Query 020172
Match_columns 330
No_of_seqs 182 out of 942
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:36:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00083 HLH Helix-loop-helix d 99.3 2E-12 4.3E-17 93.9 5.8 52 227-278 6-60 (60)
2 smart00353 HLH helix loop heli 99.3 4E-12 8.8E-17 90.9 6.2 49 230-278 1-52 (53)
3 PF00010 HLH: Helix-loop-helix 99.2 9.3E-12 2E-16 90.5 5.1 47 228-274 4-55 (55)
4 KOG1318 Helix loop helix trans 98.8 3.1E-09 6.7E-14 106.4 4.4 56 223-278 231-290 (411)
5 KOG1319 bHLHZip transcription 98.6 1.4E-08 2.9E-13 93.5 2.1 61 228-288 65-132 (229)
6 KOG4304 Transcriptional repres 98.6 3.5E-08 7.5E-13 93.3 3.2 51 228-278 35-93 (250)
7 KOG3561 Aryl-hydrocarbon recep 98.1 4E-06 8.7E-11 90.1 5.1 51 226-276 21-75 (803)
8 KOG2588 Predicted DNA-binding 97.8 1.1E-05 2.3E-10 87.7 3.4 62 226-287 277-339 (953)
9 KOG0561 bHLH transcription fac 97.6 2.7E-05 5.9E-10 76.3 2.1 55 231-285 66-122 (373)
10 KOG2483 Upstream transcription 97.5 8.6E-05 1.9E-09 70.0 4.3 54 224-277 58-114 (232)
11 KOG3960 Myogenic helix-loop-he 97.5 0.00038 8.2E-09 66.9 8.5 59 229-287 122-182 (284)
12 PLN03217 transcription factor 97.0 0.00061 1.3E-08 56.2 3.1 52 237-288 19-76 (93)
13 KOG4029 Transcription factor H 96.8 0.0011 2.4E-08 61.1 4.0 56 229-284 113-172 (228)
14 KOG4447 Transcription factor T 95.5 0.027 5.8E-07 51.1 5.4 73 205-277 45-132 (173)
15 KOG3910 Helix loop helix trans 93.1 0.053 1.2E-06 56.7 2.1 52 229-280 530-585 (632)
16 KOG3558 Hypoxia-inducible fact 88.3 0.25 5.4E-06 53.5 1.8 45 230-274 51-99 (768)
17 KOG3560 Aryl-hydrocarbon recep 85.6 0.89 1.9E-05 48.5 4.0 39 233-271 33-75 (712)
18 KOG3559 Transcriptional regula 85.4 0.94 2E-05 47.0 4.0 44 230-273 6-53 (598)
19 KOG3898 Transcription factor N 72.8 2.2 4.8E-05 40.8 1.9 47 230-276 77-126 (254)
20 KOG3582 Mlx interactors and re 65.0 1.1 2.4E-05 48.9 -2.1 63 228-290 654-721 (856)
21 KOG4395 Transcription factor A 58.3 16 0.00036 35.9 4.7 48 230-277 179-229 (285)
22 KOG4447 Transcription factor T 43.3 18 0.00038 33.3 2.2 42 232-273 29-72 (173)
23 COG3074 Uncharacterized protei 30.5 37 0.00081 27.6 1.9 27 263-289 13-39 (79)
24 KOG3584 cAMP response element 30.3 24 0.00053 35.4 1.1 21 267-287 311-331 (348)
25 PRK13702 replication protein; 28.0 1.3E+02 0.0028 25.1 4.7 42 227-268 22-76 (85)
26 TIGR00986 3a0801s05tom22 mitoc 25.6 34 0.00075 30.9 1.1 37 237-273 48-84 (145)
27 PF02150 RNA_POL_M_15KD: RNA p 24.3 28 0.00062 23.9 0.3 13 48-60 1-13 (35)
28 PRK15422 septal ring assembly 21.3 62 0.0014 26.6 1.7 28 262-289 12-39 (79)
No 1
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=99.33 E-value=2e-12 Score=93.87 Aligned_cols=52 Identities=31% Similarity=0.569 Sum_probs=48.9
Q ss_pred CcccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHH
Q 020172 227 DPQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVK 278 (330)
Q Consensus 227 ~~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq 278 (330)
..|+.+||+||++||+.|..|+.|||.. .|+||++||+.||+||++|+.+++
T Consensus 6 ~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~ 60 (60)
T cd00083 6 EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60 (60)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 3689999999999999999999999988 899999999999999999998863
No 2
>smart00353 HLH helix loop helix domain.
