Query 036175
Match_columns 361
No_of_seqs 117 out of 334
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:10:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036175.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036175hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00353 HLH helix loop heli 99.2 4.7E-11 1E-15 86.2 5.9 47 311-357 3-52 (53)
2 cd00083 HLH Helix-loop-helix d 99.1 1.3E-10 2.8E-15 85.0 5.4 50 308-357 8-60 (60)
3 PF00010 HLH: Helix-loop-helix 98.9 2.6E-09 5.6E-14 78.4 5.2 45 309-353 6-55 (55)
4 KOG1318 Helix loop helix trans 97.8 3E-05 6.5E-10 79.0 5.6 50 308-357 237-290 (411)
5 KOG4304 Transcriptional repres 97.6 2.8E-05 6E-10 74.5 2.3 46 311-356 39-92 (250)
6 KOG1319 bHLHZip transcription 97.5 0.00011 2.4E-09 68.9 4.7 50 308-357 66-122 (229)
7 KOG3561 Aryl-hydrocarbon recep 97.3 0.00023 5.1E-09 77.6 4.8 46 310-355 26-75 (803)
8 KOG2483 Upstream transcription 96.6 0.0037 8.1E-08 59.8 5.7 49 310-358 65-116 (232)
9 KOG3960 Myogenic helix-loop-he 96.4 0.0068 1.5E-07 59.1 6.2 50 311-360 125-176 (284)
10 KOG0561 bHLH transcription fac 95.7 0.011 2.3E-07 59.2 3.9 48 309-356 65-114 (373)
11 PLN03217 transcription factor 95.3 0.024 5.1E-07 47.6 4.2 47 313-359 16-68 (93)
12 KOG4029 Transcription factor H 92.8 0.12 2.5E-06 48.3 3.9 47 311-357 116-166 (228)
13 KOG2588 Predicted DNA-binding 90.8 0.14 2.9E-06 57.5 2.2 51 309-359 281-332 (953)
14 KOG3910 Helix loop helix trans 83.2 1.1 2.4E-05 47.8 3.5 50 311-360 533-586 (632)
15 KOG3558 Hypoxia-inducible fact 73.6 2.8 6E-05 46.3 3.1 45 309-353 51-99 (768)
16 KOG3560 Aryl-hydrocarbon recep 73.6 2.8 6.1E-05 45.4 3.0 38 313-350 34-75 (712)
17 KOG4447 Transcription factor T 66.4 3.3 7.2E-05 38.4 1.5 44 310-353 84-129 (173)
18 PF11040 DGF-1_C: Dispersed ge 66.3 5.3 0.00012 33.3 2.6 62 200-280 19-83 (87)
19 PF11332 DUF3134: Protein of u 44.8 17 0.00037 29.7 2.1 20 192-211 45-64 (73)
20 PRK15365 type III secretion sy 43.1 36 0.00079 29.6 3.9 42 319-360 49-93 (107)
21 KOG3898 Transcription factor N 42.3 19 0.0004 35.0 2.3 45 309-353 77-124 (254)
22 TIGR00986 3a0801s05tom22 mitoc 34.1 22 0.00047 32.6 1.3 38 316-353 48-85 (145)
23 KOG4447 Transcription factor T 25.9 61 0.0013 30.3 2.8 23 312-334 30-52 (173)
24 PF04281 Tom22: Mitochondrial 25.6 36 0.00077 30.7 1.2 39 315-353 49-87 (137)
25 PF05320 Pox_RNA_Pol_19: Poxvi 23.9 46 0.00099 31.1 1.6 15 195-210 2-16 (167)
26 PF14689 SPOB_a: Sensor_kinase 21.8 1.5E+02 0.0033 22.6 3.9 41 312-359 16-56 (62)
27 PTZ00405 cytochrome c; Provisi 21.3 1.5E+02 0.0032 25.5 4.0 38 316-353 72-113 (114)
28 PHA03282 envelope glycoprotein 20.3 71 0.0015 34.5 2.3 32 197-228 457-488 (540)
No 1
>smart00353 HLH helix loop helix domain.
