Query 042291
Match_columns 241
No_of_seqs 118 out of 272
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 04:47:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042291hhsearch_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 99.0 4.3E-10 9.4E-15 77.0 5.5 44 189-232 6-52 (53)
2 cd00083 HLH Helix-loop-helix d 98.9 1.8E-09 3.9E-14 75.0 5.2 44 189-232 14-60 (60)
3 PF00010 HLH: Helix-loop-helix 98.6 4.2E-08 9.1E-13 68.3 4.8 40 189-228 11-55 (55)
4 KOG1318 Helix loop helix trans 97.6 6.3E-05 1.4E-09 72.9 4.7 44 189-232 243-290 (411)
5 KOG4304 Transcriptional repres 97.3 6.8E-05 1.5E-09 68.2 1.1 44 189-232 42-93 (250)
6 KOG3561 Aryl-hydrocarbon recep 97.0 0.00076 1.6E-08 70.1 4.4 47 184-230 24-75 (803)
7 KOG1319 bHLHZip transcription 96.8 0.0012 2.6E-08 59.1 4.0 52 181-233 65-123 (229)
8 KOG2483 Upstream transcription 95.8 0.018 3.9E-07 52.3 5.4 46 189-234 69-117 (232)
9 KOG0561 bHLH transcription fac 95.8 0.0093 2E-07 56.7 3.7 46 186-231 66-114 (373)
10 PLN03217 transcription factor 95.5 0.021 4.5E-07 45.5 4.3 45 191-235 19-69 (93)
11 KOG3960 Myogenic helix-loop-he 93.8 0.14 3E-06 47.7 5.9 48 188-235 126-176 (284)
12 KOG3560 Aryl-hydrocarbon recep 92.5 0.13 2.9E-06 52.4 3.9 64 163-226 8-76 (712)
13 KOG2588 Predicted DNA-binding 91.5 0.093 2E-06 55.8 1.6 50 187-236 283-334 (953)
14 KOG4029 Transcription factor H 74.1 3.6 7.8E-05 36.4 3.4 44 190-233 120-167 (228)
15 KOG3910 Helix loop helix trans 69.0 4.4 9.6E-05 41.3 3.1 50 188-237 534-588 (632)
16 PF11332 DUF3134: Protein of u 56.6 7.3 0.00016 30.0 1.7 22 115-136 45-66 (73)
17 PRK15365 type III secretion sy 39.0 51 0.0011 27.2 4.0 42 195-236 50-94 (107)
18 PF10542 Vitelline_membr: Vite 36.5 20 0.00043 24.6 1.1 12 54-65 3-14 (38)
19 PRK06666 fliM flagellar motor 30.1 35 0.00077 31.5 2.1 14 120-133 8-21 (337)
20 KOG3558 Hypoxia-inducible fact 29.3 43 0.00093 35.6 2.6 39 190-228 57-99 (768)
21 PF02845 CUE: CUE domain; Int 28.9 79 0.0017 20.8 3.1 33 195-227 2-41 (42)
22 PF05320 Pox_RNA_Pol_19: Poxvi 28.5 86 0.0019 27.7 4.0 15 118-132 2-16 (167)
23 KOG4447 Transcription factor T 28.0 31 0.00067 30.5 1.2 40 189-228 88-129 (173)
24 TIGR00986 3a0801s05tom22 mitoc 26.8 39 0.00085 29.2 1.6 38 191-228 48-85 (145)
25 PRK02877 hypothetical protein; 24.9 1.5E+02 0.0033 24.0 4.6 45 193-238 31-76 (106)
26 TIGR01397 fliM_switch flagella 23.4 66 0.0014 29.5 2.5 15 120-134 5-19 (320)
27 PTZ00048 cytochrome c; Provisi 22.0 1.2E+02 0.0025 24.4 3.4 39 191-229 72-114 (115)
28 PTZ00405 cytochrome c; Provisi 21.1 1.6E+02 0.0034 23.8 4.0 37 191-228 72-113 (114)
29 KOG3559 Transcriptional regula 20.9 85 0.0018 31.9 2.8 40 189-228 11-54 (598)
30 PF10046 BLOC1_2: Biogenesis o 20.6 64 0.0014 25.3 1.6 44 191-234 51-99 (99)
No 1
>smart00353 HLH helix loop helix domain.
