Query psy17810
Match_columns 62
No_of_seqs 112 out of 191
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 23:37:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17810.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17810hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3558|consensus 99.5 2.6E-15 5.6E-20 121.5 3.1 56 1-57 71-126 (768)
2 KOG3559|consensus 99.3 5.6E-13 1.2E-17 105.0 2.1 58 1-58 26-87 (598)
3 KOG3560|consensus 99.2 4.4E-12 9.5E-17 102.0 3.2 60 1-60 50-114 (712)
4 PF00010 HLH: Helix-loop-helix 95.2 0.0099 2.1E-07 32.8 1.2 26 1-26 26-52 (55)
5 cd00083 HLH Helix-loop-helix d 95.1 0.013 2.9E-07 32.0 1.4 26 2-28 30-55 (60)
6 smart00353 HLH helix loop heli 94.9 0.015 3.3E-07 31.4 1.4 20 8-27 27-46 (53)
7 KOG3561|consensus 69.8 3.1 6.6E-05 35.3 1.8 27 6-32 50-76 (803)
8 KOG4029|consensus 54.9 6.9 0.00015 27.2 1.2 23 9-31 142-164 (228)
9 KOG4304|consensus 48.1 14 0.00031 26.9 2.0 24 9-32 69-92 (250)
10 TIGR03331 SAM_DCase_Eco S-aden 36.0 13 0.00029 27.9 0.2 13 3-15 98-110 (259)
11 PRK05462 S-adenosylmethionine 33.8 15 0.00033 27.7 0.2 13 3-15 102-114 (266)
12 COG5485 Predicted ester cyclas 31.7 15 0.00033 25.2 -0.0 13 7-19 116-128 (131)
No 1
>KOG3558|consensus
Probab=99.54 E-value=2.6e-15 Score=121.52 Aligned_cols=56 Identities=59% Similarity=0.895 Sum_probs=43.0
Q ss_pred CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCCCCCCCCCCCCCCCcccCcccccc
Q psy17810 1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPWSRDGPSPSKSVKGIPHNLQ 57 (62)
Q Consensus 1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~~~w~~~~~~~~~t~~lgshlLQ 57 (62)
+||||++|++||||||||||||||||||+|+.+++++ ...++.++.-.-.+.|.||
T Consensus 71 ~lPlp~aisshLDkaSimRLtISyLRlrk~a~~g~~p-~~e~~~~~~e~~l~~~iLq 126 (768)
T KOG3558|consen 71 LLPLPAAISSHLDKASIMRLTISYLRLRKFAGAGDPP-RAEGEPENLEQHLGDHILQ 126 (768)
T ss_pred hCCCcchhhhhhhhHHHHHHHHHHHHHHHHhhcCCcc-cccCCCcchhhhhhhhHHh
Confidence 5999999999999999999999999999999999765 2233333322235566665
No 2
>KOG3559|consensus
Probab=99.32 E-value=5.6e-13 Score=105.05 Aligned_cols=58 Identities=50% Similarity=0.651 Sum_probs=49.6
Q ss_pred CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCCC-CCCCCC---CCCCCCcccCccccccc
Q psy17810 1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGD-PPWSRD---GPSPSKSVKGIPHNLQE 58 (62)
Q Consensus 1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~-~~w~~~---~~~~~~t~~lgshlLQe 58 (62)
+||||.+|++|||||||+|||.||||||.+|+.|+ ..|+.. .+-......+|+|+||+
T Consensus 26 lLPLa~AItsQlDKasiiRLtTsYlKmr~vFPeGLGeawg~~S~a~~~~g~~~elgshlLqt 87 (598)
T KOG3559|consen 26 LLPLASAITSQLDKASIIRLTTSYLKMRNVFPEGLGEAWGASSRADPLDGVDKELGSHLLQT 87 (598)
T ss_pred hccchhhhhhccchhhhhhHHHHHHHHHHhcccccchhccCCCccccccchHHHHHHhHHHh
Confidence 69999999999999999999999999999998876 688753 34445566888999986
No 3
>KOG3560|consensus
Probab=99.23 E-value=4.4e-12 Score=101.97 Aligned_cols=60 Identities=35% Similarity=0.492 Sum_probs=46.1
Q ss_pred CCCCchHHhhccchhhhhHhhHHHHHHHHhhcCCCCCC--CCCCCCCCCcc-c-Cc-ccccccCC
Q psy17810 1 MLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDPPW--SRDGPSPSKSV-K-GI-PHNLQEGQ 60 (62)
Q Consensus 1 lLPlp~~v~s~LDKaSImRLtisyLr~r~~~~~~~~~w--~~~~~~~~~t~-~-lg-shlLQeg~ 60 (62)
|||||.+|+++|||.||+||++||||.|+||+...... ...+..+++.. . .+ +..|+||.
