Query psy11122
Match_columns 212
No_of_seqs 131 out of 381
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 18:35:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11122.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11122hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03366 YEATS: YEATS family; 100.0 9E-34 2E-38 213.7 8.6 82 108-192 1-82 (84)
2 KOG3149|consensus 100.0 4.5E-29 9.8E-34 220.1 11.4 107 83-192 11-117 (249)
3 COG5033 TFG3 Transcription ini 99.9 8.4E-27 1.8E-31 201.7 8.8 101 87-193 13-115 (225)
4 PF09154 DUF1939: Domain of un 63.2 4.2 9E-05 28.8 1.2 14 153-166 36-49 (57)
5 PLN00172 ubiquitin conjugating 42.9 96 0.0021 25.3 6.3 48 105-154 27-75 (147)
6 PF10983 DUF2793: Protein of u 35.8 22 0.00047 27.3 1.4 17 8-24 2-18 (87)
7 smart00212 UBCc Ubiquitin-conj 24.9 3.4E+02 0.0074 21.4 6.7 49 106-156 26-75 (145)
8 PF14766 RPA_interact_N: Repli 23.8 69 0.0015 21.3 2.0 17 3-19 23-40 (42)
9 PF10437 Lip_prot_lig_C: Bacte 20.8 75 0.0016 23.1 1.9 21 149-169 1-24 (86)
10 PF12854 PPR_1: PPR repeat 15.5 98 0.0021 18.8 1.3 14 5-18 21-34 (34)
No 1
>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=9e-34 Score=213.71 Aligned_cols=82 Identities=41% Similarity=0.779 Sum_probs=67.4
Q ss_pred ceeEEEEEECCCCCCccccCeeeeEEEEeCCCCCCCCeEEEecCCeEEEeeeEeeEeEEEEEEEecCCCCceeEEEEEEE
Q psy11122 108 THKWTVYVRNCESNPENIVRHIAHVKFMLHESYAPNNVVIVRKAPFKITREGWGEFPMKITIGFVDRENNRNVELVHPVN 187 (212)
Q Consensus 108 tH~WtVyVR~~~~~~d~ls~~I~KV~F~LHpTF~pnp~rvV~~PPFeVtE~GWGEF~I~I~I~Fk~~~~~p~v~i~H~L~ 187 (212)
||+|+||||+.+++ | ++.+|+||+|+|||||+ ||+|++++|||+|+|+|||||+|.|+|+|++.++.++++|.|+|+
T Consensus 1 th~W~v~Vr~~~~~-d-~~~~i~kV~f~LHpsF~-~p~r~v~~pPFevte~GWGeF~i~I~i~f~~~~~~~~~~~~h~L~ 77 (84)
T PF03366_consen 1 THKWTVYVRGLDNE-D-LSYFIKKVTFKLHPSFP-NPVRVVTKPPFEVTETGWGEFEIPIKIHFKDPSNEKPVTIQHDLK 77 (84)
T ss_dssp -EEEEEEEEECCCT----TTTEEEEEEES-TTSS-S-EEECSSTTEEEEEEESS--EEEEEEECCCGGCTCEEEEEEE--
T ss_pred CcEEEEEEEeCCCC-C-ccceEEEEEEECCCCCC-CCceEecCCCCEEEEeEeccEEEEEEEEEeCCCCCCcEEEEEEEE
Confidence 79999999999875 5 99999999999999995 899999999999999999999999999999975445599999999
Q ss_pred eCCCC
Q psy11122 188 FLHVK 192 (212)
Q Consensus 188 l~~~~ 192 (212)
|+++.