Probab=99.04 E-value=4.3e-10 Score=77.03 Aligned_cols=44 Identities=30% Similarity=0.565 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHhhccCC---CCCCcchhhHHHHHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVP---GGNELNTVGVLDEAVRHLKSLKVEVQ 232 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVP---g~~~~D~asvLdEaI~YLKsLk~qV~ 232 (241)
+||++|++.|..|+.+|| ++.++++++||++||+||+.|+.+++
T Consensus 6 ~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~ 52 (53)
T smart00353 6 RRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ 52 (53)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 499999999999999999 57899999999999999999999986
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=98.92 E-value=1.8e-09 Score=74.98 Aligned_cols=44 Identities=27% Similarity=0.489 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHhhccCCCC---CCcchhhHHHHHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVPGG---NELNTVGVLDEAVRHLKSLKVEVQ 232 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg~---~~~D~asvLdEaI~YLKsLk~qV~ 232 (241)
+||++|++.|..|+.+||+. .++|+++||+.||+||+.|+.+++
T Consensus 14 ~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~ 60 (60)
T cd00083 14 RRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60 (60)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 49999999999999999998 899999999999999999998863
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=98.65 E-value=4.2e-08 Score=68.32 Aligned_cols=40 Identities=23% Similarity=0.550 Sum_probs=37.7
Q ss_pred hhHHHHHHHHHHhhccCCCC-----CCcchhhHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVPGG-----NELNTVGVLDEAVRHLKSLK 228 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg~-----~~~D~asvLdEaI~YLKsLk 228 (241)
+||++|+..|..|+.+||.. .++++++||..||+||+.||
T Consensus 11 ~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 11 RRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 48999999999999999987 67899999999999999997
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=97.62 E-value=6.3e-05 Score=72.89 Aligned_cols=44 Identities=16% Similarity=0.345 Sum_probs=39.3
Q ss_pred hhHHHHHHHHHHhhccCCCC----CCcchhhHHHHHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVPGG----NELNTVGVLDEAVRHLKSLKVEVQ 232 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg~----~~~D~asvLdEaI~YLKsLk~qV~ 232 (241)
|||++||.+++.|..|||.+ .+.+|-.||.-+++|++.||..-+
T Consensus 243 RRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q 290 (411)
T KOG1318|consen 243 RRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ 290 (411)
T ss_pred HHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence 58999999999999999997 244689999999999999998766
No 5
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=97.35 E-value=6.8e-05 Score=68.20 Aligned_cols=44 Identities=25% Similarity=0.578 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHhhccCCCC--------CCcchhhHHHHHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVPGG--------NELNTVGVLDEAVRHLKSLKVEVQ 232 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg~--------~~~D~asvLdEaI~YLKsLk~qV~ 232 (241)
|||+|||+-|..|+.|||.. .+++||-||+=|++|||.|+...+
T Consensus 42 kRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~ 93 (250)
T KOG4304|consen 42 KRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ 93 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence 69999999999999999973 456899999999999999997643
No 6
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=96.97 E-value=0.00076 Score=70.09 Aligned_cols=47 Identities=28% Similarity=0.461 Sum_probs=42.4
Q ss_pred cccchh-hHHHHHHHHHHhhccCCCCC----CcchhhHHHHHHHHHHHHHHH
Q 042291 184 KCHNGK-KRQKLKKMVNVLRGFVPGGN----ELNTVGVLDEAVRHLKSLKVE 230 (241)
Q Consensus 184 ~c~~~k-RRekI~e~~~~L~~lVPg~~----~~D~asvLdEaI~YLKsLk~q 230 (241)
.|..|| ||+|+|.-|.-|-.|||++. |+||.+||..||+.||.++..