Probab=99.31 E-value=4e-12 Score=90.93 Aligned_cols=49 Identities=31% Similarity=0.547 Sum_probs=45.6
Q ss_pred cHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhchHHHHHHHHHHHHHHHH
Q 020172 230 TVAARQRRERISERIRVLQRLVPG---GSKMDTASMLDEAANYLKFLRSQVK 278 (330)
Q Consensus 230 s~aER~RRerINer~~~LrsLVPg---~~KmDKASILeeAIdYIK~LQ~QVq 278 (330)
+.+||+||++||++|..|+.|||. ..|+||++||.+||+||+.|+.+++
T Consensus 1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~ 52 (53)
T smart00353 1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ 52 (53)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 368999999999999999999994 6799999999999999999999886
No 3
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=99.25 E-value=9.3e-12 Score=90.55 Aligned_cols=47 Identities=34% Similarity=0.593 Sum_probs=44.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHhcCCCC-----CCCChhchHHHHHHHHHHHH
Q 020172 228 PQTVAARQRRERISERIRVLQRLVPGG-----SKMDTASMLDEAANYLKFLR 274 (330)
Q Consensus 228 ~Hs~aER~RRerINer~~~LrsLVPg~-----~KmDKASILeeAIdYIK~LQ 274 (330)
.|+..||+||++||+.|..|+.+||.+ .|++|++||+.||+||+.||
T Consensus 4 ~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 4 KHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 588999999999999999999999986 68999999999999999997
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=98.81 E-value=3.1e-09 Score=106.38 Aligned_cols=56 Identities=29% Similarity=0.551 Sum_probs=50.0
Q ss_pred CCCCCcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHHHHHHH
Q 020172 223 RISTDPQTVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFLRSQVK 278 (330)
Q Consensus 223 r~ss~~Hs~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~LQ~QVq 278 (330)
|.+++.|+..|||||++||++|++|..|||.+ .|..|..||..++|||+.||+..+
T Consensus 231 r~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q 290 (411)
T KOG1318|consen 231 RRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ 290 (411)
T ss_pred HHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence 45567999999999999999999999999998 356799999999999999998654
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=98.62 E-value=1.4e-08 Score=93.47 Aligned_cols=61 Identities=30% Similarity=0.427 Sum_probs=54.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCCC
Q 020172 228 PQTVAARQRRERISERIRVLQRLVPGG-------SKMDTASMLDEAANYLKFLRSQVKALENPGHQKP 288 (330)
Q Consensus 228 ~Hs~aER~RRerINer~~~LrsLVPg~-------~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L~ 288 (330)
.|..+||+||+.|+..+..|+.|||.| .|+.||.||..+|+||.+|+.++.+-+.++..|.
T Consensus 65 aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~ 132 (229)
T KOG1319|consen 65 AHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR 132 (229)
T ss_pred HHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999999999965 3788999999999999999999888877766553
No 6
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.56 E-value=3.5e-08 Score=93.28 Aligned_cols=51 Identities=27% Similarity=0.492 Sum_probs=45.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHhcCCCC--------CCCChhchHHHHHHHHHHHHHHHH
Q 020172 228 PQTVAARQRRERISERIRVLQRLVPGG--------SKMDTASMLDEAANYLKFLRSQVK 278 (330)
Q Consensus 228 ~Hs~aER~RRerINer~~~LrsLVPg~--------~KmDKASILeeAIdYIK~LQ~QVq 278 (330)
.+-+.||+||+|||+.|..|+.|||.. .|++||.||+-||+|++.|+.+..