Probab=99.18 E-value=4.7e-11 Score=86.19 Aligned_cols=47 Identities=26% Similarity=0.419 Sum_probs=44.2
Q ss_pred hhhhhHHHHHHHHHHHHhcCCC---CCCCChhhhHHHHHHHHHHHHHHHH
Q 036175 311 NMQSRKDKIHTALRILQGIIPG---ANGKDPLSLLDEAIDYLQSLKLKAV 357 (361)
Q Consensus 311 seR~RReKI~erl~~Lq~LVPg---~~k~DkaSvLdeAI~YlK~Lq~qVk 357 (361)
.||+||++|++.|..|+.+||. ..++|+++||++||+||+.|+.+++
T Consensus 3 ~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~ 52 (53)
T smart00353 3 RERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ 52 (53)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999999994 6689999999999999999999986
No 2
>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=99.10 E-value=1.3e-10 Score=85.04 Aligned_cols=50 Identities=22% Similarity=0.353 Sum_probs=46.2
Q ss_pred ccchhhhhHHHHHHHHHHHHhcCCCC---CCCChhhhHHHHHHHHHHHHHHHH
Q 036175 308 ILGNMQSRKDKIHTALRILQGIIPGA---NGKDPLSLLDEAIDYLQSLKLKAV 357 (361)
Q Consensus 308 ~~~seR~RReKI~erl~~Lq~LVPg~---~k~DkaSvLdeAI~YlK~Lq~qVk 357 (361)
....||+||++|++.|..|+.+||+. .++|+++||..||+||++|+.+++
T Consensus 8 ~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~ 60 (60)
T cd00083 8 HNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60 (60)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 34579999999999999999999999 789999999999999999999864
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=98.89 E-value=2.6e-09 Score=78.43 Aligned_cols=45 Identities=27% Similarity=0.519 Sum_probs=42.0
Q ss_pred cchhhhhHHHHHHHHHHHHhcCCCC-----CCCChhhhHHHHHHHHHHHH
Q 036175 309 LGNMQSRKDKIHTALRILQGIIPGA-----NGKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 309 ~~seR~RReKI~erl~~Lq~LVPg~-----~k~DkaSvLdeAI~YlK~Lq 353 (361)
...||+||++|++.|..|+.+||.. .++|+++||..||+||+.||
T Consensus 6 ~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 6 NERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 3579999999999999999999997 57899999999999999997
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=97.79 E-value=3e-05 Score=79.03 Aligned_cols=50 Identities=20% Similarity=0.350 Sum_probs=44.4
Q ss_pred ccchhhhhHHHHHHHHHHHHhcCCCCC----CCChhhhHHHHHHHHHHHHHHHH
Q 036175 308 ILGNMQSRKDKIHTALRILQGIIPGAN----GKDPLSLLDEAIDYLQSLKLKAV 357 (361)
Q Consensus 308 ~~~seR~RReKI~erl~~Lq~LVPg~~----k~DkaSvLdeAI~YlK~Lq~qVk 357 (361)
+.--|||||++||++|+.|..|||.+. +..|..||..+.+|++.||..-+
T Consensus 237 HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q 290 (411)
T KOG1318|consen 237 HNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ 290 (411)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence 344599999999999999999999993 56799999999999999998765
No 5
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=97.61 E-value=2.8e-05 Score=74.53 Aligned_cols=46 Identities=22% Similarity=0.385 Sum_probs=41.1
Q ss_pred hhhhhHHHHHHHHHHHHhcCCCC--------CCCChhhhHHHHHHHHHHHHHHH
Q 036175 311 NMQSRKDKIHTALRILQGIIPGA--------NGKDPLSLLDEAIDYLQSLKLKA 356 (361)
Q Consensus 311 seR~RReKI~erl~~Lq~LVPg~--------~k~DkaSvLdeAI~YlK~Lq~qV 356 (361)
=|||||.|||+-|..|+.|||.. .|++||.||+-|++|||.|+...