T Consensus 24 ~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 24 RSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 356675 89999999999999999965 899999999999999999875
No 7
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=96.84 E-value=0.0012 Score=59.07 Aligned_cols=52 Identities=19% Similarity=0.359 Sum_probs=42.1
Q ss_pred CCccccchhhHHHHHHHHHHhhccCCCCC-------CcchhhHHHHHHHHHHHHHHHHHH
Q 042291 181 SSSKCHNGKKRQKLKKMVNVLRGFVPGGN-------ELNTVGVLDEAVRHLKSLKVEVQN 233 (241)
Q Consensus 181 a~s~c~~~kRRekI~e~~~~L~~lVPg~~-------~~D~asvLdEaI~YLKsLk~qV~~ 233 (241)
++..|.. +||+-||.-..-||.|||-+. +.-+|.||-.||+|+..|+.+...
T Consensus 65 aHtqaEq-kRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~k 123 (229)
T KOG1319|consen 65 AHTQAEQ-KRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKK 123 (229)
T ss_pred HHHHHHH-HHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444544 799999999999999999754 445899999999999999876543
No 8
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=95.76 E-value=0.018 Score=52.34 Aligned_cols=46 Identities=30% Similarity=0.448 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHhhccCCCCCC--c-chhhHHHHHHHHHHHHHHHHHHh
Q 042291 189 KKRQKLKKMVNVLRGFVPGGNE--L-NTVGVLDEAVRHLKSLKVEVQNL 234 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg~~~--~-D~asvLdEaI~YLKsLk~qV~~L 234 (241)
+||+.|++.+..|+.+||.+.. . +.++||+.|+.|+++|+.+....
T Consensus 69 ~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~ 117 (232)
T KOG2483|consen 69 RRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQ 117 (232)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHH
Confidence 4999999999999999998532 2 46999999999999998876543
No 9
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=95.76 E-value=0.0093 Score=56.72 Aligned_cols=46 Identities=20% Similarity=0.398 Sum_probs=39.9
Q ss_pred cchh-hHHHHHHHHHHhhccCCC--CCCcchhhHHHHHHHHHHHHHHHH
Q 042291 186 HNGK-KRQKLKKMVNVLRGFVPG--GNELNTVGVLDEAVRHLKSLKVEV 231 (241)
Q Consensus 186 ~~~k-RRekI~e~~~~L~~lVPg--~~~~D~asvLdEaI~YLKsLk~qV 231 (241)
+||| |-.-||.-|..||.|+|- |+|.-||.||..|.+|+-+|+-+-
T Consensus 66 sNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K 114 (373)
T KOG0561|consen 66 SNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK 114 (373)
T ss_pred chHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence 3455 458899999999999998 899999999999999999886543
No 10
>PLN03217 transcription factor ATBS1; Provisional
Probab=95.53 E-value=0.021 Score=45.48 Aligned_cols=45 Identities=18% Similarity=0.431 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhhccCCCC------CCcchhhHHHHHHHHHHHHHHHHHHhc
Q 042291 191 RQKLKKMVNVLRGFVPGG------NELNTVGVLDEAVRHLKSLKVEVQNLG 235 (241)
Q Consensus 191 RekI~e~~~~L~~lVPg~------~~~D~asvLdEaI~YLKsLk~qV~~L~ 235 (241)
-+.|++-+..||.|+|.. .+.-.+-||.||-.|+++|..+|..|.