T Consensus 35 ~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~ 93 (250)
T KOG4304|consen 35 RKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ 93 (250)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence 456899999999999999999999943 678999999999999999998653
No 7
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=98.06 E-value=4e-06 Score=90.13 Aligned_cols=51 Identities=24% Similarity=0.475 Sum_probs=47.6
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHhcCCCCC----CCChhchHHHHHHHHHHHHHH
Q 020172 226 TDPQTVAARQRRERISERIRVLQRLVPGGS----KMDTASMLDEAANYLKFLRSQ 276 (330)
Q Consensus 226 s~~Hs~aER~RRerINer~~~LrsLVPg~~----KmDKASILeeAIdYIK~LQ~Q 276 (330)
...|+.+||+||+++|..|.+|.+|||.+. |+||-+||.+||++||.++.+
T Consensus 21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 457899999999999999999999999884 999999999999999999985
No 8
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=97.83 E-value=1.1e-05 Score=87.72 Aligned_cols=62 Identities=23% Similarity=0.424 Sum_probs=55.5
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172 226 TDPQTVAARQRRERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQK 287 (330)
Q Consensus 226 s~~Hs~aER~RRerINer~~~LrsLVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L 287 (330)
+..|+++||+.|-.||++|.+|+.+||+. .|+.|..+|..||+||++|+...+.+..+++.+
T Consensus 277 RtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l 339 (953)
T KOG2588|consen 277 RTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL 339 (953)
T ss_pred cchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence 56799999999999999999999999987 799999999999999999999887776655543
No 9
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.60 E-value=2.7e-05 Score=76.25 Aligned_cols=55 Identities=25% Similarity=0.458 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCC--CCCCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172 231 VAARQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKFLRSQVKALENPGH 285 (330)
Q Consensus 231 ~aER~RRerINer~~~LrsLVPg--~~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~ 285 (330)
.-||+|=.-||-.|..||.|+|. +.|+.||.||+.+.+||..|..+.-+|-.++.
T Consensus 66 sNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~ 122 (373)
T KOG0561|consen 66 SNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNG 122 (373)
T ss_pred chHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccc
Confidence 34999999999999999999995 68999999999999999999887654444333
No 10
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=97.53 E-value=8.6e-05 Score=70.04 Aligned_cols=54 Identities=22% Similarity=0.272 Sum_probs=46.0
Q ss_pred CCCCcccHHHHHHHHHHHHHHHHHHhcCCCC--CCCC-hhchHHHHHHHHHHHHHHH
Q 020172 224 ISTDPQTVAARQRRERISERIRVLQRLVPGG--SKMD-TASMLDEAANYLKFLRSQV 277 (330)
Q Consensus 224 ~ss~~Hs~aER~RRerINer~~~LrsLVPg~--~KmD-KASILeeAIdYIK~LQ~QV 277 (330)
.+...|+.-||+||..|.++|..|+.+||.+ .+.. .++||..|+.||+.|+.+.
