Query 009676
Match_columns 529
No_of_seqs 297 out of 1154
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 16:00:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009676hhsearch_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 99.4 6.9E-13 1.5E-17 103.6 6.3 54 333-386 4-60 (60)
2 PF00010 HLH: Helix-loop-helix 99.4 7.4E-13 1.6E-17 103.0 5.4 49 334-382 2-55 (55)
3 smart00353 HLH helix loop heli 99.3 7.6E-12 1.6E-16 96.0 6.7 49 338-386 1-52 (53)
4 KOG1318 Helix loop helix trans 99.2 7.4E-12 1.6E-16 132.6 5.8 60 327-386 227-290 (411)
5 KOG1319 bHLHZip transcription 98.9 4.6E-10 9.9E-15 107.7 3.7 63 325-390 57-126 (229)
6 KOG4304 Transcriptional repres 98.9 1.2E-09 2.6E-14 110.1 3.6 54 334-387 33-94 (250)
7 KOG3561 Aryl-hydrocarbon recep 98.5 1E-07 2.2E-12 108.5 6.4 51 334-384 21-75 (803)
8 KOG2588 Predicted DNA-binding 98.0 2.4E-06 5.2E-11 98.1 2.4 58 332-389 275-333 (953)
9 KOG2483 Upstream transcription 98.0 1.8E-05 3.8E-10 79.3 7.7 54 334-387 60-116 (232)
10 KOG3960 Myogenic helix-loop-he 98.0 1.8E-05 3.9E-10 79.5 7.1 54 337-390 122-177 (284)
11 KOG0561 bHLH transcription fac 97.5 8.5E-05 1.8E-09 76.4 4.6 52 334-385 61-114 (373)
12 KOG4029 Transcription factor H 97.5 8E-05 1.7E-09 73.9 4.1 55 336-390 112-170 (228)
13 PLN03217 transcription factor 97.2 0.00069 1.5E-08 58.3 5.8 46 345-390 19-70 (93)
14 KOG3910 Helix loop helix trans 97.0 0.001 2.2E-08 72.5 5.8 57 334-390 527-587 (632)
15 KOG4447 Transcription factor T 95.0 0.012 2.6E-07 55.8 1.7 50 334-383 79-130 (173)
16 KOG3898 Transcription factor N 94.3 0.09 1.9E-06 53.7 6.3 48 336-383 75-125 (254)
17 KOG3560 Aryl-hydrocarbon recep 94.2 0.04 8.8E-07 61.1 3.6 39 342-380 34-76 (712)
18 KOG3558 Hypoxia-inducible fact 91.1 0.16 3.6E-06 57.8 3.2 44 337-380 50-97 (768)
19 KOG4395 Transcription factor A 88.0 0.75 1.6E-05 47.1 4.9 51 336-386 177-230 (285)
20 KOG3559 Transcriptional regula 86.5 0.63 1.4E-05 50.5 3.5 43 340-382 8-54 (598)
21 KOG4447 Transcription factor T 52.3 9.2 0.0002 36.8 1.9 49 340-388 29-79 (173)
22 KOG3582 Mlx interactors and re 44.4 5.7 0.00012 45.9 -0.8 52 335-386 653-709 (856)
23 KOG1924 RhoA GTPase effector D 38.6 38 0.00082 40.2 4.4 12 481-492 594-605 (1102)
24 KOG4571 Activating transcripti 27.9 1.1E+02 0.0023 32.4 5.3 50 338-387 236-290 (294)
25 PF07908 D-aminoacyl_C: D-amin 21.6 49 0.0011 25.5 1.1 16 28-43 18-33 (48)
26 PRK13702 replication protein; 20.9 2.2E+02 0.0048 25.0 5.0 42 335-376 22-76 (85)
27 PTZ00405 cytochrome c; Provisi 20.4 1.5E+02 0.0032 26.8 4.1 38 345-382 72-113 (114)
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=99.38 E-value=6.9e-13 Score=103.64 Aligned_cols=54 Identities=50% Similarity=0.773 Sum_probs=50.2
Q ss_pred hhhccchhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHH
Q 009676 333 AAEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQ 386 (529)
Q Consensus 333 ~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~ 386 (529)
.+..|+..||+||++||+.|..|+.+||.+ .|++|++||..||+||+.|+.+++
T Consensus 4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~ 60 (60)
T cd00083 4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60 (60)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 355799999999999999999999999998 799999999999999999998763
No 2
>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=99.36 E-value=7.4e-13 Score=103.01 Aligned_cols=49 Identities=55% Similarity=0.889 Sum_probs=46.3
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCC-----CCCchhhHHHHHHHHHHHHH
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHC-----NKTDKASMLDEAIEYLKSLQ 382 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~-----~K~dKAsIL~~AI~YIk~Lq 382 (529)
+..|+..||+||++||+.|.+|+.+||.+ .|++|++||+.||+||++||
T Consensus 2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 45799999999999999999999999998 48999999999999999997
No 3
>smart00353 HLH helix loop helix domain.