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLS 69 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLS 69 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 588999999999999973 456678899999999999999998875
No 11
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=93.83 E-value=0.14 Score=47.72 Aligned_cols=48 Identities=19% Similarity=0.316 Sum_probs=39.6
Q ss_pred hh-hHHHHHHHHHHhhc-cCCCC-CCcchhhHHHHHHHHHHHHHHHHHHhc
Q 042291 188 GK-KRQKLKKMVNVLRG-FVPGG-NELNTVGVLDEAVRHLKSLKVEVQNLG 235 (241)
Q Consensus 188 ~k-RRekI~e~~~~L~~-lVPg~-~~~D~asvLdEaI~YLKsLk~qV~~L~ 235 (241)
|| |-.||||.|.+|+. -+++- -..=|+-||--||+||..||.-+++++
T Consensus 126 ERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~ 176 (284)
T KOG3960|consen 126 ERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQD 176 (284)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhh
Confidence 55 45899999999975 45663 556899999999999999999888775
No 12
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=92.46 E-value=0.13 Score=52.36 Aligned_cols=64 Identities=19% Similarity=0.284 Sum_probs=45.8
Q ss_pred CCCccccccccccccCCCCCcc-ccchhhHHHHHHHHHHhhccCCC----CCCcchhhHHHHHHHHHHH
Q 042291 163 YDSEPQHNKFSSMLKSSGSSSK-CHNGKKRQKLKKMVNVLRGFVPG----GNELNTVGVLDEAVRHLKS 226 (241)
Q Consensus 163 ~g~kkr~k~~sS~~~ss~a~s~-c~~~kRRekI~e~~~~L~~lVPg----~~~~D~asvLdEaI~YLKs 226 (241)
|..|||||.+-+++..-.+..+ +-+-|-|+|+|.-|..|.+|+|= ..+.|+.|||-=+|.||..
T Consensus 8 YAsrkRrrp~qk~rpp~~a~tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 8 YASRKRRRPLQKQRPPPKALTKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV 76 (712)
T ss_pred ehhhhccCCccccCCCccccccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence 5567777754344433333222 22324599999999999999996 5888999999999999863
No 13
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=91.45 E-value=0.093 Score=55.77 Aligned_cols=50 Identities=28% Similarity=0.425 Sum_probs=43.9
Q ss_pred chhh-HHHHHHHHHHhhccCCC-CCCcchhhHHHHHHHHHHHHHHHHHHhcC
Q 042291 187 NGKK-RQKLKKMVNVLRGFVPG-GNELNTVGVLDEAVRHLKSLKVEVQNLGV 236 (241)
Q Consensus 187 ~~kR-RekI~e~~~~L~~lVPg-~~~~D~asvLdEaI~YLKsLk~qV~~L~~ 236 (241)
.||| |--||.++.-|+.+||| .-++.+..+|.-||+|++.|+..-+.+..
T Consensus 283 IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~ 334 (953)
T KOG2588|consen 283 IEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKL 334 (953)
T ss_pred HHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccch
Confidence 4776 88999999999999999 57889999999999999999987666643
No 14
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=74.13 E-value=3.6 Score=36.39 Aligned_cols=44 Identities=20% Similarity=0.298 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHhhccCCC----CCCcchhhHHHHHHHHHHHHHHHHHH
Q 042291 190 KRQKLKKMVNVLRGFVPG----GNELNTVGVLDEAVRHLKSLKVEVQN 233 (241)
Q Consensus 190 RRekI~e~~~~L~~lVPg----~~~~D~asvLdEaI~YLKsLk~qV~~ 233 (241)
|-.-||..+..||.+||- .++.-|+..|-.||.||+.|+.-++.
T Consensus 120 Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~ 167 (228)
T KOG4029|consen 120 RVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLAT 167 (228)
T ss_pred cccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcc
Confidence 667799999999999986 45679999999999999999876554
No 15
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=69.01 E-value=4.4 Score=41.32 Aligned_cols=50 Identities=16% Similarity=0.274 Sum_probs=40.2
