Query psy17997
Match_columns 120
No_of_seqs 54 out of 56
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 19:38:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17997.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17997hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00570 cdk7 CDK-activating 99.9 2.5E-23 5.5E-28 173.2 3.8 102 7-111 207-308 (309)
2 KOG3800|consensus 99.9 5.4E-23 1.2E-27 170.6 5.2 87 21-110 214-300 (300)
3 PF06391 MAT1: CDK-activating 96.5 0.00064 1.4E-08 54.3 0.0 42 11-55 159-200 (200)
4 COG5220 TFB3 Cdk activating ki 64.4 5 0.00011 34.2 2.1 43 53-108 265-307 (314)
5 PF08727 P3A: Poliovirus 3A pr 48.7 11 0.00023 25.3 1.2 24 46-71 1-25 (57)
6 COG4537 ComGC Competence prote 37.7 17 0.00037 27.0 1.0 24 62-85 70-93 (107)
7 PF12960 DUF3849: Protein of u 31.8 35 0.00075 26.0 1.9 23 89-111 22-44 (133)
8 KOG4447|consensus 31.6 26 0.00056 27.9 1.2 42 56-110 62-103 (173)
9 PF09585 Lin0512_fam: Conserve 30.8 31 0.00067 25.7 1.5 13 93-105 19-31 (113)
10 PF13501 SoxY: Sulfur oxidatio 26.7 17 0.00036 26.4 -0.6 46 3-50 54-99 (111)
11 PF02518 HATPase_c: Histidine 25.6 85 0.0018 20.6 2.8 51 52-106 38-90 (111)
12 PRK07474 sulfur oxidation prot 24.8 34 0.00074 26.4 0.8 48 3-52 95-142 (154)
13 PF15161 Neuropep_like: Neurop 24.2 41 0.00089 22.9 1.0 10 95-104 24-33 (65)
14 TIGR02058 lin0512_fam conserve 22.7 54 0.0012 24.6 1.5 13 93-105 19-31 (116)
15 PF05322 NinE: NINE Protein; 22.1 58 0.0013 22.0 1.4 32 48-79 15-47 (60)
No 1
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.87 E-value=2.5e-23 Score=173.17 Aligned_cols=102 Identities=35% Similarity=0.689 Sum_probs=91.9
Q ss_pred ccccccCCCCCCCCCccccceeeccccccccCCccCCccCCCceeeccccccCCCCCCCHHHhhhchhhhhcccccchhh
Q psy17997 7 DLPALFSQPSQDLPKHFSSGIRIGSNLGLSVPAIVKPELGPLYKYEPTIKMIDGPDYPSWDDVRRGNYLKHVRTETVEEK 86 (120)
Q Consensus 7 ~~~~~~~~~~~~k~~~FSTGIk~g~~~s~~~~pvpk~eeG~lY~Y~Pl~~~~~GP~~P~~e~L~~~GYl~HVR~~s~~e~ 86 (120)
.+....+..+..|++.|+|||+++.+.+++ |+++.++ +.|.|+|+..+.+||..|+++++...||+.|||+++++.+
T Consensus 207 ~~k~~~~r~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~py~Pf~g~~~~p~~y~~~~~~~~~y~~~~r~~~~~~~ 283 (309)
T TIGR00570 207 KLEMQVEKPKPEKPNTFSTGIKMGYQISLV--PVQKSEE-ALYPYQPLNIETEGPPVPTLEELVRQGYLNHVRAASPQDI 283 (309)
T ss_pred HHHhhhhhccccchhhhhhccccccccccc--ccCCCCC-CCCCcCCCCCCCCCCCCCCccccccccHHHHHhccCcccc
Confidence 344555666666777899999998777888 9988776 9999999999999999999999999999999999999999
Q ss_pred cCchhhHHhHHHHHHHHhhcccCCC
Q psy17997 87 AGGYVCAIATMRALNDAFAGLYHTN 111 (120)
Q Consensus 87 AGGfts~laC~RALQEAfsgL~~~~ 111 (120)
||||++.+.|.|||||||+||++..