Probab=99.28 E-value=7.6e-12 Score=96.02 Aligned_cols=49 Identities=53% Similarity=0.736 Sum_probs=45.5
Q ss_pred chhHHHHHHHHHHHHHHHHhhCCC---CCCCchhhHHHHHHHHHHHHHHHHH
Q 009676 338 NLSERRRRDRINEKMRALQELIPH---CNKTDKASMLDEAIEYLKSLQLQLQ 386 (529)
Q Consensus 338 ~~~ERrRRerIN~~~~~Lr~LVP~---~~K~dKAsIL~~AI~YIk~Lq~qv~ 386 (529)
+..||+||++||+.|..|+.+||. ..|++|++||.+||+||++|+.+++
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 468999999999999999999995 5589999999999999999999875
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=99.23 E-value=7.4e-12 Score=132.55 Aligned_cols=60 Identities=42% Similarity=0.758 Sum_probs=53.9
Q ss_pred CcccchhhhccchhHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHH
Q 009676 327 SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQ 386 (529)
Q Consensus 327 ~~rr~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq~qv~ 386 (529)
..|.+++|+.||++|||||++||++|++|..|||.|+ |..|..||..+++||+.||+..+
T Consensus 227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q 290 (411)
T KOG1318|consen 227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ 290 (411)
T ss_pred hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence 3455566779999999999999999999999999995 67899999999999999998776
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=98.95 E-value=4.6e-10 Score=107.69 Aligned_cols=63 Identities=35% Similarity=0.527 Sum_probs=53.5
Q ss_pred CCCcccchhhhccchhHHHHHHHHHHHHHHHHhhCCCCC-------CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009676 325 SGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-------KTDKASMLDEAIEYLKSLQLQLQVMWM 390 (529)
Q Consensus 325 ~~~~rr~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~-------K~dKAsIL~~AI~YIk~Lq~qv~~L~~ 390 (529)
+.+.||++ .|..+||+||+-||..+..|+.|||.|. |+.||.||.++|+||.+|++++...+.
T Consensus 57 syk~rrr~---aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~ 126 (229)
T KOG1319|consen 57 SYKDRRRR---AHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEE 126 (229)
T ss_pred hHHHHHHH---HHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444443 6999999999999999999999999883 889999999999999999887766553
No 6
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.86 E-value=1.2e-09 Score=110.06 Aligned_cols=54 Identities=35% Similarity=0.531 Sum_probs=47.9
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCC--------CCCchhhHHHHHHHHHHHHHHHHHH
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHC--------NKTDKASMLDEAIEYLKSLQLQLQV 387 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--------~K~dKAsIL~~AI~YIk~Lq~qv~~ 387 (529)
+..|.++|||||+|||+.|.+|++||+.+ .|++||.||+.||+|||.|+.....
