Query psy3607
Match_columns 95
No_of_seqs 103 out of 377
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 20:55:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3607.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3607hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1318|consensus 99.7 3.5E-18 7.7E-23 139.5 5.6 71 15-85 220-293 (411)
2 PF00010 HLH: Helix-loop-helix 99.7 3.6E-17 7.8E-22 98.5 5.8 51 28-78 1-55 (55)
3 KOG3561|consensus 99.7 1.5E-16 3.1E-21 138.1 6.9 70 16-85 8-80 (803)
4 cd00083 HLH Helix-loop-helix d 99.7 4.2E-16 9.2E-21 93.7 6.8 56 26-81 2-59 (60)
5 KOG4304|consensus 99.5 4.2E-15 9.1E-20 114.7 4.8 64 20-83 24-94 (250)
6 smart00353 HLH helix loop heli 99.5 3.1E-14 6.7E-19 84.3 6.6 49 33-81 1-51 (53)
7 KOG1319|consensus 99.4 5.4E-13 1.2E-17 101.1 5.8 72 9-80 37-120 (229)
8 KOG2588|consensus 98.7 5.6E-09 1.2E-13 92.4 2.9 60 26-85 274-333 (953)
9 KOG0561|consensus 98.5 2.1E-07 4.5E-12 75.0 5.4 67 22-88 54-121 (373)
10 KOG2483|consensus 98.5 3.4E-07 7.3E-12 70.5 5.6 56 26-81 57-114 (232)
11 KOG4029|consensus 98.2 1.7E-06 3.6E-11 65.1 3.4 56 26-81 107-165 (228)
12 KOG3960|consensus 98.0 1.2E-05 2.7E-10 63.3 6.3 53 28-80 118-171 (284)
13 KOG3560|consensus 97.5 7.1E-05 1.5E-09 64.5 3.3 41 36-76 33-76 (712)
14 KOG3910|consensus 97.4 0.00026 5.7E-09 60.4 4.8 59 23-81 521-582 (632)
15 KOG3558|consensus 97.3 0.00032 7E-09 61.5 4.6 60 26-86 44-106 (768)
16 PLN03217 transcription factor 97.3 0.0006 1.3E-08 46.3 4.8 45 40-84 19-68 (93)
17 KOG4447|consensus 95.6 0.006 1.3E-07 45.4 1.6 53 27-79 77-130 (173)
18 KOG3559|consensus 95.5 0.016 3.4E-07 49.2 3.7 44 35-78 8-54 (598)
19 KOG3898|consensus 95.4 0.011 2.4E-07 45.8 2.4 55 26-80 70-126 (254)
20 KOG4395|consensus 94.5 0.083 1.8E-06 42.1 4.9 55 26-80 172-228 (285)
21 KOG3582|consensus 63.5 2.2 4.7E-05 38.4 -0.2 58 27-84 650-711 (856)
22 KOG4447|consensus 53.6 5 0.00011 30.0 0.3 50 35-84 29-79 (173)
23 PF15392 Joubert: Joubert synd 52.1 17 0.00037 29.8 3.1 32 25-56 53-84 (329)
24 PF15566 Imm18: Immunity prote 35.3 37 0.00081 20.8 2.1 13 83-95 19-31 (52)
25 PF02186 TFIIE_beta: TFIIE bet 28.2 49 0.0011 20.7 1.8 15 63-77 3-17 (65)
26 cd07977 TFIIE_beta_winged_heli 26.8 56 0.0012 20.8 2.0 18 61-78 5-22 (75)
27 PTZ00405 cytochrome c; Provisi 26.6 1.3E+02 0.0029 20.4 3.9 39 40-78 72-113 (114)
28 PF02344 Myc-LZ: Myc leucine z 24.2 92 0.002 17.4 2.2 21 32-52 9-29 (32)
29 PF08079 Ribosomal_L30_N: Ribo 21.1 87 0.0019 19.7 2.0 34 60-93 28-69 (71)
No 1
>KOG1318|consensus
Probab=99.73 E-value=3.5e-18 Score=139.47 Aligned_cols=71 Identities=25% Similarity=0.380 Sum_probs=63.3
Q ss_pred CCcCCCCCchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607 15 DDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYNGTYYFGC 85 (95)
Q Consensus 15 ~d~~~~~~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~L~~~~~~~~ 85 (95)
.+.+-....++++||++||++|||||++||+||.+|+.|||.| ..+++|++||+.+++||+.|++...+..