T Consensus 58 ~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~ 114 (232)
T KOG2483|consen 58 SSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS 114 (232)
T ss_pred cchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence 3445689999999999999999999999976 2333 6999999999999998765
No 11
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.52 E-value=0.00038 Score=66.86 Aligned_cols=59 Identities=17% Similarity=0.345 Sum_probs=49.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHh-cCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172 229 QTVAARQRRERISERIRVLQR-LVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQK 287 (330)
Q Consensus 229 Hs~aER~RRerINer~~~Lrs-LVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L 287 (330)
-++.||+|=.||||.|.+|++ -+++. .++-|..||..||+||..||.-++++..+..-+
T Consensus 122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~ 182 (284)
T KOG3960|consen 122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL 182 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence 467899999999999999985 34554 678999999999999999999998887665544
No 12
>PLN03217 transcription factor ATBS1; Provisional
Probab=96.98 E-value=0.00061 Score=56.16 Aligned_cols=52 Identities=27% Similarity=0.423 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHhcCCCC------CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCCC
Q 020172 237 RERISERIRVLQRLVPGG------SKMDTASMLDEAANYLKFLRSQVKALENPGHQKP 288 (330)
Q Consensus 237 RerINer~~~LrsLVPg~------~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L~ 288 (330)
-+.|++-+..||.|+|.. .|...+-||+||..||+.|+.+|..|.+....|-
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL 76 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL 76 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999953 5677888999999999999999999988766653
No 13
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=96.84 E-value=0.0011 Score=61.11 Aligned_cols=56 Identities=23% Similarity=0.427 Sum_probs=48.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHhcCCC----CCCCChhchHHHHHHHHHHHHHHHHHHhCCC
Q 020172 229 QTVAARQRRERISERIRVLQRLVPG----GSKMDTASMLDEAANYLKFLRSQVKALENPG 284 (330)
Q Consensus 229 Hs~aER~RRerINer~~~LrsLVPg----~~KmDKASILeeAIdYIK~LQ~QVq~Le~~~ 284 (330)
++..||.|=+.+|..|..||.+||. ..|+.|..+|..||.||++|+.-++.-+...
T Consensus 113 ~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~ 172 (228)
T KOG4029|consen 113 RNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL 172 (228)
T ss_pred hhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence 4566999999999999999999994 4689999999999999999999777666443
No 14
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=95.49 E-value=0.027 Score=51.10 Aligned_cols=73 Identities=29% Similarity=0.452 Sum_probs=58.3
Q ss_pred CCCCCCcccccCcccCCCCCCCCc-------------ccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHH
Q 020172 205 RPVNLGLEVVEKPKRKNVRISTDP-------------QTVAARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANY 269 (330)
Q Consensus 205 rP~s~g~~ss~K~rrkr~r~ss~~-------------Hs~aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdY 269 (330)
+....|.++..|++++.-++.++. |++.||+|-..+|+.|..||.++|.. .|+.|.--|.-|..|
T Consensus 45 g~l~pgspa~gk~~~ktlr~~~~~~~~~dE~q~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ry 124 (173)
T KOG4447|consen 45 GKLEPGSPADGKRGKKTLRIGTDSIQSLDELQKQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARY 124 (173)
T ss_pred cccCCCCCCcccccccccccCCCchhhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccC
Confidence 444556666677766655555543 78889999999999999999999954 899999999999999
Q ss_pred HHHHHHHH
Q 020172 270 LKFLRSQV 277 (330)
Q Consensus 270 IK~LQ~QV 277 (330)
|.+|=.-.
T Consensus 125 idfl~~vl 132 (173)
T KOG4447|consen 125 IDFLYQVL 132 (173)
T ss_pred Cchhhhcc
Confidence 99996543
No 15
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=93.07 E-value=0.053 Score=56.71 Aligned_cols=52 Identities=23% Similarity=0.257 Sum_probs=41.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHhcCCCCCCC----ChhchHHHHHHHHHHHHHHHHHH
Q 020172 229 QTVAARQRRERISERIRVLQRLVPGGSKM----DTASMLDEAANYLKFLRSQVKAL 280 (330)
Q Consensus 229 Hs~aER~RRerINer~~~LrsLVPg~~Km----DKASILeeAIdYIK~LQ~QVq~L 280 (330)
.+..||.|=..|||.|++|.++.----|. -|--||..||.-|-.|++||++-
T Consensus 530 NNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER 585 (632)
T KOG3910|consen 530 NNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER 585 (632)
T ss_pred hhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence 34557777677999999999987543333 37789999999999999999863
No 16
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=88.27 E-value=0.25 Score=53.47 Aligned_cols=45 Identities=33% Similarity=0.499 Sum_probs=39.0
Q ss_pred cHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHHH
Q 020172 230 TVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFLR 274 (330)
Q Consensus 230 s~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~LQ 274 (330)
.-|.|.||.|-|+-|.+|..+||-. .-+|||+|+.-||-|+|-=+