T Consensus 39 ~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~ 92 (250)
T KOG4304|consen 39 LEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ 92 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence 38999999999999999999975 35679999999999999998754
No 6
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=97.52 E-value=0.00011 Score=68.86 Aligned_cols=50 Identities=26% Similarity=0.346 Sum_probs=43.5
Q ss_pred ccchhhhhHHHHHHHHHHHHhcCCCCC-------CCChhhhHHHHHHHHHHHHHHHH
Q 036175 308 ILGNMQSRKDKIHTALRILQGIIPGAN-------GKDPLSLLDEAIDYLQSLKLKAV 357 (361)
Q Consensus 308 ~~~seR~RReKI~erl~~Lq~LVPg~~-------k~DkaSvLdeAI~YlK~Lq~qVk 357 (361)
+.-+||+||+-|+.-..-||.|||-+- |+-+|.||-.||+|+.+|+.+..
T Consensus 66 HtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~ 122 (229)
T KOG1319|consen 66 HTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKK 122 (229)
T ss_pred HHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445799999999999999999999764 55699999999999999987654
No 7
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=97.30 E-value=0.00023 Score=77.64 Aligned_cols=46 Identities=24% Similarity=0.391 Sum_probs=43.2
Q ss_pred chhhhhHHHHHHHHHHHHhcCCCCC----CCChhhhHHHHHHHHHHHHHH
Q 036175 310 GNMQSRKDKIHTALRILQGIIPGAN----GKDPLSLLDEAIDYLQSLKLK 355 (361)
Q Consensus 310 ~seR~RReKI~erl~~Lq~LVPg~~----k~DkaSvLdeAI~YlK~Lq~q 355 (361)
..|||||+|+|.-|..|.+|||.+. |+||..||..||++||.++..
T Consensus 26 ~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 26 EIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 4689999999999999999999986 899999999999999999875
No 8
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=96.59 E-value=0.0037 Score=59.75 Aligned_cols=49 Identities=29% Similarity=0.487 Sum_probs=42.6
Q ss_pred chhhhhHHHHHHHHHHHHhcCCCCCC--C-ChhhhHHHHHHHHHHHHHHHHH
Q 036175 310 GNMQSRKDKIHTALRILQGIIPGANG--K-DPLSLLDEAIDYLQSLKLKAVA 358 (361)
Q Consensus 310 ~seR~RReKI~erl~~Lq~LVPg~~k--~-DkaSvLdeAI~YlK~Lq~qVk~ 358 (361)
--||+||..|++.|..|+.+||.+.. . ++++||+.|+.|++.|+.+...
T Consensus 65 ~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~ 116 (232)
T KOG2483|consen 65 ALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSAT 116 (232)
T ss_pred hhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHH
Confidence 35799999999999999999999853 2 4699999999999999987654
No 9
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=96.40 E-value=0.0068 Score=59.13 Aligned_cols=50 Identities=20% Similarity=0.280 Sum_probs=43.6
Q ss_pred hhhhhHHHHHHHHHHHH-hcCCCCC-CCChhhhHHHHHHHHHHHHHHHHHhC
Q 036175 311 NMQSRKDKIHTALRILQ-GIIPGAN-GKDPLSLLDEAIDYLQSLKLKAVALG 360 (361)
Q Consensus 311 seR~RReKI~erl~~Lq-~LVPg~~-k~DkaSvLdeAI~YlK~Lq~qVk~Lg 360 (361)
.||||=.||||.|.+|+ .-+++-+ ..-|+.||..||+||..||.=+++++
T Consensus 125 RERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~ 176 (284)
T KOG3960|consen 125 RERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQD 176 (284)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhh
Confidence 58999999999999996 4677766 47999999999999999998887764
No 10
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=95.67 E-value=0.011 Score=59.17 Aligned_cols=48 Identities=19% Similarity=0.389 Sum_probs=43.3
