Query 040760
Match_columns 108
No_of_seqs 144 out of 275
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 11:32:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040760.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040760hhsearch_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 98.3 9.2E-07 2E-11 53.6 3.2 34 74-107 5-41 (60)
2 smart00353 HLH helix loop heli 98.1 3.6E-06 7.9E-11 50.4 3.3 30 78-107 1-33 (53)
3 PF00010 HLH: Helix-loop-helix 97.9 9E-06 2E-10 49.7 2.6 27 76-102 4-30 (55)
4 KOG1318 Helix loop helix trans 97.8 8.5E-06 1.8E-10 69.8 2.3 35 71-105 231-265 (411)
5 KOG4304 Transcriptional repres 96.3 0.0022 4.8E-08 51.5 1.9 31 76-106 35-65 (250)
6 KOG1319 bHLHZip transcription 96.0 0.0058 1.3E-07 49.4 2.9 31 76-106 65-95 (229)
7 KOG3561 Aryl-hydrocarbon recep 95.7 0.0069 1.5E-07 55.9 2.6 35 74-108 21-59 (803)
8 KOG2483 Upstream transcription 77.9 2.6 5.7E-05 34.0 3.2 32 73-104 59-90 (232)
9 KOG2588 Predicted DNA-binding 75.9 4.1 8.8E-05 39.0 4.3 39 65-103 264-306 (953)
10 PF08781 DP: Transcription fac 46.9 18 0.0004 27.4 2.4 19 81-99 9-28 (142)
11 smart00546 CUE Domain that may 36.0 30 0.00066 20.0 1.7 17 88-104 2-18 (43)
12 PF00714 IFN-gamma: Interferon 27.7 38 0.00083 25.8 1.5 23 82-104 113-135 (138)
13 PF02845 CUE: CUE domain; Int 25.2 65 0.0014 18.6 1.9 16 89-104 2-17 (42)
14 KOG4447 Transcription factor T 25.2 71 0.0015 25.3 2.6 27 76-102 81-107 (173)
15 PF09321 DUF1978: Domain of un 25.0 58 0.0013 26.8 2.2 18 86-103 116-133 (241)
16 smart00733 Mterf Mitochondrial 24.9 63 0.0014 15.8 1.6 14 85-98 15-28 (31)
17 PLN03217 transcription factor 22.5 65 0.0014 23.3 1.8 21 82-102 16-36 (93)
18 PF09278 MerR-DNA-bind: MerR, 21.8 1.2E+02 0.0026 18.2 2.7 18 81-98 41-58 (65)
19 TIGR03776 RPE5 Rickettsial pal 20.3 44 0.00095 21.1 0.5 25 78-102 16-40 (43)
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=98.26 E-value=9.2e-07 Score=53.62 Aligned_cols=34 Identities=29% Similarity=0.506 Sum_probs=30.4
Q ss_pred CCcchHHHHHHHHHHHHHHHHHhhhccCC---cccCC
Q 040760 74 TNSHSLVERVRREKISERMKFLQNLSLAI---EETGR 107 (108)
Q Consensus 74 t~~hSlaER~RRerInErmk~LQ~LVP~~---~K~Dk 107 (108)
-..|+++||.||++||+.+..|+.|||.+ .|+||
T Consensus 5 r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k 41 (60)
T cd00083 5 REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSK 41 (60)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCH
Confidence 35799999999999999999999999999 66664
No 2
>smart00353 HLH helix loop helix domain.