T Consensus 78 l~~~~ 82 (84)
T PF03366_consen 78 LHQDG 82 (84)
T ss_dssp SSSCE
T ss_pred cCCCC
Confidence 99864
No 2
>KOG3149|consensus
Probab=99.96 E-value=4.5e-29 Score=220.14 Aligned_cols=107 Identities=35% Similarity=0.569 Sum_probs=99.4
Q ss_pred CceEEeEEEEccceEEcCCCCCCCCceeEEEEEECCCCCCccccCeeeeEEEEeCCCCCCCCeEEEecCCeEEEeeeEee
Q psy11122 83 LTQRNFRFYVGTMCKSLGSPACGQSTHKWTVYVRNCESNPENIVRHIAHVKFMLHESYAPNNVVIVRKAPFKITREGWGE 162 (212)
Q Consensus 83 ~~~~~k~IviGn~a~~l~~~~~~~~tH~WtVyVR~~~~~~d~ls~~I~KV~F~LHpTF~pnp~rvV~~PPFeVtE~GWGE 162 (212)
+.++.++|++||.|++++++.++.+||.|+||||+..+ .| ++.||+||+|+||+|| +||+|+|++|||+|+|+||||
T Consensus 11 ~~~~~~~iv~G~~a~~~~~~~~~~~th~w~v~v~~~~~-ed-~~~~V~KV~f~LH~sf-~~P~Rvv~~pPf~i~EtGwge 87 (249)
T KOG3149|consen 11 ECTISVPIVPGNRAAILGKRLPDGFTHIWEVYVRGPGK-ED-ISAFVDKVVFKLHESF-PNPRRVVESPPFEITETGWGE 87 (249)
T ss_pred eeeEEeeeecCccccccCCCCCcccceeeEEEecCcCc-cc-cceeeeeeeeeccccc-ccccccccCCCceEEeecccc
Confidence 55678999999999999998888999999999999975 34 9999999999999999 599999999999999999999
Q ss_pred EeEEEEEEEecCCCCceeEEEEEEEeCCCC
Q psy11122 163 FPMKITIGFVDRENNRNVELVHPVNFLHVK 192 (212)
Q Consensus 163 F~I~I~I~Fk~~~~~p~v~i~H~L~l~~~~ 192 (212)
|+|.|+|+|.+..+++++.+.|.|.++..+
T Consensus 88 F~i~i~i~f~d~~~~~~v~~~~~l~l~~~~ 117 (249)
T KOG3149|consen 88 FEIQIEIFFTDDANEKKVTLYHDLKLHSYG 117 (249)
T ss_pred ceEEEEEEeccCCCCceeeeeeeEEeeccC
Confidence 999999999988888889999999999764
No 3
>COG5033 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=99.94 E-value=8.4e-27 Score=201.70 Aligned_cols=101 Identities=28% Similarity=0.491 Sum_probs=88.0
Q ss_pred EeEEEEccceEEcCCC--CCCCCceeEEEEEECCCCCCccccCeeeeEEEEeCCCCCCCCeEEEecCCeEEEeeeEeeEe
Q psy11122 87 NFRFYVGTMCKSLGSP--ACGQSTHKWTVYVRNCESNPENIVRHIAHVKFMLHESYAPNNVVIVRKAPFKITREGWGEFP 164 (212)
Q Consensus 87 ~k~IviGn~a~~l~~~--~~~~~tH~WtVyVR~~~~~~d~ls~~I~KV~F~LHpTF~pnp~rvV~~PPFeVtE~GWGEF~ 164 (212)
.+.|+.| +|..++.+ .+-.+||-|.+||++..+ .+ +++||+||+|+||||| +||.|++++|||+|.|+|||||+
T Consensus 13 ~r~Iipg-ea~~~~~e~~~P~r~th~w~v~v~~~g~-E~-~~~iv~KVifkLH~Tf-~NP~Rti~~pPFeI~EtGWGEF~ 88 (225)
T COG5033 13 QRVIIPG-EAKPLGNEERFPVRHTHIWLVFVRAPGK-ED-IATIVKKVIFKLHPTF-SNPTRTIESPPFEIKETGWGEFD 88 (225)
T ss_pred eceeccC-ccccCCccccCCchhhEEEEEEEeCCCC-cc-hhhhhheeeEEecccc-CCCcccccCCCcEEEecccccce
Confidence 4556666 99999985 566799999999999865 34 8999999999999999 59999999999999999999999
Q ss_pred EEEEEEEecCCCCceeEEEEEEEeCCCCC
Q psy11122 165 MKITIGFVDRENNRNVELVHPVNFLHVKS 193 (212)
Q Consensus 165 I~I~I~Fk~~~~~p~v~i~H~L~l~~~~~ 193 (212)
|.|+|+|.+..++ .++.|+|.|.+...
T Consensus 89 i~I~iff~~~age--~~~~fyl~f~~~~Y 115 (225)
T COG5033 89 IQIKIFFAEKAGE--KTIHFYLHFGDEPY 115 (225)
T ss_pred EEEEEEEecCCCc--eEeehhhhcccccc
Confidence 9999999999997 58888888877543
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=63.16 E-value=4.2 Score=28.77 Aligned_cols=14 Identities=50% Similarity=1.282 Sum_probs=10.4
Q ss_pred eEEEeeeEeeEeEE
Q psy11122 153 FKITREGWGEFPMK 166 (212)
Q Consensus 153 FeVtE~GWGEF~I~ 166 (212)
-.+.+.|||+|.++
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 46789999999986
No 5
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=42.85 E-value=96 Score=25.25 Aligned_cols=48 Identities=10% Similarity=0.236 Sum_probs=31.3
Q ss_pred CCCceeEEEEEECCCCCCccccCeeeeEEEEeCCCCC-CCCeEEEecCCeE
Q psy11122 105 GQSTHKWTVYVRNCESNPENIVRHIAHVKFMLHESYA-PNNVVIVRKAPFK 154 (212)
Q Consensus 105 ~~~tH~WtVyVR~~~~~~d~ls~~I~KV~F~LHpTF~-pnp~rvV~~PPFe 154 (212)
+++.++|.+.+.|+.+.+= -+. +=++.+.+.+.|. ..|.+.+..+.|.