Q ss_pred cchhhhhHHHHHHHHHHHHhcCCC--CCCCChhhhHHHHHHHHHHHHHHH
Q 036175 309 LGNMQSRKDKIHTALRILQGIIPG--ANGKDPLSLLDEAIDYLQSLKLKA 356 (361)
Q Consensus 309 ~~seR~RReKI~erl~~Lq~LVPg--~~k~DkaSvLdeAI~YlK~Lq~qV 356 (361)
.++||||-.-||.-|..||.|+|. |.|..||.||..+.+||-.|+.+-
T Consensus 65 NsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K 114 (373)
T KOG0561|consen 65 NSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK 114 (373)
T ss_pred cchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence 368999999999999999999998 568999999999999999987653
No 11
>PLN03217 transcription factor ATBS1; Provisional
Probab=95.34 E-value=0.024 Score=47.61 Aligned_cols=47 Identities=19% Similarity=0.381 Sum_probs=41.3
Q ss_pred hhhHHHHHHHHHHHHhcCCCC------CCCChhhhHHHHHHHHHHHHHHHHHh
Q 036175 313 QSRKDKIHTALRILQGIIPGA------NGKDPLSLLDEAIDYLQSLKLKAVAL 359 (361)
Q Consensus 313 R~RReKI~erl~~Lq~LVPg~------~k~DkaSvLdeAI~YlK~Lq~qVk~L 359 (361)
|--.+.|++-+..||.|+|.. .+.-.+-||.||-.|+|.|..+|..|
T Consensus 16 risddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdL 68 (93)
T PLN03217 16 RISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDL 68 (93)
T ss_pred CCCHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 566889999999999999974 35677889999999999999999876
No 12
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=92.82 E-value=0.12 Score=48.32 Aligned_cols=47 Identities=17% Similarity=0.281 Sum_probs=41.5
Q ss_pred hhhhhHHHHHHHHHHHHhcCCCC----CCCChhhhHHHHHHHHHHHHHHHH
Q 036175 311 NMQSRKDKIHTALRILQGIIPGA----NGKDPLSLLDEAIDYLQSLKLKAV 357 (361)
Q Consensus 311 seR~RReKI~erl~~Lq~LVPg~----~k~DkaSvLdeAI~YlK~Lq~qVk 357 (361)
.||.|-+-||..|..||.+||.. +|.-|+.+|-.||.||++|+.-++
T Consensus 116 RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~ 166 (228)
T KOG4029|consen 116 RERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLA 166 (228)
T ss_pred hhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhc
Confidence 48899999999999999999974 467999999999999999987554
No 13
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=90.82 E-value=0.14 Score=57.47 Aligned_cols=51 Identities=22% Similarity=0.322 Sum_probs=44.9
Q ss_pred cchhhhhHHHHHHHHHHHHhcCCCCC-CCChhhhHHHHHHHHHHHHHHHHHh
Q 036175 309 LGNMQSRKDKIHTALRILQGIIPGAN-GKDPLSLLDEAIDYLQSLKLKAVAL 359 (361)
Q Consensus 309 ~~seR~RReKI~erl~~Lq~LVPg~~-k~DkaSvLdeAI~YlK~Lq~qVk~L 359 (361)
.--|||=|--||+|+..|+.+|||.. |+.|..+|..||+|+++|+..-+.+
T Consensus 281 N~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~l 332 (953)
T KOG2588|consen 281 NIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKL 332 (953)
T ss_pred hHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhcccccc
Confidence 34588889999999999999999975 8899999999999999998765544
No 14
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=83.23 E-value=1.1 Score=47.76 Aligned_cols=50 Identities=18% Similarity=0.190 Sum_probs=41.5
Q ss_pred hhhhhHHHHHHHHHHHHhcCCCCCC----CChhhhHHHHHHHHHHHHHHHHHhC
Q 036175 311 NMQSRKDKIHTALRILQGIIPGANG----KDPLSLLDEAIDYLQSLKLKAVALG 360 (361)
Q Consensus 311 seR~RReKI~erl~~Lq~LVPg~~k----~DkaSvLdeAI~YlK~Lq~qVk~Lg 360 (361)
.||.|-+.|||.|+.|..++=---| .-|.-||..||.-|-.|+.||.+-.