T Consensus 220 ~~~~~~~~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~ 293 (411)
T KOG1318|consen 220 PKTDATALERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR 293 (411)
T ss_pred CCcccchhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence 3555557789999999999999999999999999999999997 5799999999999999999998776544
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=99.70 E-value=3.6e-17 Score=98.47 Aligned_cols=51 Identities=29% Similarity=0.601 Sum_probs=48.2
Q ss_pred hhhhcchHHHhHHHHHHHHHHHHHhhcCCC----CCCCCHHHHHHHHHHHHHHhh
Q psy3607 28 KRKSRNLSEKKRRDQFNMLINELCTMVSTN----NRKMDKSTVLKSTIAFLKNYN 78 (95)
Q Consensus 28 ~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~----~~K~dK~sIL~~aI~ylk~L~ 78 (95)
+|..|+..||+||+.||.+|.+|+.+||.+ ..|++|++||+.||+||+.||
T Consensus 1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 578999999999999999999999999986 589999999999999999986
No 3
>KOG3561|consensus
Probab=99.66 E-value=1.5e-16 Score=138.14 Aligned_cols=70 Identities=40% Similarity=0.491 Sum_probs=62.5
Q ss_pred CcCCCCCchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCC---CCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607 16 DTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGTYYFGC 85 (95)
Q Consensus 16 d~~~~~~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~---~K~dK~sIL~~aI~ylk~L~~~~~~~~ 85 (95)
+++.+.+.+++.+|++||.+||||||++|.+|.||++|||.|. +|+||++||++||++||.+++.+...+
T Consensus 8 ~d~~~~d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~~~~~~ 80 (803)
T KOG3561|consen 8 SDDAESDSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQESENS 80 (803)
T ss_pred CCcccccchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhhhcccc
Confidence 4555677888888999999999999999999999999999986 999999999999999999998754444
No 4
>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=99.65 E-value=4.2e-16 Score=93.67 Aligned_cols=56 Identities=27% Similarity=0.576 Sum_probs=51.7
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGTY 81 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~--~~K~dK~sIL~~aI~ylk~L~~~~ 81 (95)
..+|.+|+..||+||++||.+|.+|+.+||.. ..|++|++||..||+||+.|+...
T Consensus 2 ~~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~ 59 (60)
T cd00083 2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59 (60)
T ss_pred cHHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 35788999999999999999999999999997 589999999999999999998653
No 5
>KOG4304|consensus
Probab=99.55 E-value=4.2e-15 Score=114.68 Aligned_cols=64 Identities=22% Similarity=0.389 Sum_probs=54.9
Q ss_pred CCCchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-------CCCCCHHHHHHHHHHHHHHhhhhhhc
Q psy3607 20 DTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-------NRKMDKSTVLKSTIAFLKNYNGTYYF 83 (95)
Q Consensus 20 ~~~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-------~~K~dK~sIL~~aI~ylk~L~~~~~~ 83 (95)
+......-+|.+|.++|||||++||.+|++|+.|||+. ..|++|+.||++||+||++|+.....
T Consensus 24 ~~~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~ 94 (250)
T KOG4304|consen 24 RSSKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA 94 (250)
T ss_pred cchhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence 44445567788999999999999999999999999973 37999999999999999999965443
No 6
>smart00353 HLH helix loop helix domain.
Probab=99.53 E-value=3.1e-14 Score=84.29 Aligned_cols=49 Identities=29% Similarity=0.542 Sum_probs=45.1
Q ss_pred chHHHhHHHHHHHHHHHHHhhcCCC--CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607 33 NLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKNYNGTY 81 (95)
Q Consensus 33 n~~EKrRRd~iN~~i~eL~~LIP~~--~~K~dK~sIL~~aI~ylk~L~~~~ 81 (95)
|..||+||++||.+|.+|+.+||.+ ..+++|++||..||+||+.|++..