Probab=98.09 E-value=3.6e-06 Score=50.44 Aligned_cols=30 Identities=30% Similarity=0.409 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHHHHHHHHhhhccCC---cccCC
Q 040760 78 SLVERVRREKISERMKFLQNLSLAI---EETGR 107 (108)
Q Consensus 78 SlaER~RRerInErmk~LQ~LVP~~---~K~Dk 107 (108)
+++||.||++||+.+..|+.|||.+ .|+||
T Consensus 1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k 33 (53)
T smart00353 1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSK 33 (53)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCH
Confidence 4789999999999999999999964 45554
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=97.90 E-value=9e-06 Score=49.70 Aligned_cols=27 Identities=30% Similarity=0.407 Sum_probs=26.0
Q ss_pred cchHHHHHHHHHHHHHHHHHhhhccCC
Q 040760 76 SHSLVERVRREKISERMKFLQNLSLAI 102 (108)
Q Consensus 76 ~hSlaER~RRerInErmk~LQ~LVP~~ 102 (108)
.|+..||.||.+||+.+..|+.|||.+
T Consensus 4 ~h~~~Er~RR~~i~~~~~~L~~llp~~ 30 (55)
T PF00010_consen 4 KHNERERRRRDRINDCFDELRELLPSC 30 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCCSSH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccch
Confidence 589999999999999999999999997
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=97.84 E-value=8.5e-06 Score=69.84 Aligned_cols=35 Identities=34% Similarity=0.456 Sum_probs=30.9
Q ss_pred ccCCCcchHHHHHHHHHHHHHHHHHhhhccCCccc
Q 040760 71 GQATNSHSLVERVRREKISERMKFLQNLSLAIEET 105 (108)
Q Consensus 71 g~At~~hSlaER~RRerInErmk~LQ~LVP~~~K~ 105 (108)
.+-.+.|++.||+||++||.+||.|-.|||.|+--
T Consensus 231 r~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~ 265 (411)
T KOG1318|consen 231 RRKRDNHNEVERRRRENINDRIKELGQLIPKCNSE 265 (411)
T ss_pred HHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcc
Confidence 34458899999999999999999999999999643
No 5
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=96.30 E-value=0.0022 Score=51.45 Aligned_cols=31 Identities=23% Similarity=0.337 Sum_probs=28.5
Q ss_pred cchHHHHHHHHHHHHHHHHHhhhccCCcccC
Q 040760 76 SHSLVERVRREKISERMKFLQNLSLAIEETG 106 (108)
Q Consensus 76 ~hSlaER~RRerInErmk~LQ~LVP~~~K~D 106 (108)
.+-|.||+||.|||+=|..|++|||-+.|.|
T Consensus 35 ~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~ 65 (250)
T KOG4304|consen 35 RKPLLEKKRRARINRCLDELKDLIPEALKKD 65 (250)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4679999999999999999999999998876
No 6
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=95.98 E-value=0.0058 Score=49.38 Aligned_cols=31 Identities=26% Similarity=0.350 Sum_probs=28.7
Q ss_pred cchHHHHHHHHHHHHHHHHHhhhccCCcccC
Q 040760 76 SHSLVERVRREKISERMKFLQNLSLAIEETG 106 (108)
Q Consensus 76 ~hSlaER~RRerInErmk~LQ~LVP~~~K~D 106 (108)
.|--|||.||+.|+.-..-||+|||-|.-.|
T Consensus 65 aHtqaEqkRRdAIk~GYddLq~LvP~cq~~d 95 (229)
T KOG1319|consen 65 AHTQAEQKRRDAIKRGYDDLQTLVPTCQQQD 95 (229)
T ss_pred HHHHHHHHHHHHHHhchHHHHHhcccccccc
Confidence 5888999999999999999999999998766
No 7
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=95.73 E-value=0.0069 Score=55.91 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=32.4
Q ss_pred CCcchHHHHHHHHHHHHHHHHHhhhccCCc----ccCCC
Q 040760 74 TNSHSLVERVRREKISERMKFLQNLSLAIE----ETGRS 108 (108)
Q Consensus 74 t~~hSlaER~RRerInErmk~LQ~LVP~~~----K~Dks 108 (108)
-.+|+.+||+||++.|.=|..|=+|||.|. |.||.
T Consensus 21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~ 59 (803)
T KOG3561|consen 21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKL 59 (803)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHH
Confidence 578999999999999999999999999998 88873
No 8
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=77.87 E-value=2.6 Score=33.97 Aligned_cols=32 Identities=16% Similarity=0.310 Sum_probs=28.9
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhhccCCcc
Q 040760 73 ATNSHSLVERVRREKISERMKFLQNLSLAIEE 104 (108)
Q Consensus 73 At~~hSlaER~RRerInErmk~LQ~LVP~~~K 104 (108)
+...|+--||.||.-|.+.+-.|.++||+.+-
T Consensus 59 ~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~ 90 (232)
T KOG2483|consen 59 SRAHHNALEKRRRAHLKDCFESLKDSVPLLNG 90 (232)
T ss_pred chhhhhhhhHHHHHHHHHHHHHHHHhCCCCCC
Confidence 46789999999999999999999999998764
No 9
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=75.86 E-value=4.1 Score=39.05 Aligned_cols=39 Identities=21% Similarity=0.337 Sum_probs=31.9
Q ss_pred ccccccccC----CCcchHHHHHHHHHHHHHHHHHhhhccCCc
Q 040760 65 HVRARRGQA----TNSHSLVERVRREKISERMKFLQNLSLAIE 103 (108)
Q Consensus 65 ~~RakRg~A----t~~hSlaER~RRerInErmk~LQ~LVP~~~ 103 (108)
+++.+|-.. ...|++-|++=|.-||.||-.|++|||+..