T Consensus 533 RERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN 586 (632)
T KOG3910|consen 533 RERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN 586 (632)
T ss_pred hhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence 5777888899999999988654322 4588999999999999999998754
No 15
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=73.61 E-value=2.8 Score=46.31 Aligned_cols=45 Identities=24% Similarity=0.310 Sum_probs=38.7
Q ss_pred cchhhhhHHHHHHHHHHHHhcCCCC----CCCChhhhHHHHHHHHHHHH
Q 036175 309 LGNMQSRKDKIHTALRILQGIIPGA----NGKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 309 ~~seR~RReKI~erl~~Lq~LVPg~----~k~DkaSvLdeAI~YlK~Lq 353 (361)
+.++|.||-|=++-|..|..++|=- ...|||||+.-||-|||-=+
T Consensus 51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk 99 (768)
T KOG3558|consen 51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRK 99 (768)
T ss_pred hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHH
Confidence 4578999999999999999999853 36799999999999998543
No 16
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=73.58 E-value=2.8 Score=45.39 Aligned_cols=38 Identities=26% Similarity=0.511 Sum_probs=35.1
Q ss_pred hhhHHHHHHHHHHHHhcCCC----CCCCChhhhHHHHHHHHH
Q 036175 313 QSRKDKIHTALRILQGIIPG----ANGKDPLSLLDEAIDYLQ 350 (361)
Q Consensus 313 R~RReKI~erl~~Lq~LVPg----~~k~DkaSvLdeAI~YlK 350 (361)
||-|||+|.-|..|.+|+|- +.|.||.|||.-+|.||+
T Consensus 34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr 75 (712)
T KOG3560|consen 34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR 75 (712)
T ss_pred hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence 67799999999999999997 468999999999999986
No 17
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=66.41 E-value=3.3 Score=38.36 Aligned_cols=44 Identities=23% Similarity=0.314 Sum_probs=39.3
Q ss_pred chhhhhHHHHHHHHHHHHhcCCCC--CCCChhhhHHHHHHHHHHHH
Q 036175 310 GNMQSRKDKIHTALRILQGIIPGA--NGKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 310 ~seR~RReKI~erl~~Lq~LVPg~--~k~DkaSvLdeAI~YlK~Lq 353 (361)
..||+|-.-+++.|.+||.|||-. +|..++--|.-|-.|+-+|=
T Consensus 84 vrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~ 129 (173)
T KOG4447|consen 84 VRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLY 129 (173)
T ss_pred HHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhh
Confidence 468899999999999999999984 68899999999999998873
No 18
>PF11040 DGF-1_C: Dispersed gene family protein 1 of Trypanosoma cruzi C-terminus ; InterPro: IPR021053 Dispersed gene family protein 1 of Trypanosoma cruzi is likely to be highly expressed, and is expressed from the sub-telomeric region []. However, its function is not known. This entry represents the C-terminal domain on this protein.
Probab=66.35 E-value=5.3 Score=33.26 Aligned_cols=62 Identities=27% Similarity=0.302 Sum_probs=36.1
Q ss_pred HhhhhccCCCCCCCCCCCCCcccccccCCCcccccccccccccccccccccccCC-CCccchhhccCCC--CCCCccccc
Q 036175 200 INALLYSDGDDDYSNGDDSEDDEVKSTDHSPVAIEGKYEKHDLTLEISEEVASSD-GPNKRQKLLNGGY--NKSSQTDTA 276 (361)
Q Consensus 200 InALLySDdd~~~~~~~~~~ddEV~STghSP~~~~~~~~~~~~~~~s~eevaSs~-~p~KrrKl~d~~~--~~~s~vdta 276 (361)
+.|||--|+++|. +--.-.|+||.-. + .+| -||||+ .|+.-....-|.- |.-|+.|.+
T Consensus 19 LeALLrDdeesdE---etqkphd~tsssy---A-----------sgt--t~assYrPPA~~lqpmagdtrsdalsl~dra 79 (87)
T PF11040_consen 19 LEALLRDDEESDE---ETQKPHDMTSSSY---A-----------SGT--TVASSYRPPAPPLQPMAGDTRSDALSLLDRA 79 (87)
T ss_pred HHHHhccccccch---hhcchhhhccccc---c-----------CCc--eeeeccCCCCCccccccCCccccccchhccc
Confidence 6799987666541 1112255554211 1 112 468888 5566656666655 556899999
Q ss_pred cccc
Q 036175 277 CSVQ 280 (361)
Q Consensus 277 SS~~ 280 (361)
||+.