T Consensus 284 aGGy~~~~~~~RaL~EAF~GL~~fi 308 (309)
T TIGR00570 284 AGGYTSNLACERALQEAFSGLFWQP 308 (309)
T ss_pred cCCcCHHHHHHHHHHHHHccCCccC
Confidence 9999999999999999999999865
No 2
>KOG3800|consensus
Probab=99.87 E-value=5.4e-23 Score=170.63 Aligned_cols=87 Identities=31% Similarity=0.565 Sum_probs=83.2
Q ss_pred CccccceeeccccccccCCccCCccCCCceeeccccccCCCCCCCHHHhhhchhhhhcccccchhhcCchhhHHhHHHHH
Q psy17997 21 KHFSSGIRIGSNLGLSVPAIVKPELGPLYKYEPTIKMIDGPDYPSWDDVRRGNYLKHVRTETVEEKAGGYVCAIATMRAL 100 (120)
Q Consensus 21 ~~FSTGIk~g~~~s~~~~pvpk~eeG~lY~Y~Pl~~~~~GP~~P~~e~L~~~GYl~HVR~~s~~e~AGGfts~laC~RAL 100 (120)
+.|+|+|+++ +.++. |+++.+++++|.|+|+..+.+||++|+...+..+||++|+|+.+++++||||+++++|.|||
T Consensus 214 ~s~nt~ir~~-~~s~~--~~~n~~~~~~~pf~pl~~~~~g~~~~~~~~~v~~~~~~~~r~~~~~~~aggf~~~~~~~r~l 290 (300)
T KOG3800|consen 214 TSFNTIIRVS-SISLE--PNENSEESAAFPFEPLRGEKEGPPMPGTKKIVARGYFAHIRAHTPEELAGGFTSNLACERAL 290 (300)
T ss_pred cchhheeecc-ccccc--cchhhhhccccccccccccccCCCCcChhhhhhhhhhHHhhcCChHHhhcCCcchHHHHHHH
Confidence 5799999998 66777 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcccCC
Q psy17997 101 NDAFAGLYHT 110 (120)
Q Consensus 101 QEAfsgL~~~ 110 (120)
||||+||||.
T Consensus 291 ~ea~~Gl~~~ 300 (300)
T KOG3800|consen 291 QEAFSGLFYE 300 (300)
T ss_pred HHHhcccccC
Confidence 9999999973
No 3
>PF06391 MAT1: CDK-activating kinase assembly factor MAT1; InterPro: IPR015877 MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. This entry represents the central region of MAT1. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle []. CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 []. The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus; PDB: 1G25_A.
Probab=96.51 E-value=0.00064 Score=54.33 Aligned_cols=42 Identities=36% Similarity=0.426 Sum_probs=0.0
Q ss_pred ccCCCCCCCCCccccceeeccccccccCCccCCccCCCceeeccc
Q psy17997 11 LFSQPSQDLPKHFSSGIRIGSNLGLSVPAIVKPELGPLYKYEPTI 55 (120)
Q Consensus 11 ~~~~~~~~k~~~FSTGIk~g~~~s~~~~pvpk~eeG~lY~Y~Pl~ 55 (120)
.-++....+.+.|++|++++++.++. |+|++++ ++|.|+|++
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~e-~~~~y~P~~ 200 (200)
T PF06391_consen 159 ARRQEEQLKRKLFSTGIKKSQNQSFL--PVPKVEE-PLYPYTPLN 200 (200)
T ss_dssp ---------------------------------------------
T ss_pred HHHhHhhhhHHHhhhhhhhccccccc--ccccccC-CCCCCCCCC