T Consensus 33 k~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~ 94 (250)
T KOG4304|consen 33 KVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA 94 (250)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence 44689999999999999999999999965 5789999999999999999975443
No 7
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=98.53 E-value=1e-07 Score=108.54 Aligned_cols=51 Identities=33% Similarity=0.531 Sum_probs=48.1
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHH
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQ 384 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq~q 384 (529)
+++|+.+||||||++|..|.+|.+|||.|. |+||..||++||.+||.+++.
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 568999999999999999999999999986 999999999999999998874
No 8
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=98.01 E-value=2.4e-06 Score=98.06 Aligned_cols=58 Identities=34% Similarity=0.549 Sum_probs=52.0
Q ss_pred hhhhccchhHHHHHHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHHHh
Q 009676 332 RAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMW 389 (529)
Q Consensus 332 ~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIk~Lq~qv~~L~ 389 (529)
.+|.+||++|||.|..||++|.+|+.+||+.. |+.|..+|..||+||++|+...+.+-
T Consensus 275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk 333 (953)
T KOG2588|consen 275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLK 333 (953)
T ss_pred cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccc
Confidence 34568999999999999999999999999875 99999999999999999998766554
No 9
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=97.98 E-value=1.8e-05 Score=79.33 Aligned_cols=54 Identities=30% Similarity=0.483 Sum_probs=46.6
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCCC--CCc-hhhHHHHHHHHHHHHHHHHHH
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHCN--KTD-KASMLDEAIEYLKSLQLQLQV 387 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~--K~d-KAsIL~~AI~YIk~Lq~qv~~ 387 (529)
+..||..||+||+.|.+.|..|+.+||... |.. .++||++|++||+.|+.+...
T Consensus 60 R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~ 116 (232)
T KOG2483|consen 60 RAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSAT 116 (232)
T ss_pred hhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHH
Confidence 457999999999999999999999999764 333 799999999999999875443
No 10
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.95 E-value=1.8e-05 Score=79.54 Aligned_cols=54 Identities=31% Similarity=0.423 Sum_probs=46.2
Q ss_pred cchhHHHHHHHHHHHHHHHHhh-CCCCC-CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009676 337 HNLSERRRRDRINEKMRALQEL-IPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM 390 (529)
Q Consensus 337 H~~~ERrRRerIN~~~~~Lr~L-VP~~~-K~dKAsIL~~AI~YIk~Lq~qv~~L~~ 390 (529)
-.+.||||=.|+||.|.+|+.- +++-+ .+-|..||..||+||+.||.-++.+..
T Consensus 122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~ 177 (284)
T KOG3960|consen 122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ 177 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3689999999999999999875 34433 689999999999999999998888754
No 11
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.53 E-value=8.5e-05 Score=76.43 Aligned_cols=52 Identities=33% Similarity=0.556 Sum_probs=46.4
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHH
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQL 385 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~qv 385 (529)
++.-|--||||=.-||..|..||.|||.. .|++||.||+.+.+||.+|+.+.
T Consensus 61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K 114 (373)
T KOG0561|consen 61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK 114 (373)
T ss_pred HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence 45667889999999999999999999975 59999999999999999997643
No 12
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=97.52 E-value=8e-05 Score=73.93 Aligned_cols=55 Identities=27% Similarity=0.378 Sum_probs=48.9
Q ss_pred ccchhHHHHHHHHHHHHHHHHhhCCC----CCCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009676 336 VHNLSERRRRDRINEKMRALQELIPH----CNKTDKASMLDEAIEYLKSLQLQLQVMWM 390 (529)
Q Consensus 336 ~H~~~ERrRRerIN~~~~~Lr~LVP~----~~K~dKAsIL~~AI~YIk~Lq~qv~~L~~ 390 (529)
.+|..||.|=..+|..|..||.+||. -+|+.|..+|..||+||++|+.-++.-+.