T Consensus 1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~ 51 (53)
T smart00353 1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEEL 51 (53)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999973 689999999999999999998764
No 7
>KOG1319|consensus
Probab=99.39 E-value=5.4e-13 Score=101.14 Aligned_cols=72 Identities=29% Similarity=0.443 Sum_probs=61.9
Q ss_pred cccCCCCCcCCCCCc------hhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC------CCCCCHHHHHHHHHHHHHH
Q psy3607 9 SFNRNSDDTMDDTDD------KDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN------NRKMDKSTVLKSTIAFLKN 76 (95)
Q Consensus 9 ~~~~~~~d~~~~~~~------k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~------~~K~dK~sIL~~aI~ylk~ 76 (95)
+|.+|.+|++++... .++.+|+.|...|++|||-||..++.|+.|||.| +.|+.|+-||.+||+||.+
T Consensus 37 sSApNtdd~ds~~hS~a~k~syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~ 116 (229)
T KOG1319|consen 37 SSAPNTDDEDSDYHSEAYKESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQF 116 (229)
T ss_pred CCCCCCCcccccchhHHHHhhHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHH
Confidence 567888888887443 3456789999999999999999999999999986 3499999999999999999
Q ss_pred hhhh
Q psy3607 77 YNGT 80 (95)
Q Consensus 77 L~~~ 80 (95)
|+..
T Consensus 117 L~~~ 120 (229)
T KOG1319|consen 117 LHKE 120 (229)
T ss_pred HHHH
Confidence 9854
No 8
>KOG2588|consensus
Probab=98.73 E-value=5.6e-09 Score=92.41 Aligned_cols=60 Identities=30% Similarity=0.400 Sum_probs=55.0
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHhhhhhhccc
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYYFGC 85 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~~K~dK~sIL~~aI~ylk~L~~~~~~~~ 85 (95)
..+|..||.||||-|..||++|.||+.+||+...|+.|..+|+.||+||+.+++....+.
T Consensus 274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk 333 (953)
T KOG2588|consen 274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLK 333 (953)
T ss_pred CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccc
Confidence 367899999999999999999999999999988999999999999999999997665554
No 9
>KOG0561|consensus
Probab=98.49 E-value=2.1e-07 Score=75.01 Aligned_cols=67 Identities=19% Similarity=0.311 Sum_probs=57.9
Q ss_pred CchhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhhcccchh
Q psy3607 22 DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGTYYFGCSLN 88 (95)
Q Consensus 22 ~~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~~~~~~~~~~ 88 (95)
++..+-+|+--|-.||||-.-||..|.-|+.|||-. ..|+.|+.||+.|.+||.+|.+...++...|
T Consensus 54 D~erRmRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn 121 (373)
T KOG0561|consen 54 DPERRMRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQN 121 (373)
T ss_pred CHHHHHHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccccccc
Confidence 345567778888899999999999999999999963 5899999999999999999998877765443
No 10
>KOG2483|consensus
Probab=98.45 E-value=3.4e-07 Score=70.53 Aligned_cols=56 Identities=20% Similarity=0.261 Sum_probs=47.6
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCCCCCCCC--HHHHHHHHHHHHHHhhhhh
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMD--KSTVLKSTIAFLKNYNGTY 81 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~~~K~d--K~sIL~~aI~ylk~L~~~~ 81 (95)
...|..||..||+||+.|-.+|..|+.+||....... -++||++|+.||+.|+...
T Consensus 57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~ 114 (232)
T KOG2483|consen 57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS 114 (232)
T ss_pred CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence 4577899999999999999999999999997432222 5899999999999998543
No 11
>KOG4029|consensus
Probab=98.16 E-value=1.7e-06 Score=65.07 Aligned_cols=56 Identities=21% Similarity=0.411 Sum_probs=49.5
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC--C-CCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--N-NRKMDKSTVLKSTIAFLKNYNGTY 81 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~--~-~~K~dK~sIL~~aI~ylk~L~~~~ 81 (95)
...+..+|..||.|=..+|.+|.+|+.+||. . ..|+.|+.+|+.||.||+.|.+.-
T Consensus 107 ~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL 165 (228)
T KOG4029|consen 107 SAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLL 165 (228)
T ss_pred hhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHh
Confidence 4555677888999999999999999999997 3 689999999999999999998653
No 12
>KOG3960|consensus
Probab=98.05 E-value=1.2e-05 Score=63.34 Aligned_cols=53 Identities=23% Similarity=0.434 Sum_probs=44.6
Q ss_pred hhhhcchHHHhHHHHHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHhhhh
Q psy3607 28 KRKSRNLSEKKRRDQFNMLINELCTMVS-TNNRKMDKSTVLKSTIAFLKNYNGT 80 (95)
Q Consensus 28 ~r~~hn~~EKrRRd~iN~~i~eL~~LIP-~~~~K~dK~sIL~~aI~ylk~L~~~ 80 (95)
||+.-.+-||||=-++|+.|..|+.=-- ..++++-|+.||+.||+||..||..