Confidence 33444444556699999999888899 9999876 999999984
No 4
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=64.37 E-value=5 Score=34.20 Aligned_cols=43 Identities=33% Similarity=0.363 Sum_probs=31.5
Q ss_pred ccccccCCCCCCCHHHhhhchhhhhcccccchhhcCchhhHHhHHHHHHHHhhccc
Q psy17997 53 PTIKMIDGPDYPSWDDVRRGNYLKHVRTETVEEKAGGYVCAIATMRALNDAFAGLY 108 (120)
Q Consensus 53 Pl~~~~~GP~~P~~e~L~~~GYl~HVR~~s~~e~AGGfts~laC~RALQEAfsgL~ 108 (120)
-+...++| -|.+++|+ | ...+|-||..+.+-.|-|-|||+||=
T Consensus 265 sl~~s~y~--dp~ik~l~------H-----k~~~~~GF~~~~~~~R~L~EAF~Gl~ 307 (314)
T COG5220 265 SLAISSYG--DPNIKDLE------H-----KEFIASGFNTNYAYERVLTEAFMGLG 307 (314)
T ss_pred EEeccccC--Ccchhhhc------c-----chhhhcCcccHHHHHHHHHHHHccCC
Confidence 33444554 35666653 3 45679999999999999999999973
No 5
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=48.65 E-value=11 Score=25.26 Aligned_cols=24 Identities=29% Similarity=0.520 Sum_probs=13.3
Q ss_pred CCCceeecccccc-CCCCCCCHHHhhh
Q psy17997 46 GPLYKYEPTIKMI-DGPDYPSWDDVRR 71 (120)
Q Consensus 46 G~lY~Y~Pl~~~~-~GP~~P~~e~L~~ 71 (120)
||. |+++.+++ +.|.++-+.+|.+
T Consensus 1 gp~--~k~l~I~~~~~P~P~~I~DLL~ 25 (57)
T PF08727_consen 1 GPP--YKDLKISVEETPPPPAIADLLR 25 (57)
T ss_dssp -SS---SS-S--SSS--SS-TTHHHHH
T ss_pred CCC--CcceeeeccCCCCCHHHHHHHH
Confidence 567 99999998 8999999988854
No 6
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=37.69 E-value=17 Score=27.00 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=19.4
Q ss_pred CCCCHHHhhhchhhhhcccccchh
Q psy17997 62 DYPSWDDVRRGNYLKHVRTETVEE 85 (120)
Q Consensus 62 ~~P~~e~L~~~GYl~HVR~~s~~e 85 (120)
..|++++|.+.||+.|-....+.+
T Consensus 70 ~~pSl~~L~s~G~i~~~Q~~c~ng 93 (107)
T COG4537 70 LPPSLSDLKSDGYIKEKQKSCPNG 93 (107)
T ss_pred CCCCHHHHHhCCceehhhhcCCCC
Confidence 479999999999999976655543
No 7
>PF12960 DUF3849: Protein of unknown function (DUF3849); InterPro: IPR024383 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences [].
Probab=31.83 E-value=35 Score=25.98 Aligned_cols=23 Identities=22% Similarity=0.252 Sum_probs=19.7
Q ss_pred chhhHHhHHHHHHHHhhcccCCC
Q psy17997 89 GYVCAIATMRALNDAFAGLYHTN 111 (120)
Q Consensus 89 Gfts~laC~RALQEAfsgL~~~~ 111 (120)
.+.++++|.+||.+|.+.=|-.-
T Consensus 22 S~~aN~~Ck~aIE~aI~~~~~~~ 44 (133)
T PF12960_consen 22 SRKANIACKEAIEQAIREHFDGN 44 (133)