T Consensus 51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk 99 (768)
T KOG3558|consen 51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRK 99 (768)
T ss_pred hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHH
Confidence 4579999999999999999999933 56999999999999997433
No 17
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=85.55 E-value=0.89 Score=48.49 Aligned_cols=39 Identities=31% Similarity=0.564 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHH
Q 020172 233 ARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLK 271 (330)
Q Consensus 233 ER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK 271 (330)
-|+-|+|+|..|+.|-+|+|=. .|+||-+||.-+|-|++
T Consensus 33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr 75 (712)
T KOG3560|consen 33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR 75 (712)
T ss_pred chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence 4567999999999999999943 89999999999999986
No 18
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=85.43 E-value=0.94 Score=47.02 Aligned_cols=44 Identities=36% Similarity=0.508 Sum_probs=39.0
Q ss_pred cHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHH
Q 020172 230 TVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFL 273 (330)
Q Consensus 230 s~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~L 273 (330)
.-+.|.||++-|-.|.+|-.|+|-. ..+||++|+.-|..|||.-
T Consensus 6 KnaA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr 53 (598)
T KOG3559|consen 6 KNAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR 53 (598)
T ss_pred hhHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence 3578999999999999999999954 5699999999999999863
No 19
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=72.84 E-value=2.2 Score=40.79 Aligned_cols=47 Identities=26% Similarity=0.465 Sum_probs=40.6
Q ss_pred cHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHH
Q 020172 230 TVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQ 276 (330)
Q Consensus 230 s~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~Q 276 (330)
+..||+|=-.+|+.|+.||.+||.+ .|+.|+..|.-|-.||..|+.-
T Consensus 77 NaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~ 126 (254)
T KOG3898|consen 77 NARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV 126 (254)
T ss_pred cchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence 3558888888999999999999943 7899999999999999998853
No 20
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=64.95 E-value=1.1 Score=48.91 Aligned_cols=63 Identities=17% Similarity=0.293 Sum_probs=52.1
Q ss_pred cccHHHHHHHHHHHHHHHHHHhcCCCC-----CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCCCcc
Q 020172 228 PQTVAARQRRERISERIRVLQRLVPGG-----SKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDH 290 (330)
Q Consensus 228 ~Hs~aER~RRerINer~~~LrsLVPg~-----~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L~~~ 290 (330)
.|+.+|.+||+.|.-++..|-+++-+. .||.++.-|..+++||-.++.+...+.++...|...
T Consensus 654 t~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~ 721 (856)
T KOG3582|consen 654 THISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKE 721 (856)
T ss_pred cCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhh
Confidence 588999999999999999999999865 567788889999999999988777666665555433
No 21
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=58.30 E-value=16 Score=35.85 Aligned_cols=48 Identities=23% Similarity=0.369 Sum_probs=41.9
Q ss_pred cHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHH
Q 020172 230 TVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQV 277 (330)
Q Consensus 230 s~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QV 277 (330)
...||+|=..+|..|+.||.+||.+ .|+.|-.-|..|-.||--|-...
T Consensus 179 narErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l 229 (285)
T KOG4395|consen 179 NARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL 229 (285)
T ss_pred chHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence 4668888899999999999999976 57889999999999999887655
No 22
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=43.26 E-value=18 Score=33.31 Aligned_cols=42 Identities=24% Similarity=0.388 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHHHHHH
Q 020172 232 AARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANYLKFL 273 (330)
Q Consensus 232 aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdYIK~L 273 (330)
.|+.|..++++.+.-|+.|+|+. .++.+.--|.-+-+||.+|
T Consensus 29 ~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~ 72 (173)
T KOG4447|consen 29 KERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSL 72 (173)
T ss_pred HHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhH
Confidence 47888899999999999999986 3444333354455555444
No 23
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.46 E-value=37 Score=27.62 Aligned_cols=27 Identities=11% Similarity=0.345 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCCc
Q 020172 263 LDEAANYLKFLRSQVKALENPGHQKPD 289 (330)
Q Consensus 263 LeeAIdYIK~LQ~QVq~Le~~~~~L~~ 289 (330)
+..||+-|.-||.+|++|++.+..|..