T Consensus 118 RRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~L 171 (284)
T KOG3960|consen 118 RRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQAL 171 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHH
Confidence 3445567799999999999999986544 4578999999999999999999864
No 13
>KOG3560|consensus
Probab=97.53 E-value=7.1e-05 Score=64.47 Aligned_cols=41 Identities=27% Similarity=0.544 Sum_probs=37.7
Q ss_pred HHhHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHH
Q psy3607 36 EKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKN 76 (95)
Q Consensus 36 EKrRRd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~ 76 (95)
-||.||++|.-++-|++|+|-. ..|+||.+||+.+|.||+-
T Consensus 33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV 76 (712)
T ss_pred chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence 6899999999999999999963 5799999999999999984
No 14
>KOG3910|consensus
Probab=97.37 E-value=0.00026 Score=60.42 Aligned_cols=59 Identities=17% Similarity=0.308 Sum_probs=49.6
Q ss_pred chhhhhhhhcchHHHhHHHHHHHHHHHHHhhcCC---CCCCCCHHHHHHHHHHHHHHhhhhh
Q psy3607 23 DKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIAFLKNYNGTY 81 (95)
Q Consensus 23 ~k~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~---~~~K~dK~sIL~~aI~ylk~L~~~~ 81 (95)
++++.||...|..||-|=.-||+.|+||..|.-- ...--.|..||..||.-|-.|++..
T Consensus 521 eREkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQV 582 (632)
T KOG3910|consen 521 EREKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQV 582 (632)
T ss_pred hHHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHH
Confidence 4566778888999999999999999999999875 2334579999999999999998754
No 15
>KOG3558|consensus
Probab=97.29 E-value=0.00032 Score=61.48 Aligned_cols=60 Identities=18% Similarity=0.309 Sum_probs=49.6
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC---CCCCCCHHHHHHHHHHHHHHhhhhhhcccc
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST---NNRKMDKSTVLKSTIAFLKNYNGTYYFGCS 86 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~---~~~K~dK~sIL~~aI~ylk~L~~~~~~~~~ 86 (95)
+.||+.-..+-|-||-+-|.-|-||+.++|- ....+||++|++.||.||| |+...+.+|.
T Consensus 44 ~~rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR-lrk~a~~g~~ 106 (768)
T KOG3558|consen 44 ELRKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR-LRKFAGAGDP 106 (768)
T ss_pred HHHhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH-HHHHhhcCCc
Confidence 3456666677899999999999999999994 2578999999999999999 6666666665
No 16
>PLN03217 transcription factor ATBS1; Provisional
Probab=97.27 E-value=0.0006 Score=46.27 Aligned_cols=45 Identities=24% Similarity=0.284 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHhhcCCC-----CCCCCHHHHHHHHHHHHHHhhhhhhcc
Q psy3607 40 RDQFNMLINELCTMVSTN-----NRKMDKSTVLKSTIAFLKNYNGTYYFG 84 (95)
Q Consensus 40 Rd~iN~~i~eL~~LIP~~-----~~K~dK~sIL~~aI~ylk~L~~~~~~~ 84 (95)
-|.||+.+..|+.|+|.. ..|..-+-||++|+.||+.|+.+...+
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdL 68 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDL 68 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 488999999999999972 457888899999999999999766544
No 17
>KOG4447|consensus
Probab=95.65 E-value=0.006 Score=45.37 Aligned_cols=53 Identities=21% Similarity=0.302 Sum_probs=47.5
Q ss_pred hhhhhcchHHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhh
Q psy3607 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNG 79 (95)
Q Consensus 27 ~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~ 79 (95)
..|.-||.-|++|=..+|+.|..|+.+||.. ..|+.|..-|+.|-.||-.|-+
T Consensus 77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~ 130 (173)
T KOG4447|consen 77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ 130 (173)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence 4567899999999999999999999999983 5799999999999999987754
No 18
>KOG3559|consensus
Probab=95.50 E-value=0.016 Score=49.17 Aligned_cols=44 Identities=25% Similarity=0.473 Sum_probs=38.4
Q ss_pred HHHhHHHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhh
Q psy3607 35 SEKKRRDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYN 78 (95)
Q Consensus 35 ~EKrRRd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~L~ 78 (95)
.-|.||++-|.-|-||+.++|-. ...+||++|++.|-.|||.-+
T Consensus 8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~ 54 (598)
T KOG3559|consen 8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN 54 (598)
T ss_pred HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence 46889999999999999999952 356999999999999999654
No 19
>KOG3898|consensus
Probab=95.40 E-value=0.011 Score=45.80 Aligned_cols=55 Identities=16% Similarity=0.289 Sum_probs=47.9
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHhhhh
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLKNYNGT 80 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~--~~~K~dK~sIL~~aI~ylk~L~~~ 80 (95)
..+|..-|.-||+|--.+|+.++.|+.+||. ...|+.|+..|+.|-.||..|.+.