T Consensus 27 ~~nl~~w~~~i~GP~~tpy-egg-~f~~~i~fp~~YP~~pP~v~f~t~i~H 75 (147)
T PLN00172 27 DENLFRWTASIIGPSDSPY-AGG-VFFLSILFPPDYPFKPPKVQFTTKIYH 75 (147)
T ss_pred CCChheEEEEEECCCCCCC-CCC-EEEEEEECCcccCCCCCEEEEecCccc
Confidence 3589999999998875432 222 3368888888885 2355555555554
No 6
>PF10983 DUF2793: Protein of unknown function (DUF2793); InterPro: IPR021251 This entry is represented by Bacteriophage D3112, Orf54. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=35.76 E-value=22 Score=27.26 Aligned_cols=17 Identities=41% Similarity=0.446 Sum_probs=13.2
Q ss_pred HHHHHHHHHhhhheeeh
Q psy11122 8 NETLRLFRALKRSVVTQ 24 (212)
Q Consensus 8 ~~~~~~~~~l~~~i~~~ 24 (212)
|||||+||.|--..|.|
T Consensus 2 NEAL~~LD~lvql~V~s 18 (87)
T PF10983_consen 2 NEALRRLDALVQLAVLS 18 (87)
T ss_pred cHHHHHHHhhhhhheec
Confidence 79999999887666554
No 7
>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=24.88 E-value=3.4e+02 Score=21.36 Aligned_cols=49 Identities=10% Similarity=0.090 Sum_probs=31.5
Q ss_pred CCceeEEEEEECCCCCCccccCeeeeEEEEeCCCCC-CCCeEEEecCCeEEE
Q psy11122 106 QSTHKWTVYVRNCESNPENIVRHIAHVKFMLHESYA-PNNVVIVRKAPFKIT 156 (212)
Q Consensus 106 ~~tH~WtVyVR~~~~~~d~ls~~I~KV~F~LHpTF~-pnp~rvV~~PPFeVt 156 (212)
++...|.+-+.|..+.+= -...+ ++++.+.+.|- ..|...+..++|.-.
T Consensus 26 ~~~~~w~~~i~gp~~~~y-~g~~f-~~~l~~p~~yP~~pP~v~f~~~i~Hp~ 75 (145)
T smart00212 26 DNLLEWTGTIVGPPGTPY-EGGIF-KLTIEFPPDYPFKPPKVKFITKIYHPN 75 (145)
T ss_pred CChheEEEEEEcCCCCCc-CCcEE-EEEEECCcccCCCCCEEEEeCCceEee
Confidence 478999999987654321 12223 78888999994 235556666655544
No 8
>PF14766 RPA_interact_N: Replication protein A interacting N-terminal
Probab=23.80 E-value=69 Score=21.34 Aligned_cols=17 Identities=18% Similarity=0.614 Sum_probs=13.2
Q ss_pred chHHHHHHH-HHHHHhhh
Q psy11122 3 CFDELNETL-RLFRALKR 19 (212)
Q Consensus 3 ~~~~~~~~~-~~~~~l~~ 19 (212)
|.++|.+-| ++|+++|-
T Consensus 23 C~~R~r~~R~~lL~k~R~ 40 (42)
T PF14766_consen 23 CLERVRESRTQLLWKYRQ 40 (42)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 899998887 57777763
No 9
>PF10437 Lip_prot_lig_C: Bacterial lipoate protein ligase C-terminus; InterPro: IPR019491 This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with IPR004143 from INTERPRO, further upstream. This C-terminal domain is more stable than IPR004143 from INTERPRO and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues. ; PDB: 1X2G_A 3A7R_A 3A7A_A 1X2H_C 1VQZ_A 3R07_C.
Probab=20.78 E-value=75 Score=23.12 Aligned_cols=21 Identities=19% Similarity=0.727 Sum_probs=13.9
Q ss_pred ecCCeEEEee---eEeeEeEEEEE
Q psy11122 149 RKAPFKITRE---GWGEFPMKITI 169 (212)
Q Consensus 149 ~~PPFeVtE~---GWGEF~I~I~I 169 (212)
++|+|+++.. .||..+|.+.|
T Consensus 1 ksP~f~~~~~~rf~~G~v~v~~~V 24 (86)
T PF10437_consen 1 KSPEFTFSKERRFPWGTVEVHLNV 24 (86)
T ss_dssp TS-CESEEEEEEETTEEEEEEEEE
T ss_pred CcCCCcEeeeeEcCCceEEEEEEE
Confidence 3678877655 78996666665
No 10
>PF12854 PPR_1: PPR repeat
Probab=15.50 E-value=98 Score=18.84 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHhh
Q psy11122 5 DELNETLRLFRALK 18 (212)
Q Consensus 5 ~~~~~~~~~~~~l~ 18 (212)
.++.+|+++|++.+
T Consensus 21 G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 21 GRVDEAFELFDEMK 34 (34)
T ss_pred CCHHHHHHHHHhCc
Confidence 46889999998764
Done!