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l~~ 39 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSLSQ 39 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHhHH
Confidence 567999999999999999988876653
No 24
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=30.34 E-value=24 Score=35.39 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCC
Q 020172 267 ANYLKFLRSQVKALENPGHQK 287 (330)
Q Consensus 267 IdYIK~LQ~QVq~Le~~~~~L 287 (330)
-+|||.|+.+|..||.++..|
T Consensus 311 KEYVKCLENRVAVLENQNKaL 331 (348)
T KOG3584|consen 311 KEYVKCLENRVAVLENQNKAL 331 (348)
T ss_pred hHHHHHHHhHHHHHhcccHHH
Confidence 378899999998888887655
No 25
>PRK13702 replication protein; Provisional
Probab=27.95 E-value=1.3e+02 Score=25.07 Aligned_cols=42 Identities=17% Similarity=0.336 Sum_probs=30.0
Q ss_pred CcccHHHHHHH--HHHHHHHHHHHhcCCCC-----------CCCChhchHHHHHH
Q 020172 227 DPQTVAARQRR--ERISERIRVLQRLVPGG-----------SKMDTASMLDEAAN 268 (330)
Q Consensus 227 ~~Hs~aER~RR--erINer~~~LrsLVPg~-----------~KmDKASILeeAId 268 (330)
.|.+.+||.|. -|..+--++|.-+|++. ..+..|.||+..|+
T Consensus 22 ~Pls~aErQr~svaRKr~THkei~vfi~n~lK~~L~elc~~~glTQAe~IE~LIe 76 (85)
T PRK13702 22 NPLSAAEKQRASVARKRATHKEIKVFIQNPLKDKLMELCEEEGLTQAEMIERLIE 76 (85)
T ss_pred CCCCHHHHHHHHHHHHHHhhhhhheeecHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 68899999885 45566667788788755 33567777777665
No 26
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit Tom22. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins.
Probab=25.60 E-value=34 Score=30.87 Aligned_cols=37 Identities=22% Similarity=0.315 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhcCCCCCCCChhchHHHHHHHHHHH
Q 020172 237 RERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFL 273 (330)
Q Consensus 237 RerINer~~~LrsLVPg~~KmDKASILeeAIdYIK~L 273 (330)
-|-|-+||.+|+.+||+..+---.+...-+..++|.+
T Consensus 48 ~ETl~ERi~ALkDm~Pp~~R~~i~~~~s~t~s~~ks~ 84 (145)
T TIGR00986 48 EETFTDRIYALKDIVPPTTRGWIYHKYSTTTNFVKST 84 (145)
T ss_pred cCcHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3568889999999999775544444444444444443
No 27
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=24.33 E-value=28 Score=23.86 Aligned_cols=13 Identities=31% Similarity=0.588 Sum_probs=9.2
Q ss_pred EEeccchhhhccc
Q 020172 48 ILFSSDCRNLWNF 60 (330)
Q Consensus 48 ~~~~~~~~~~~~~ 60 (330)
|+|-++|.||+-.
T Consensus 1 m~FCp~C~nlL~p 13 (35)
T PF02150_consen 1 MRFCPECGNLLYP 13 (35)
T ss_dssp --BETTTTSBEEE
T ss_pred CeeCCCCCccceE
Confidence 6788999999854
No 28
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=21.26 E-value=62 Score=26.60 Aligned_cols=28 Identities=11% Similarity=0.316 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCCCc
Q 020172 262 MLDEAANYLKFLRSQVKALENPGHQKPD 289 (330)
Q Consensus 262 ILeeAIdYIK~LQ~QVq~Le~~~~~L~~ 289 (330)
=+..|||-|.-||.+|++|++.+..|..
T Consensus 12 KIqqAvdtI~LLqmEieELKekn~~L~~ 39 (79)
T PRK15422 12 KVQQAIDTITLLQMEIEELKEKNNSLSQ 39 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999988766643
Done!