T Consensus 70 ~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~ 126 (254)
T KOG3898|consen 70 TLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV 126 (254)
T ss_pred hhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence 4556667778999999999999999999994 468999999999999999998853
No 20
>KOG4395|consensus
Probab=94.46 E-value=0.083 Score=42.07 Aligned_cols=55 Identities=18% Similarity=0.328 Sum_probs=47.9
Q ss_pred hhhhhhcchHHHhHHHHHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHhhhh
Q psy3607 26 DSKRKSRNLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLKNYNGT 80 (95)
Q Consensus 26 ~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~--~~~K~dK~sIL~~aI~ylk~L~~~ 80 (95)
..+|-.-|..||||-.-+|..|+.|+..||. ...|+.|-.-|++|--||--|-..
T Consensus 172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~ 228 (285)
T KOG4395|consen 172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCL 228 (285)
T ss_pred HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHh
Confidence 4556678889999999999999999999997 468999999999999999877543
No 21
>KOG3582|consensus
Probab=63.50 E-value=2.2 Score=38.43 Aligned_cols=58 Identities=17% Similarity=0.200 Sum_probs=49.5
Q ss_pred hhhhhcchHHHhHHHHHHHHHHHHHhhcCCC----CCCCCHHHHHHHHHHHHHHhhhhhhcc
Q psy3607 27 SKRKSRNLSEKKRRDQFNMLINELCTMVSTN----NRKMDKSTVLKSTIAFLKNYNGTYYFG 84 (95)
Q Consensus 27 ~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~~----~~K~dK~sIL~~aI~ylk~L~~~~~~~ 84 (95)
.+...|.-+|.+||..|-..+..|-+++... +.|+.+..-|+.+++||-.++++....
T Consensus 650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v 711 (856)
T KOG3582|consen 650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPV 711 (856)
T ss_pred CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhcccc
Confidence 6677899999999999999999999999863 568888888999999998888665443
No 22
>KOG4447|consensus
Probab=53.63 E-value=5 Score=30.05 Aligned_cols=50 Identities=8% Similarity=0.038 Sum_probs=35.8
Q ss_pred HHHhHHHHHHHHHHHHHhhcCCC-CCCCCHHHHHHHHHHHHHHhhhhhhcc
Q psy3607 35 SEKKRRDQFNMLINELCTMVSTN-NRKMDKSTVLKSTIAFLKNYNGTYYFG 84 (95)
Q Consensus 35 ~EKrRRd~iN~~i~eL~~LIP~~-~~K~dK~sIL~~aI~ylk~L~~~~~~~ 84 (95)
.|+-|-.++|..+.-|+.|+|+. ..++.+.--|+-+-+|+..+.+.+.+.
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 57788888999999999999985 234444444777777777666655543
No 23
>PF15392 Joubert: Joubert syndrome-associated
Probab=52.06 E-value=17 Score=29.82 Aligned_cols=32 Identities=13% Similarity=0.354 Sum_probs=28.0
Q ss_pred hhhhhhhcchHHHhHHHHHHHHHHHHHhhcCC
Q psy3607 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVST 56 (95)
Q Consensus 25 ~~~~r~~hn~~EKrRRd~iN~~i~eL~~LIP~ 56 (95)
++.+|+-..++.|+|+++|-+++.+|..+.-.
