 106 (228)
++.++|.+.+.|+.+..-..-+=++.+.+.+.|+ .|...+..+.|
T Consensus 28 ~nl~~w~~~i~GP~~tpyegg~f~~~i~fp~~YP~~pP~v~f~t~i~ 74 (147)
T PLN00172 28 ENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIY 74 (147)
T ss_pred CChheEEEEEECCCCCCCCCCEEEEEEECCcccCCCCCEEEEecCcc
Confidence 5799999999998765544334478888888886 35554544444
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=26.59 E-value=2.6e+02 Score=22.30 Aligned_cols=45 Identities=13% Similarity=0.235 Sum_probs=30.0
Q ss_pred CCceeEEEEEeCCCCCCcccceeeEEEEeCCCCCC--CceeeecCCc
Q 027120 62 SQSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFNN--PTRVVESPPF 106 (228)
Q Consensus 62 ~~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~n--P~Rvv~~PPF 106 (228)
++...|.+-+.|+.+..-..-+=++++.+.+.|+. |.-.+..++|
T Consensus 26 ~~~~~w~~~i~gp~~~~y~g~~f~~~l~~p~~yP~~pP~v~f~~~i~ 72 (145)
T smart00212 26 DNLLEWTGTIVGPPGTPYEGGIFKLTIEFPPDYPFKPPKVKFITKIY 72 (145)
T ss_pred CChheEEEEEEcCCCCCcCCcEEEEEEECCcccCCCCCEEEEeCCce
Confidence 37889999999876543322233888889999974 5555555443
No 7
>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=18.51 E-value=4.1e+02 Score=21.09 Aligned_cols=34 Identities=12% Similarity=0.207 Sum_probs=23.8
Q ss_pred CceeEEEEEeCCCCCCcccceeeEEEEeCCCCCC
Q 027120 63 QSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFNN 96 (228)
Q Consensus 63 ~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~n 96 (228)
....|.+-+.|+.+.....=+=++.+.+++.|+.
T Consensus 27 ~~~~w~~~i~g~~~t~y~g~~~~~~~~~p~~yP~ 60 (141)
T cd00195 27 NLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPF 60 (141)
T ss_pred ChhEEEEEEecCCCCCccCCEEEEEEECCCccCC
Confidence 6788999999985443333345577788888873
No 8
>KOG0417 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=16.90 E-value=4.4e+02 Score=22.59 Aligned_cols=35 Identities=6% Similarity=0.142 Sum_probs=23.6
Q ss_pred CCCceeEEEEEeCCCCCCcccceeeEEEEeCCCCC
Q 027120 61 ESQSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFN 95 (228)
Q Consensus 61 e~~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~ 95 (228)
++++.+|++.+.|+.+..-..=+=++...+++.|+
T Consensus 27 ~dnl~~w~a~I~GP~~SpYEgG~F~l~I~~p~~YP 61 (148)
T KOG0417|consen 27 GDNLFHWQATILGPPGSPYEGGVFFLEIHFPEDYP 61 (148)
T ss_pred CCceeeEEEEEECCCCCCcCCCEEEEEEECCCCCC
Confidence 56888899999998764433334455566666654
No 9
>PTZ00390 ubiquitin-conjugating enzyme; Provisional
Probab=16.31 E-value=4.6e+02 Score=21.73 Aligned_cols=42 Identities=7% Similarity=0.112 Sum_probs=28.0
Q ss_pred CCceeEEEEEeCCCCCCcccceeeEEEEeCCCCCC--Cceeeec
Q 027120 62 SQSHRWTVYVRGATNEDIGVVIKRVVFQLHPSFNN--PTRVVES 103 (228)
Q Consensus 62 ~~tH~WtVyVR~~~~edls~fIkKV~F~LHpSF~n--P~Rvv~~ 103 (228)
++.+.|.+-+.|+.+..-..=+=++.+.+-+.|+. |...+..
T Consensus 29 ~d~~~w~~~i~GP~~tpY~gg~f~~~i~~p~~YP~~pP~v~F~t 72 (152)
T PTZ00390 29 GNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLT 72 (152)
T ss_pred CCccEEEEEEEcCCCCCCcCcEEEEEEECccccCCCCCEEEEec
Confidence 46899999999987655443455566777777763 4444433
No 10
>COG3055 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=13.75 E-value=1.6e+02 Score=28.75 Aligned_cols=41 Identities=37% Similarity=0.528 Sum_probs=26.8
Q ss_pred HHcCCCccCCCCCCCCCcCCCCCcccccccceEEeec--cceeeeee
Q 027120 177 VLNHPAVVVPRLPAGFVLPTPGKASCLFLFGVWVGVG--GVANFCLL 221 (228)
Q Consensus 177 L~~~~~~~~p~~~~~~~~p~p~~~~~~~~~~~~~~~~--~~~~~~~~ 221 (228)
|...-+-.+|.+|.++ ..- +-..--.++|||+| |.++|-|-
T Consensus 22 ~~~~~a~~lPdlPvg~--KnG--~Ga~ig~~~YVGLGs~G~afy~ld 64 (381)
T COG3055 22 LVAAYAGQLPDLPVGF--KNG--AGALIGDTVYVGLGSAGTAFYVLD 64 (381)
T ss_pred HHHHhhccCCCCCccc--ccc--ccceecceEEEEeccCCccceehh
Confidence 3333455688888877 222 12233448999999 99999773
Done!