T Consensus 80 ssas 83 (87)
T PF11040_consen 80 SSAS 83 (87)
T ss_pred cccc
Confidence 8763
No 19
>PF11332 DUF3134: Protein of unknown function (DUF3134); InterPro: IPR021481 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=44.79 E-value=17 Score=29.68 Aligned_cols=20 Identities=30% Similarity=0.401 Sum_probs=15.6
Q ss_pred ccccChHHHhhhhccCCCCC
Q 036175 192 EMHEDTEEINALLYSDGDDD 211 (361)
Q Consensus 192 e~hEDTeEInALLySDdd~~ 211 (361)
..-++-|||.+|+..|++.+
T Consensus 45 ~~~~eeEEiselm~~dd~~~ 64 (73)
T PF11332_consen 45 DSLDEEEEISELMGDDDDYY 64 (73)
T ss_pred cccccHHHHHHHhcCCcccc
Confidence 33456699999999887776
No 20
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=43.07 E-value=36 Score=29.61 Aligned_cols=42 Identities=14% Similarity=0.287 Sum_probs=37.5
Q ss_pred HHHHHHHHHhcCCCCC---CCChhhhHHHHHHHHHHHHHHHHHhC
Q 036175 319 IHTALRILQGIIPGAN---GKDPLSLLDEAIDYLQSLKLKAVALG 360 (361)
Q Consensus 319 I~erl~~Lq~LVPg~~---k~DkaSvLdeAI~YlK~Lq~qVk~Lg 360 (361)
-+|.+..|-.+.|.|- +-.++-+|.-...-.|.|+.|++.|+
T Consensus 49 aRE~l~rLd~aFP~G~~~~~qE~~k~m~~i~~~FKQLEt~LKnln 93 (107)
T PRK15365 49 SRETESILHNLFPQGVAGVNQEAEKDLKKIVSLFKQLEVRLKQLN 93 (107)
T ss_pred HHHHHHHHHHHCcchhhHHhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3678999999999998 78899999988899999999999886
No 21
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=42.26 E-value=19 Score=35.00 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=38.1
Q ss_pred cchhhhhHHHHHHHHHHHHhcCCCC---CCCChhhhHHHHHHHHHHHH
Q 036175 309 LGNMQSRKDKIHTALRILQGIIPGA---NGKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 309 ~~seR~RReKI~erl~~Lq~LVPg~---~k~DkaSvLdeAI~YlK~Lq 353 (361)
...||.|--.+|+.|..||++||-+ .|+-|+..|--|=.|+..|+
T Consensus 77 NaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als 124 (254)
T KOG3898|consen 77 NARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALS 124 (254)
T ss_pred cchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhc
Confidence 3468999999999999999999943 37788889988888988876
No 22
>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=34.10 E-value=22 Score=32.55 Aligned_cols=38 Identities=11% Similarity=0.192 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHhcCCCCCCCChhhhHHHHHHHHHHHH
Q 036175 316 KDKIHTALRILQGIIPGANGKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 316 ReKI~erl~~Lq~LVPg~~k~DkaSvLdeAI~YlK~Lq 353 (361)
.|-|-|||-+|+.|||...+.-..+...-+..++|.+=
T Consensus 48 ~ETl~ERi~ALkDm~Pp~~R~~i~~~~s~t~s~~ks~~ 85 (145)
T TIGR00986 48 EETFTDRIYALKDIVPPTTRGWIYHKYSTTTNFVKSTL 85 (145)
T ss_pred cCcHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999988888888889999998864
No 23
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=25.95 E-value=61 Score=30.31 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=20.3
Q ss_pred hhhhHHHHHHHHHHHHhcCCCCC
Q 036175 312 MQSRKDKIHTALRILQGIIPGAN 334 (361)
Q Consensus 312 eR~RReKI~erl~~Lq~LVPg~~ 334 (361)
|+-|+.+++.++..|++|+||..