T Consensus 112 ~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~ 170 (228)
T KOG4029|consen 112 ARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA 170 (228)
T ss_pred hhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence 46778999999999999999999995 35899999999999999999987776654
No 13
>PLN03217 transcription factor ATBS1; Provisional
Probab=97.22 E-value=0.00069 Score=58.26 Aligned_cols=46 Identities=26% Similarity=0.507 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHhhCCCC------CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009676 345 RDRINEKMRALQELIPHC------NKTDKASMLDEAIEYLKSLQLQLQVMWM 390 (529)
Q Consensus 345 RerIN~~~~~Lr~LVP~~------~K~dKAsIL~~AI~YIk~Lq~qv~~L~~ 390 (529)
-|.||+.+..|+.|+|.. .|..-+-||++|+.||+.|+.+|..|+.
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSe 70 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSE 70 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999964 4678889999999999999999999974
No 14
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=96.99 E-value=0.001 Score=72.45 Aligned_cols=57 Identities=26% Similarity=0.307 Sum_probs=48.6
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCCCCC----chhhHHHHHHHHHHHHHHHHHHHhc
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHCNKT----DKASMLDEAIEYLKSLQLQLQVMWM 390 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~K~----dKAsIL~~AI~YIk~Lq~qv~~L~~ 390 (529)
+...|..||.|-..||+.|++|..+.-..-|. -|..||..||..|-.|++||.+--+
T Consensus 527 R~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERNL 587 (632)
T KOG3910|consen 527 RMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERNL 587 (632)
T ss_pred HhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHccC
Confidence 34678999999999999999999987655443 4999999999999999999997643
No 15
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=94.98 E-value=0.012 Score=55.78 Aligned_cols=50 Identities=32% Similarity=0.471 Sum_probs=45.7
Q ss_pred hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHH
Q 009676 334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQL 383 (529)
Q Consensus 334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~ 383 (529)
+--||+.||+|-..+|+.|.+||.+||.. .|++|+-.|+.|..||-+|=+
T Consensus 79 rv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~ 130 (173)
T KOG4447|consen 79 RVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ 130 (173)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence 34699999999999999999999999975 699999999999999998864
No 16
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=94.31 E-value=0.09 Score=53.66 Aligned_cols=48 Identities=35% Similarity=0.486 Sum_probs=42.4
Q ss_pred ccchhHHHHHHHHHHHHHHHHhhCCC---CCCCchhhHHHHHHHHHHHHHH
Q 009676 336 VHNLSERRRRDRINEKMRALQELIPH---CNKTDKASMLDEAIEYLKSLQL 383 (529)
Q Consensus 336 ~H~~~ERrRRerIN~~~~~Lr~LVP~---~~K~dKAsIL~~AI~YIk~Lq~ 383 (529)
.=|..||+|=-.+|+.|+.||++||. ..|+.|+..|.-|-.||..|++
T Consensus 75 kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~ 125 (254)
T KOG3898|consen 75 KANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE 125 (254)
T ss_pred cccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence 35677998889999999999999994 3489999999999999999985
No 17
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=94.18 E-value=0.04 Score=61.10 Aligned_cols=39 Identities=38% Similarity=0.692 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHhhCCC----CCCCchhhHHHHHHHHHHH
Q 009676 342 RRRRDRINEKMRALQELIPH----CNKTDKASMLDEAIEYLKS 380 (529)
Q Consensus 342 RrRRerIN~~~~~Lr~LVP~----~~K~dKAsIL~~AI~YIk~ 380 (529)
||-|||+|..++.|..|+|- ++|+||.+||.-+|.||+.