T ss_pred HHHhhHHHHHHHHHHHHHHcCCC
Confidence 46789999999999999877654
No 8
>KOG4447|consensus
Probab=31.58 E-value=26 Score=27.94 Aligned_cols=42 Identities=26% Similarity=0.355 Sum_probs=30.0
Q ss_pred cccCCCCCCCHHHhhhchhhhhcccccchhhcCchhhHHhHHHHHHHHhhcccCC
Q psy17997 56 KMIDGPDYPSWDDVRRGNYLKHVRTETVEEKAGGYVCAIATMRALNDAFAGLYHT 110 (120)
Q Consensus 56 ~~~~GP~~P~~e~L~~~GYl~HVR~~s~~e~AGGfts~laC~RALQEAfsgL~~~ 110 (120)
+-+-++.+=++|||.+.-|+++||...- || -|||||..|=-+
T Consensus 62 lr~~~~~~~~~dE~q~qrv~anvrerqR-----tq--------sLn~AF~~lr~i 103 (173)
T KOG4447|consen 62 LRIGTDSIQSLDELQKQRVMANVRERQR-----TQ--------SLNEAFAALRKI 103 (173)
T ss_pred cccCCCchhhHHHHHHHHHHHHHHHHHh-----hh--------hHHHHHHHHHhh
Confidence 3344455559999999999999997432 22 489999887543
No 9
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=30.84 E-value=31 Score=25.66 Aligned_cols=13 Identities=38% Similarity=0.552 Sum_probs=10.9
Q ss_pred HHhHHHHHHHHhh
Q psy17997 93 AIATMRALNDAFA 105 (120)
Q Consensus 93 ~laC~RALQEAfs 105 (120)
.-||.||++||++
T Consensus 19 TkAA~RAv~DAI~ 31 (113)
T PF09585_consen 19 TKAAVRAVRDAIS 31 (113)
T ss_pred HHHHHHHHHHHHh
Confidence 4589999999975
No 10
>PF13501 SoxY: Sulfur oxidation protein SoxY; PDB: 2OXG_B 2OX5_B 2OXH_F 2NNF_A 2NNC_B.
Probab=26.71 E-value=17 Score=26.39 Aligned_cols=46 Identities=24% Similarity=0.294 Sum_probs=28.5
Q ss_pred CcccccccccCCCCCCCCCccccceeeccccccccCCccCCccCCCce
Q psy17997 3 ENVTDLPALFSQPSQDLPKHFSSGIRIGSNLGLSVPAIVKPELGPLYK 50 (120)
Q Consensus 3 ~~~~~~~~~~~~~~~~k~~~FSTGIk~g~~~s~~~~pvpk~eeG~lY~ 50 (120)
+|-.-+-+.|+-+-..-.-.|||.|||++..... .+.+...|.+|.
T Consensus 54 ~NP~P~~a~f~~~p~~~~~~~stRir~~~~s~V~--ava~t~dG~~~~ 99 (111)
T PF13501_consen 54 KNPSPLAATFELTPAGGEPYVSTRIRMAQTSPVR--AVAETSDGKLYM 99 (111)
T ss_dssp TSSSSEEEEEEE-TTCCEEEEEEEEE-SSSEEEE--EEEEETTTEEEE
T ss_pred CCCCcEEEEEEEcCCCCCceeEEEEEecCcccEE--EEEEecCCeEEE
Confidence 3444455555553334445699999999877555 666776677775
No 11
>PF02518 HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; InterPro: IPR003594 This domain is found in several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed beta-sheet. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0005524 ATP binding; PDB: 3JZ3_A 3DGE_A 2C2A_A 2BU5_A 2BU8_A 2BU6_A 2BU7_A 2BU2_A 2BTZ_A 3K99_D ....