T Consensus 264 k~Pi~rl~~G~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~ 306 (953)
T KOG2588|consen 264 KKPIKRLLPGGEKRTAHNIIEKRYRSSINDKIIELKDLVPGTE 306 (953)
T ss_pred cCchhhcCCCCcccchhhHHHHHhhcchhHHHHHHHHhcCccH
Confidence 445555433 778999999999999999999999999753
No 10
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=46.86 E-value=18 Score=27.39 Aligned_cols=19 Identities=42% Similarity=0.615 Sum_probs=15.8
Q ss_pred HH-HHHHHHHHHHHHHhhhc
Q 040760 81 ER-VRREKISERMKFLQNLS 99 (108)
Q Consensus 81 ER-~RRerInErmk~LQ~LV 99 (108)
|| .|++||..+-..||+|+
T Consensus 9 ek~~~~~rI~~K~~~LqEL~ 28 (142)
T PF08781_consen 9 EKQRRRERIKKKKEQLQELI 28 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44 46788999999999986
No 11
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=36.02 E-value=30 Score=20.00 Aligned_cols=17 Identities=18% Similarity=0.272 Sum_probs=13.8
Q ss_pred HHHHHHHHhhhccCCcc
Q 040760 88 ISERMKFLQNLSLAIEE 104 (108)
Q Consensus 88 InErmk~LQ~LVP~~~K 104 (108)
+.+-+..||+++|+.+.
T Consensus 2 ~~~~v~~L~~mFP~l~~ 18 (43)
T smart00546 2 NDEALHDLKDMFPNLDE 18 (43)
T ss_pred hHHHHHHHHHHCCCCCH
Confidence 35678999999999764
No 12
>PF00714 IFN-gamma: Interferon gamma This family is a subset of the SCOP family.; InterPro: IPR002069 Interferon gamma (IFN-gamma) is produced by lymphocytes activated by specific antigens or mitogens. IFN-gamma shows antiviral activity and has important immunoregulatory functions. It is a potent activator of microphages and had antiproliferative effects on transformed cells. It can potentiate the antiviral and antitumor effects of the type I interferons. The crystal structures of a number IFN-gamma proteins have been solved, including bovine interferon-gamma at 2.0-A [] and human IFN-gamma at 2.9-A [].; GO: 0005133 interferon-gamma receptor binding, 0006955 immune response, 0005576 extracellular region; PDB: 1FG9_A 1FYH_D 1EKU_B 3BES_L 1RFB_A 1D9G_A 1D9C_B.
Probab=27.69 E-value=38 Score=25.81 Aligned_cols=23 Identities=35% Similarity=0.424 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHhhhccCCcc
Q 040760 82 RVRREKISERMKFLQNLSLAIEE 104 (108)
Q Consensus 82 R~RRerInErmk~LQ~LVP~~~K 104 (108)
++.|..|+|=++.+|+|+|..+.
T Consensus 113 ~vQrKAi~EL~~V~~~Lsp~~~l 135 (138)
T PF00714_consen 113 QVQRKAINELFKVMQKLSPKSNL 135 (138)
T ss_dssp HHHHHHHHCHHHHHHCCS-GCGS
T ss_pred HHHHHHHHHHHHHHHHhCCcccc
Confidence 57999999999999999998764
No 13
>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=25.24 E-value=65 Score=18.59 Aligned_cols=16 Identities=19% Similarity=0.283 Sum_probs=12.1
Q ss_pred HHHHHHHhhhccCCcc
Q 040760 89 SERMKFLQNLSLAIEE 104 (108)
Q Consensus 89 nErmk~LQ~LVP~~~K 104 (108)
.+.+..||+++|+...