T Consensus 34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV 76 (712)
T ss_pred hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence 67899999999999999995 4799999999999999874
No 18
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=91.07 E-value=0.16 Score=57.83 Aligned_cols=44 Identities=34% Similarity=0.505 Sum_probs=38.1
Q ss_pred cchhHHHHHHHHHHHHHHHHhhCCCC----CCCchhhHHHHHHHHHHH
Q 009676 337 HNLSERRRRDRINEKMRALQELIPHC----NKTDKASMLDEAIEYLKS 380 (529)
Q Consensus 337 H~~~ERrRRerIN~~~~~Lr~LVP~~----~K~dKAsIL~~AI~YIk~ 380 (529)
-.-+.|-||-|-|+-|.+|..+||-- .-+|||+|+.-||-|+|-
T Consensus 50 SRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl 97 (768)
T KOG3558|consen 50 SRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL 97 (768)
T ss_pred hhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence 34567999999999999999999932 368999999999999984
No 19
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=88.00 E-value=0.75 Score=47.11 Aligned_cols=51 Identities=29% Similarity=0.405 Sum_probs=45.2
Q ss_pred ccchhHHHHHHHHHHHHHHHHhhCCCCC---CCchhhHHHHHHHHHHHHHHHHH
Q 009676 336 VHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQ 386 (529)
Q Consensus 336 ~H~~~ERrRRerIN~~~~~Lr~LVP~~~---K~dKAsIL~~AI~YIk~Lq~qv~ 386 (529)
.-|..||||=..+|..|+.||.+||..+ |++|-..|..|-.||--|-..+.
T Consensus 177 aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~ 230 (285)
T KOG4395|consen 177 AANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD 230 (285)
T ss_pred ccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence 5688999999999999999999999764 89999999999999998866543
No 20
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=86.52 E-value=0.63 Score=50.53 Aligned_cols=43 Identities=33% Similarity=0.512 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHH
Q 009676 340 SERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ 382 (529)
Q Consensus 340 ~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq 382 (529)
..|.||++-|-.|.+|..++|-.. .+||++|+.-|..|||.-.
T Consensus 8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~ 54 (598)
T KOG3559|consen 8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN 54 (598)
T ss_pred HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence 458999999999999999999653 6899999999999999543
No 21
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=52.25 E-value=9.2 Score=36.82 Aligned_cols=49 Identities=20% Similarity=0.243 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHHHHhhCCCCC--CCchhhHHHHHHHHHHHHHHHHHHH
Q 009676 340 SERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 388 (529)
Q Consensus 340 ~ERrRRerIN~~~~~Lr~LVP~~~--K~dKAsIL~~AI~YIk~Lq~qv~~L 388 (529)
.|+-|..++|+.+.-|+.|+|+.. ++.+.-.|..+.+||.+|.+-.+.+
T Consensus 29 ~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~dE~q~qr 79 (173)
T KOG4447|consen 29 KERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSLDELQKQR 79 (173)
T ss_pred HHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhHHHHHHHH
Confidence 578899999999999999999863 5555555777778877776543333
No 22
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=44.43 E-value=5.7 Score=45.92 Aligned_cols=52 Identities=23% Similarity=0.339 Sum_probs=44.9
Q ss_pred hccchhHHHHHHHHHHHHHHHHhhCCCCC-----CCchhhHHHHHHHHHHHHHHHHH
Q 009676 335 EVHNLSERRRRDRINEKMRALQELIPHCN-----KTDKASMLDEAIEYLKSLQLQLQ 386 (529)
Q Consensus 335 ~~H~~~ERrRRerIN~~~~~Lr~LVP~~~-----K~dKAsIL~~AI~YIk~Lq~qv~ 386 (529)
-.|.-+|.+||++|.-.+..|-.++-+.. |+.++.-|..+++||..++.+..
T Consensus 653 it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~ 709 (856)
T KOG3582|consen 653 ITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERV 709 (856)
T ss_pred ccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhcc
Confidence 46999999999999999999999998764 67788889999999998876544
No 23
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=38.57 E-value=38 Score=40.23 Aligned_cols=12 Identities=25% Similarity=0.332 Sum_probs=6.1
Q ss_pred CCCCCCCCcccc
Q 009676 481 MQANSQPMNMFR 492 (529)
Q Consensus 481 ~q~~~qp~~~~~ 492 (529)
.++||+++++|.