T Consensus 53 ekERrEIq~WMkRKrkERmaEYl~qlaEkR~q 84 (329)
T PF15392_consen 53 EKERREIQAWMKRKRKERMAEYLKQLAEKREQ 84 (329)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45678889999999999999999999998753
No 24
>PF15566 Imm18: Immunity protein 18
Probab=35.29 E-value=37 Score=20.83 Aligned_cols=13 Identities=0% Similarity=-0.176 Sum_probs=11.2
Q ss_pred cccchhhhhcccC
Q psy3607 83 FGCSLNFFLSAYA 95 (95)
Q Consensus 83 ~~~~~~~~~~~~~ 95 (95)
+.-..+||+|+|+
T Consensus 19 ~~~H~Hlmtp~Wg 31 (52)
T PF15566_consen 19 PFDHEHLMTPDWG 31 (52)
T ss_pred CCCCceecccccc
Confidence 5778999999986
No 25
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=28.24 E-value=49 Score=20.67 Aligned_cols=15 Identities=27% Similarity=0.421 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHh
Q psy3607 63 KSTVLKSTIAFLKNY 77 (95)
Q Consensus 63 K~sIL~~aI~ylk~L 77 (95)
+.+.|..||+|||..
T Consensus 3 ~~tql~~~VeymK~r 17 (65)
T PF02186_consen 3 KFTQLAKAVEYMKKR 17 (65)
T ss_dssp THHHHHHHHHHHHHH
T ss_pred hhhHHHHHHHHHHhc
Confidence 568999999999976
No 26
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=26.81 E-value=56 Score=20.83 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=15.4
Q ss_pred CCHHHHHHHHHHHHHHhh
Q psy3607 61 MDKSTVLKSTIAFLKNYN 78 (95)
Q Consensus 61 ~dK~sIL~~aI~ylk~L~ 78 (95)
-...++|-.||+|||.-.
T Consensus 5 ~~~~t~l~~aV~ymK~r~ 22 (75)
T cd07977 5 THVFTQLAKIVDYMKKRH 22 (75)
T ss_pred cchhhhHHHHHHHHHhcC
Confidence 467899999999999765
No 27
>PTZ00405 cytochrome c; Provisional
Probab=26.62 E-value=1.3e+02 Score=20.41 Aligned_cols=39 Identities=10% Similarity=0.211 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhhcCCC---CCCCCHHHHHHHHHHHHHHhh
Q psy3607 40 RDQFNMLINELCTMVSTN---NRKMDKSTVLKSTIAFLKNYN 78 (95)
Q Consensus 40 Rd~iN~~i~eL~~LIP~~---~~K~dK~sIL~~aI~ylk~L~ 78 (95)
.+.|..+|..=..++|+. -..+.+..-...-|+||+.|+
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 577888888888999963 234567777888999999886
No 28
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=24.16 E-value=92 Score=17.40 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=14.9
Q ss_pred cchHHHhHHHHHHHHHHHHHh
Q psy3607 32 RNLSEKKRRDQFNMLINELCT 52 (95)
Q Consensus 32 hn~~EKrRRd~iN~~i~eL~~ 52 (95)
-...=||||+.+...+.+|+.
T Consensus 9 ekeqLrrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 9 EKEQLRRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 334458899999999988874
No 29
>PF08079 Ribosomal_L30_N: Ribosomal L30 N-terminal domain; InterPro: IPR012988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This presumed domain is found at the N terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [].; PDB: 3IZR_e 3O5H_G 3O58_G 3IZS_e 4A1A_V 4A17_V 4A1E_V 4A1C_V.
Probab=21.14 E-value=87 Score=19.67 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHHHHhhhhhhccc--------chhhhhcc
Q psy3607 60 KMDKSTVLKSTIAFLKNYNGTYYFGC--------SLNFFLSA 93 (95)
Q Consensus 60 K~dK~sIL~~aI~ylk~L~~~~~~~~--------~~~~~~~~ 93 (95)
+..+..|+..|-.|++.-.+.....+ .++||-||
T Consensus 28 ~~~r~~~~kRAekY~kEYr~~erd~Irl~R~Ak~~G~fyvpa 69 (71)
T PF08079_consen 28 KKKRKEIFKRAEKYVKEYRQKERDEIRLKREAKKAGNFYVPA 69 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCS-SEE--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHccCccCCC
Confidence 44677899999999998886655543 67888876
Done!