Q ss_pred hh-hHHHHHHHHHHhhccCCC----CCCcchhhHHHHHHHHHHHHHHHHHHhcCC
Q 042291 188 GK-KRQKLKKMVNVLRGFVPG----GNELNTVGVLDEAVRHLKSLKVEVQNLGVG 237 (241)
Q Consensus 188 ~k-RRekI~e~~~~L~~lVPg----~~~~D~asvLdEaI~YLKsLk~qV~~L~~~ 237 (241)
|| |-+-|||.|+-|-+|+=- .+---|..||-.||.-|-+|+.||.+-.++
T Consensus 534 ERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERNLN 588 (632)
T KOG3910|consen 534 ERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERNLN 588 (632)
T ss_pred hheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHccCC
Confidence 44 667899999999888654 333467999999999999999999986544
No 16
>PF11332 DUF3134: Protein of unknown function (DUF3134); InterPro: IPR021481 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=56.56 E-value=7.3 Score=29.95 Aligned_cols=22 Identities=9% Similarity=0.300 Sum_probs=16.8
Q ss_pred ccccChhhhhhhhcccCCCCCc
Q 042291 115 SFKEDSDDIDALLSLEEGDEEE 136 (241)
Q Consensus 115 ~~hEDTeEIdALL~Sddd~e~d 136 (241)
..-++-|||.+||..|++++++
T Consensus 45 ~~~~eeEEiselm~~dd~~~d~ 66 (73)
T PF11332_consen 45 DSLDEEEEISELMGDDDDYYDD 66 (73)
T ss_pred cccccHHHHHHHhcCCcccccc
Confidence 3445669999999999886654
No 17
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=38.96 E-value=51 Score=27.15 Aligned_cols=42 Identities=21% Similarity=0.378 Sum_probs=36.7
Q ss_pred HHHHHHhhccCCCCC---CcchhhHHHHHHHHHHHHHHHHHHhcC
Q 042291 195 KKMVNVLRGFVPGGN---ELNTVGVLDEAVRHLKSLKVEVQNLGV 236 (241)
Q Consensus 195 ~e~~~~L~~lVPg~~---~~D~asvLdEaI~YLKsLk~qV~~L~~ 236 (241)
+|.+.+|-.+.|.|- +-.+..+|.-...-.|.|+.|++.|+.
T Consensus 50 RE~l~rLd~aFP~G~~~~~qE~~k~m~~i~~~FKQLEt~LKnlnt 94 (107)
T PRK15365 50 RETESILHNLFPQGVAGVNQEAEKDLKKIVSLFKQLEVRLKQLNA 94 (107)
T ss_pred HHHHHHHHHHCcchhhHHhHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 578899999999987 778888888888889999999999864
No 18
>PF10542 Vitelline_membr: Vitelline membrane cysteine-rich region; InterPro: IPR013135 In Drosophila melanogaster (Fruit fly) the vitelline membrane (VM) is the first layer of the eggshell produced by the follicular epithelium. It is composed of at least four different proteins. VM proteins are similarly organised with a central highly conserved 38-amino acid domain which is flanked by unrelated regions. Since the surrounding regions have diverged significantly, it is possible that the VM domain is of key importance in VM protein structure [, ]. The VM domain contains three highly conserved cysteines.
Probab=36.50 E-value=20 Score=24.61 Aligned_cols=12 Identities=50% Similarity=1.110 Sum_probs=9.8
Q ss_pred CCCCCCCceEEE
Q 042291 54 PSEVCPKNFIIF 65 (241)
Q Consensus 54 Ps~~c~KrFlIF 65 (241)
|+..||||||.=
T Consensus 3 psPpCpknY~FS 14 (38)
T PF10542_consen 3 PSPPCPKNYVFS 14 (38)
T ss_pred CCCCCCcceeEe
Confidence 778999999853
No 19
>PRK06666 fliM flagellar motor switch protein FliM; Validated
Probab=30.14 E-value=35 Score=31.54 Aligned_cols=14 Identities=43% Similarity=0.501 Sum_probs=11.1
Q ss_pred hhhhhhhhcccCCC
Q 042291 120 SDDIDALLSLEEGD 133 (241)
Q Consensus 120 TeEIdALL~Sddd~ 133 (241)
-|||||||.+-+++
T Consensus 8 Q~EIdaLL~~~~~g 21 (337)
T PRK06666 8 QEEIDALLSGVSDG 21 (337)
T ss_pred HHHHHHHHhccccC
Confidence 38999999886653
No 20
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=29.25 E-value=43 Score=35.59 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHhhccCCC----CCCcchhhHHHHHHHHHHHHH