T Consensus 594 g~ppPP~~gm~p 605 (1102)
T KOG1924|consen 594 GPPPPPPPGMFP 605 (1102)
T ss_pred CCCCCCCCCccc
Confidence 355555555543
No 24
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=27.91 E-value=1.1e+02 Score=32.44 Aligned_cols=50 Identities=30% Similarity=0.379 Sum_probs=30.4
Q ss_pred chhHHHHHHHHHHHHHHHHhhCCCCCC-----CchhhHHHHHHHHHHHHHHHHHH
Q 009676 338 NLSERRRRDRINEKMRALQELIPHCNK-----TDKASMLDEAIEYLKSLQLQLQV 387 (529)
Q Consensus 338 ~~~ERrRRerIN~~~~~Lr~LVP~~~K-----~dKAsIL~~AI~YIk~Lq~qv~~ 387 (529)
+++--|.|+|=.....+|-.-+-...| .+.|+=|++=|.|+|.|-.++.+
T Consensus 236 k~AAtRYRqKkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~~~ 290 (294)
T KOG4571|consen 236 KAAATRYRQKKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEVYK 290 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555544444444433333333 36899999999999999776643
No 25
>PF07908 D-aminoacyl_C: D-aminoacylase, C-terminal region; InterPro: IPR012855 D-aminoacylase (Q9AGH8 from SWISSPROT, 3.5.1.81 from EC) hydrolyses a wide variety of N-acyl derivatives of neutral D-amino acids, in a zinc-dependent manner. The enzyme is composed of a small beta-barrel domain and a larger catalytic alpha/beta-barrel that contains a short alpha/beta insert. The overall structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well []. The C-terminal region featured in this entry forms part of the beta-barrel domain, together with a short N-terminal segment. This domain does not seem to contribute to the substrate-binding site or to be involved in the catalytic process.; GO: 0008270 zinc ion binding, 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; PDB: 3GIQ_B 3GIP_B 1V4Y_A 1M7J_A 1RK5_A 1RJP_A 1RJR_A 1RJQ_A 1RK6_A 1V51_A.
Probab=21.62 E-value=49 Score=25.50 Aligned_cols=16 Identities=25% Similarity=0.615 Sum_probs=13.0
Q ss_pred chhhheeeCCeEEEee
Q 009676 28 ELVELLWQNGHVVLSS 43 (529)
Q Consensus 28 dlvELLW~NGqVV~qS 43 (529)
+=||.||-||++|...
T Consensus 18 ~GI~~V~VNG~~vv~~ 33 (48)
T PF07908_consen 18 EGIDYVFVNGQIVVED 33 (48)
T ss_dssp BSEEEEEETTEEEECT
T ss_pred CCEEEEEECCEEEEEC
Confidence 4478999999999743
No 26
>PRK13702 replication protein; Provisional
Probab=20.86 E-value=2.2e+02 Score=25.03 Aligned_cols=42 Identities=19% Similarity=0.284 Sum_probs=30.2
Q ss_pred hccchhHHHHH--HHHHHHHHHHHhhCCCCC-----------CCchhhHHHHHHH
Q 009676 335 EVHNLSERRRR--DRINEKMRALQELIPHCN-----------KTDKASMLDEAIE 376 (529)
Q Consensus 335 ~~H~~~ERrRR--erIN~~~~~Lr~LVP~~~-----------K~dKAsIL~~AI~ 376 (529)
..++.+||.|. .|..+..++|.-+|++-- .+..|.+|+..|+
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 35778888884 566677788888888642 4567777777765
No 27
>PTZ00405 cytochrome c; Provisional
Probab=20.39 E-value=1.5e+02 Score=26.81 Aligned_cols=38 Identities=16% Similarity=0.351 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHH
Q 009676 345 RDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ 382 (529)
Q Consensus 345 RerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq 382 (529)
.+.|...|..=+.++|+.. .+.+..-+...|.||++|+
T Consensus 72 ~~~L~~~l~~P~~~~pgt~M~f~gl~~~~dr~~liaYL~sl~ 113 (114)
T PTZ00405 72 PEVLDVYLENPKKFMPGTKMSFAGIKKPQERADVIAYLETLK 113 (114)
T ss_pred HHHHHHHHHCHHhhCCCCCCCCCCCCCHHHHHHHHHHHHHhc
Confidence 4567777888888999542 3567788889999999986
Done!