T Consensus 30 e~~R~~~ls~~s~l~g~l~pgsp 52 (173)
T KOG4447|consen 30 ERGRKRRLSDASTLLGKLEPGSP 52 (173)
T ss_pred HHhHHhhhhhhhhhccccCCCCC
Confidence 67788889999999999999963
No 24
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane 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 represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=25.62 E-value=36 Score=30.68 Aligned_cols=39 Identities=18% Similarity=0.150 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCChhhhHHHHHHHHHHHH
Q 036175 315 RKDKIHTALRILQGIIPGANGKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 315 RReKI~erl~~Lq~LVPg~~k~DkaSvLdeAI~YlK~Lq 353 (361)
..|-|-|||-+|+.|||.....-..+++.-+..++|.+=
T Consensus 49 ~dETl~ERl~aLkdi~P~~~R~~i~~~~~~~~~~~k~~~ 87 (137)
T PF04281_consen 49 EDETLLERLWALKDIFPPSVRNWISSTVSTTSSAVKSLF 87 (137)
T ss_pred ccccHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 467799999999999999988777888888888888764
No 25
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 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. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.91 E-value=46 Score=31.06 Aligned_cols=15 Identities=47% Similarity=0.641 Sum_probs=10.3
Q ss_pred cChHHHhhhhccCCCC
Q 036175 195 EDTEEINALLYSDGDD 210 (361)
Q Consensus 195 EDTeEInALLySDdd~ 210 (361)
||+.+|++.+ ||+++
T Consensus 2 ~ds~di~~~~-sde~~ 16 (167)
T PF05320_consen 2 EDSDDIIDYE-SDEDD 16 (167)
T ss_pred cchHHHHhhh-ccCcc
Confidence 7899999664 44444
No 26
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=21.77 E-value=1.5e+02 Score=22.60 Aligned_cols=41 Identities=15% Similarity=0.378 Sum_probs=31.2
Q ss_pred hhhhHHHHHHHHHHHHhcCCCCCCCChhhhHHHHHHHHHHHHHHHHHh
Q 036175 312 MQSRKDKIHTALRILQGIIPGANGKDPLSLLDEAIDYLQSLKLKAVAL 359 (361)
Q Consensus 312 eR~RReKI~erl~~Lq~LVPg~~k~DkaSvLdeAI~YlK~Lq~qVk~L 359 (361)
-|+.|-.....|.++.+++--+. .++|.+||+.+-.+++.+
T Consensus 16 lR~~RHD~~NhLqvI~gllqlg~-------~~~a~eYi~~~~~~~~~~ 56 (62)
T PF14689_consen 16 LRAQRHDFLNHLQVIYGLLQLGK-------YEEAKEYIKELSKDLQQE 56 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--------HHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHCCC-------HHHHHHHHHHHHHHHHHH
Confidence 35667778888999988875543 578999999988877764
No 27
>PTZ00405 cytochrome c; Provisional
Probab=21.26 E-value=1.5e+02 Score=25.49 Aligned_cols=38 Identities=24% Similarity=0.404 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhcCCCCC----CCChhhhHHHHHHHHHHHH
Q 036175 316 KDKIHTALRILQGIIPGAN----GKDPLSLLDEAIDYLQSLK 353 (361)
Q Consensus 316 ReKI~erl~~Lq~LVPg~~----k~DkaSvLdeAI~YlK~Lq 353 (361)
++.|..-|.-=+.+|||.. .+-...-+++-|.|||+|+
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 6677777777788999643 3445677888999999986
No 28
>PHA03282 envelope glycoprotein E; Provisional
Probab=20.34 E-value=71 Score=34.50 Aligned_cols=32 Identities=38% Similarity=0.459 Sum_probs=25.1
Q ss_pred hHHHhhhhccCCCCCCCCCCCCCcccccccCC
Q 036175 197 TEEINALLYSDGDDDYSNGDDSEDDEVKSTDH 228 (361)
Q Consensus 197 TeEInALLySDdd~~~~~~~~~~ddEV~STgh 228 (361)
.+|+.|-|+||++.++++..+.++|+..-|+.
T Consensus 457 d~elyad~ssd~~~e~~~~~~~~~~~~~~~d~ 488 (540)
T PHA03282 457 DDELYADLSSDGEGEDSEVYDSDPDRLPGTDS 488 (540)
T ss_pred chhhhhhhccccccccccccccCcccccCCCC
Confidence 68999999999988766666777788866655
Done!