Q 042291 190 KRQKLKKMVNVLRGFVPG----GNELNTVGVLDEAVRHLKSLK 228 (241)
Q Consensus 190 RRekI~e~~~~L~~lVPg----~~~~D~asvLdEaI~YLKsLk 228 (241)
||-|=++-|--|..++|= ....|+|+|+-=||-|||-=+
T Consensus 57 RRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk 99 (768)
T KOG3558|consen 57 RRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRK 99 (768)
T ss_pred hcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHH
Confidence 778889999999999885 366799999999999998543
No 21
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=28.89 E-value=79 Score=20.77 Aligned_cols=33 Identities=24% Similarity=0.345 Sum_probs=22.8
Q ss_pred HHHHHHhhccCCCCCCcchhhHH-------HHHHHHHHHH
Q 042291 195 KKMVNVLRGFVPGGNELNTVGVL-------DEAVRHLKSL 227 (241)
Q Consensus 195 ~e~~~~L~~lVPg~~~~D~asvL-------dEaI~YLKsL 227 (241)
.+.++.|+.|.|.-..-.-..+| +.||++|-.+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 46789999999996655555554 6777777554
No 22
>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=28.49 E-value=86 Score=27.71 Aligned_cols=15 Identities=53% Similarity=0.481 Sum_probs=10.8
Q ss_pred cChhhhhhhhcccCC
Q 042291 118 EDSDDIDALLSLEEG 132 (241)
Q Consensus 118 EDTeEIdALL~Sddd 132 (241)
+|+.+|++.++-|++
T Consensus 2 ~ds~di~~~~sde~~ 16 (167)
T PF05320_consen 2 EDSDDIIDYESDEDD 16 (167)
T ss_pred cchHHHHhhhccCcc
Confidence 689999977555554
No 23
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=28.04 E-value=31 Score=30.49 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHHhhccCCC--CCCcchhhHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVPG--GNELNTVGVLDEAVRHLKSLK 228 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg--~~~~D~asvLdEaI~YLKsLk 228 (241)
+|-.-+|+.|..||.|||- ..+.-++--|.-|-+|+-+|=
T Consensus 88 qRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~ 129 (173)
T KOG4447|consen 88 QRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLY 129 (173)
T ss_pred HhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhh
Confidence 4667899999999999998 578888999999999988774
No 24
>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=26.84 E-value=39 Score=29.21 Aligned_cols=38 Identities=13% Similarity=0.126 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhhccCCCCCCcchhhHHHHHHHHHHHHH
Q 042291 191 RQKLKKMVNVLRGFVPGGNELNTVGVLDEAVRHLKSLK 228 (241)
Q Consensus 191 RekI~e~~~~L~~lVPg~~~~D~asvLdEaI~YLKsLk 228 (241)
-|-|-+||-+|+.|||.....-..+...-+..++|++=
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 35678999999999999877777888888999988864
No 25
>PRK02877 hypothetical protein; Provisional
Probab=24.87 E-value=1.5e+02 Score=23.98 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=34.9
Q ss_pred HHHHHHHHhhccCCCCCCcchhhHHHHHHH-HHHHHHHHHHHhcCCC
Q 042291 193 KLKKMVNVLRGFVPGGNELNTVGVLDEAVR-HLKSLKVEVQNLGVGN 238 (241)
Q Consensus 193 kI~e~~~~L~~lVPg~~~~D~asvLdEaI~-YLKsLk~qV~~L~~~~ 238 (241)
=++..+..|++|| ||.-..--.+|++|=+ =|+.|+.++++||.|.
T Consensus 31 ~~kd~~a~l~~i~-GG~~~~Y~~~l~~aR~~A~~rm~~~A~~lGAnA 76 (106)
T PRK02877 31 IFRDFFAGIRDIV-GGRSGAYEKELRKAREIAFEELGEQARALGADA 76 (106)
T ss_pred hHHHHHHHHHHhh-ccchhhHHHHHHHHHHHHHHHHHHHHHHcCCCE
Confidence 4577788899988 5566667788888754 4788999999999874
No 26
>TIGR01397 fliM_switch flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself.