T Consensus 2 ~~~v~~L~~mFP~~~~ 17 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDR 17 (42)
T ss_dssp HHHHHHHHHHSSSS-H
T ss_pred HHHHHHHHHHCCCCCH
Confidence 3568899999998653
No 14
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=25.16 E-value=71 Score=25.34 Aligned_cols=27 Identities=19% Similarity=0.318 Sum_probs=24.5
Q ss_pred cchHHHHHHHHHHHHHHHHHhhhccCC
Q 040760 76 SHSLVERVRREKISERMKFLQNLSLAI 102 (108)
Q Consensus 76 ~hSlaER~RRerInErmk~LQ~LVP~~ 102 (108)
.|++-||.|-.-+|+-++.||..+|-.
T Consensus 81 ~anvrerqRtqsLn~AF~~lr~iiptl 107 (173)
T KOG4447|consen 81 MANVRERQRTQSLNEAFAALRKIIPTL 107 (173)
T ss_pred HHHHHHHHhhhhHHHHHHHHHhhcCCC
Confidence 588999999999999999999999853
No 15
>PF09321 DUF1978: Domain of unknown function (DUF1978); InterPro: IPR015400 This domain is found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified. This entry includes the IncA proteins
Probab=24.98 E-value=58 Score=26.82 Aligned_cols=18 Identities=33% Similarity=0.466 Sum_probs=15.0
Q ss_pred HHHHHHHHHHhhhccCCc
Q 040760 86 EKISERMKFLQNLSLAIE 103 (108)
Q Consensus 86 erInErmk~LQ~LVP~~~ 103 (108)
++--+||+.||.|.|+..
T Consensus 116 ~ra~eRl~~LqalYp~v~ 133 (241)
T PF09321_consen 116 ERAQERLRELQALYPEVS 133 (241)
T ss_pred HHHHHHHHHHHHhCCCCc
Confidence 347799999999999863
No 16
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=24.86 E-value=63 Score=15.78 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHhhh
Q 040760 85 REKISERMKFLQNL 98 (108)
Q Consensus 85 RerInErmk~LQ~L 98 (108)
-++|..++++|+++
T Consensus 15 ~~~l~~~~~~l~~~ 28 (31)
T smart00733 15 EKKLKPKVEFLKEL 28 (31)
T ss_pred HHHhhHHHHHHHHc
Confidence 46788899998854
No 17
>PLN03217 transcription factor ATBS1; Provisional
Probab=22.52 E-value=65 Score=23.30 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHhhhccCC
Q 040760 82 RVRREKISERMKFLQNLSLAI 102 (108)
Q Consensus 82 R~RRerInErmk~LQ~LVP~~ 102 (108)
|+-=+.|++-+-.||.|+|-.
T Consensus 16 risddqi~dLvsKLq~llPe~ 36 (93)
T PLN03217 16 RISEDQINDLIIKLQQLLPEL 36 (93)
T ss_pred CCCHHHHHHHHHHHHHHChHH
Confidence 666688999999999999964
No 18
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=21.75 E-value=1.2e+02 Score=18.23 Aligned_cols=18 Identities=33% Similarity=0.351 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 040760 81 ERVRREKISERMKFLQNL 98 (108)
Q Consensus 81 ER~RRerInErmk~LQ~L 98 (108)
-+.+++.|.+++..||.+
T Consensus 41 l~~~~~~i~~~i~~L~~~ 58 (65)
T PF09278_consen 41 LEEKLEEIEEQIAELQAL 58 (65)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 345778899999999876
No 19
>TIGR03776 RPE5 Rickettsial palindromic element RPE5 domain. This model describes protein translations of a family, RPE5, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else.
Probab=20.27 E-value=44 Score=21.14 Aligned_cols=25 Identities=16% Similarity=0.097 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhhccCC
Q 040760 78 SLVERVRREKISERMKFLQNLSLAI 102 (108)
Q Consensus 78 SlaER~RRerInErmk~LQ~LVP~~ 102 (108)
++.+..-|-+|-|..|+.++-|||-
T Consensus 16 sVsr~Aeri~i~eH~r~~KddV~Nf 40 (43)
T TIGR03776 16 SVSRGAERIIIREHPRTYKDDVANF 40 (43)
T ss_pred hhcchhHHHHHHhcccchhhhcchh
Confidence 4445566789999999999999984
Done!