Probab=25.64 E-value=85 Score=20.56 Aligned_cols=51 Identities=10% Similarity=0.162 Sum_probs=34.0
Q ss_pred eccccccCCCCCCC--HHHhhhchhhhhcccccchhhcCchhhHHhHHHHHHHHhhc
Q psy17997 52 EPTIKMIDGPDYPS--WDDVRRGNYLKHVRTETVEEKAGGYVCAIATMRALNDAFAG 106 (120)
Q Consensus 52 ~Pl~~~~~GP~~P~--~e~L~~~GYl~HVR~~s~~e~AGGfts~laC~RALQEAfsg 106 (120)
-=+.+..+|+.+|. ++.+-. ............+|+.-.|.+.|.+-+.+.|
T Consensus 38 ~~i~i~d~G~gi~~~~l~~~~~----~~~~~~~~~~~~~g~GlGL~~~~~~~~~~~g 90 (111)
T PF02518_consen 38 LSIEISDNGVGIPPEELEKLFE----PFFTSDKSETSISGHGLGLYIVKQIAERHGG 90 (111)
T ss_dssp EEEEEEESSSSTTHHHHHHHCS----TTSHSSSSSGGSSSSSHHHHHHHHHHHHTTE
T ss_pred EEEEEEeccccccccccccchh----hcccccccccccCCCChHHHHHHHHHHHCCC
Confidence 33556678998885 333332 3333333555677888888889999898887
No 12
>PRK07474 sulfur oxidation protein SoxY; Provisional
Probab=24.81 E-value=34 Score=26.44 Aligned_cols=48 Identities=21% Similarity=0.142 Sum_probs=30.4
Q ss_pred CcccccccccCCCCCCCCCccccceeeccccccccCCccCCccCCCceee
Q psy17997 3 ENVTDLPALFSQPSQDLPKHFSSGIRIGSNLGLSVPAIVKPELGPLYKYE 52 (120)
Q Consensus 3 ~~~~~~~~~~~~~~~~k~~~FSTGIk~g~~~s~~~~pvpk~eeG~lY~Y~ 52 (120)
+|-.-+-+.|+-.-..-+-.|||.|||++.+... .|.+...|.+|.=.
T Consensus 95 ~NP~Pl~a~f~l~p~~~~~~vstRIRm~~ts~V~--Ava~~~dG~l~~a~ 142 (154)
T PRK07474 95 GNPQPGVATFHFGPAAGRAEASTRIRLAQTQNVI--AIAEMSDGSLWSAK 142 (154)
T ss_pred CCCCCEEEEEEecCCCCCceEEEEEEcCCCceEE--EEEEeCCCeEEEEE
Confidence 3444455556542233345699999999877665 66676568776543
No 13
>PF15161 Neuropep_like: Neuropeptide-like
Probab=24.20 E-value=41 Score=22.90 Aligned_cols=10 Identities=40% Similarity=0.271 Sum_probs=7.4
Q ss_pred hHHHHHHHHh
Q psy17997 95 ATMRALNDAF 104 (120)
Q Consensus 95 aC~RALQEAf 104 (120)
.|+|||||--
T Consensus 24 fmqRALQdlk 33 (65)
T PF15161_consen 24 FMQRALQDLK 33 (65)
T ss_pred HHHHHHhhhh
Confidence 5779999853
No 14
>TIGR02058 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus.
Probab=22.70 E-value=54 Score=24.57 Aligned_cols=13 Identities=46% Similarity=0.590 Sum_probs=10.9
Q ss_pred HHhHHHHHHHHhh
Q psy17997 93 AIATMRALNDAFA 105 (120)
Q Consensus 93 ~laC~RALQEAfs 105 (120)
.-|+.||++||+.
T Consensus 19 TkAA~RAvrDAI~ 31 (116)
T TIGR02058 19 TKAAMRAVRNAIA 31 (116)
T ss_pred HHHHHHHHHHHHh
Confidence 4589999999975
No 15
>PF05322 NinE: NINE Protein; InterPro: IPR007986 This family consists of NINE proteins from several bacteriophage and from Escherichia coli.
Probab=22.13 E-value=58 Score=22.00 Aligned_cols=32 Identities=31% Similarity=0.404 Sum_probs=27.1
Q ss_pred CceeeccccccCCCC-CCCHHHhhhchhhhhcc
Q psy17997 48 LYKYEPTIKMIDGPD-YPSWDDVRRGNYLKHVR 79 (120)
Q Consensus 48 lY~Y~Pl~~~~~GP~-~P~~e~L~~~GYl~HVR 79 (120)
--.|.|..--.+-+. .|+..++...+|+.|.-
T Consensus 15 Nc~ylpTkRs~~k~kpip~~S~vktf~y~~~L~ 47 (60)
T PF05322_consen 15 NCKYLPTKRSRNKKKPIPTESDVKTFNYTAHLW 47 (60)
T ss_pred hceeccccccccCCCCCCChhhcccccchhHHH
Confidence 457888888888887 88999999999999874
Done!