Probab=23.37 E-value=66 Score=29.47 Aligned_cols=15 Identities=40% Similarity=0.492 Sum_probs=12.0
Q ss_pred hhhhhhhhcccCCCC
Q 042291 120 SDDIDALLSLEEGDE 134 (241)
Q Consensus 120 TeEIdALL~Sddd~e 134 (241)
-|||||||.+.++++
T Consensus 5 q~EIdaLl~~~~~g~ 19 (320)
T TIGR01397 5 QDEIDALLGGLSEGD 19 (320)
T ss_pred HHHHHHHHhcccCCC
Confidence 379999999877644
No 27
>PTZ00048 cytochrome c; Provisional
Probab=21.97 E-value=1.2e+02 Score=24.36 Aligned_cols=39 Identities=13% Similarity=0.177 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhccCCCC----CCcchhhHHHHHHHHHHHHHH
Q 042291 191 RQKLKKMVNVLRGFVPGG----NELNTVGVLDEAVRHLKSLKV 229 (241)
Q Consensus 191 RekI~e~~~~L~~lVPg~----~~~D~asvLdEaI~YLKsLk~ 229 (241)
++.|..-+.-=+.++||. ..+.....+...|.||++|..
T Consensus 72 ~~~L~~~l~~P~~~~pgt~M~~~gl~~~~~~~~liaYL~s~~~ 114 (115)
T PTZ00048 72 DKHLFEYLVNPKLYIPGTKMVFAGIKKEKERADLIAYLKEASS 114 (115)
T ss_pred HHHHHHHHhCcCccCCCCccCcCCCCCHHHHHHHHHHHHHhcc
Confidence 566677777778889974 234456677789999999864
No 28
>PTZ00405 cytochrome c; Provisional
Probab=21.06 E-value=1.6e+02 Score=23.77 Aligned_cols=37 Identities=19% Similarity=0.343 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhccCCCCCCc-----chhhHHHHHHHHHHHHH
Q 042291 191 RQKLKKMVNVLRGFVPGGNEL-----NTVGVLDEAVRHLKSLK 228 (241)
Q Consensus 191 RekI~e~~~~L~~lVPg~~~~-----D~asvLdEaI~YLKsLk 228 (241)
.+.|..-|.-=+.+|||. .| -...-++..|.||++|+
T Consensus 72 ~~~L~~~l~~P~~~~pgt-~M~f~gl~~~~dr~~liaYL~sl~ 113 (114)
T PTZ00405 72 PEVLDVYLENPKKFMPGT-KMSFAGIKKPQERADVIAYLETLK 113 (114)
T ss_pred HHHHHHHHHCHHhhCCCC-CCCCCCCCCHHHHHHHHHHHHHhc
Confidence 566777777777899973 44 34556778999999986
No 29
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=20.89 E-value=85 Score=31.93 Aligned_cols=40 Identities=18% Similarity=0.233 Sum_probs=35.1
Q ss_pred hhHHHHHHHHHHhhccCCCC----CCcchhhHHHHHHHHHHHHH
Q 042291 189 KKRQKLKKMVNVLRGFVPGG----NELNTVGVLDEAVRHLKSLK 228 (241)
Q Consensus 189 kRRekI~e~~~~L~~lVPg~----~~~D~asvLdEaI~YLKsLk 228 (241)
.||+|=|--|--|..++|=. .++||++|+.-|-.|||--.
T Consensus 11 tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~ 54 (598)
T KOG3559|consen 11 TRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN 54 (598)
T ss_pred HHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence 59999999999999999963 67899999999999998543
No 30
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=20.59 E-value=64 Score=25.29 Aligned_cols=44 Identities=18% Similarity=0.285 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhccCCCCCCcc-hhhHHHHHHH----HHHHHHHHHHHh
Q 042291 191 RQKLKKMVNVLRGFVPGGNELN-TVGVLDEAVR----HLKSLKVEVQNL 234 (241)
Q Consensus 191 RekI~e~~~~L~~lVPg~~~~D-~asvLdEaI~----YLKsLk~qV~~L 234 (241)
-+.++++...|+..+=-...+| .++-|++++. |.|.|+.+++.|
T Consensus 51 ~~~l~~k~~~l~~~l~~Id~Ie~~V~~LE~~v~~LD~ysk~LE~k~k~l 99 (99)
T PF10046_consen 51 LEDLNQKYEELQPYLQQIDQIEEQVTELEQTVYELDEYSKELESKFKKL 99 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 3455556666665554444443 3667777775 778888888764
Done!