T Consensus 50 LLPfpqdiisKLDkLSVLRLSVSyLr~KSfFqvvl~~s~~~~~gg~~s~~a~~~yr~gl~llege 114 (712)
T KOG3560|consen 50 LLPFPQDIISKLDKLSVLRLSVSYLRVKSFFQVVLHQSSRQPAGGPPSPHASCPYRNGLALLEGE 114 (712)
T ss_pred hcCCCHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHhcCccccCCCCCCccccchhhccccccchH
Confidence 69999999999999999999999999999998765433 23455555422 2 33 66788874
No 4
>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=95.25 E-value=0.0099 Score=32.83 Aligned_cols=26 Identities=42% Similarity=0.648 Sum_probs=20.3
Q ss_pred CCCCc-hHHhhccchhhhhHhhHHHHH
Q psy17810 1 MLPLP-AAITSQLDKASIIRLTISYLK 26 (62)
Q Consensus 1 lLPlp-~~v~s~LDKaSImRLtisyLr 26 (62)
+||.. ......+||++|+..++.|++
T Consensus 26 llp~~~~~~~~k~~K~~iL~~ai~yI~ 52 (55)
T PF00010_consen 26 LLPSCSAGSSRKLSKASILQKAIDYIK 52 (55)
T ss_dssp CCSSHHCCTTSSSSHHHHHHHHHHHHH
T ss_pred hccchhccccccCCHHHHHHHHHHHHH
Confidence 35663 135678999999999999986
No 5
>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=95.07 E-value=0.013 Score=31.97 Aligned_cols=26 Identities=35% Similarity=0.542 Sum_probs=20.6
Q ss_pred CCCchHHhhccchhhhhHhhHHHHHHH
Q psy17810 2 LPLPAAITSQLDKASIIRLTISYLKLR 28 (62)
Q Consensus 2 LPlp~~v~s~LDKaSImRLtisyLr~r 28 (62)
+|... ...++||++|+..++.|++--
T Consensus 30 lp~~~-~~~k~~k~~iL~~a~~yI~~L 55 (60)
T cd00083 30 LPTLP-PSKKLSKAEILRKAVDYIKSL 55 (60)
T ss_pred CCCCC-CCCCCCHHHHHHHHHHHHHHH
Confidence 44444 467999999999999998754
No 6
>smart00353 HLH helix loop helix domain.
Probab=94.94 E-value=0.015 Score=31.39 Aligned_cols=20 Identities=45% Similarity=0.693 Sum_probs=17.5
Q ss_pred HhhccchhhhhHhhHHHHHH
Q psy17810 8 ITSQLDKASIIRLTISYLKL 27 (62)
Q Consensus 8 v~s~LDKaSImRLtisyLr~ 27 (62)
...++||++|+..+++|++-
T Consensus 27 ~~~k~~k~~iL~~ai~yi~~ 46 (53)
T smart00353 27 NNKKLSKAEILRLAIEYIKS 46 (53)
T ss_pred CCCCCCHHHHHHHHHHHHHH
Confidence 46789999999999999853
No 7
>KOG3561|consensus
Probab=69.75 E-value=3.1 Score=35.25 Aligned_cols=27 Identities=22% Similarity=0.429 Sum_probs=22.9
Q ss_pred hHHhhccchhhhhHhhHHHHHHHHhhc
Q psy17810 6 AAITSQLDKASIIRLTISYLKLRDFSG 32 (62)
Q Consensus 6 ~~v~s~LDKaSImRLtisyLr~r~~~~ 32 (62)
.+..-++||..|+|-||.+||..+-+.
T Consensus 50 ~~~~RK~DK~tVLr~aV~~lr~~k~~~ 76 (803)
T KOG3561|consen 50 ASLSRKPDKLTVLRMAVDHLRLIKEQE 76 (803)
T ss_pred hhcccCchHHHHHHHHHHHHHHHhhhh
Confidence 344578999999999999999988863
No 8
>KOG4029|consensus
Probab=54.86 E-value=6.9 Score=27.20 Aligned_cols=23 Identities=26% Similarity=0.434 Sum_probs=19.4
Q ss_pred hhccchhhhhHhhHHHHHHHHhh
Q psy17810 9 TSQLDKASIIRLTISYLKLRDFS 31 (62)
Q Consensus 9 ~s~LDKaSImRLtisyLr~r~~~ 31 (62)
.+.|=|..++|++++|+++-.-+
T Consensus 142 ~kklSKveTLr~A~~YI~~L~~l 164 (228)
T KOG4029|consen 142 SKKLSKVETLRLATSYIRYLTKL 164 (228)
T ss_pred ccccCcccchHHHHHHHHHHHHH
Confidence 57888999999999999875544
No 9
>KOG4304|consensus
Probab=48.07 E-value=14 Score=26.88 Aligned_cols=24 Identities=38% Similarity=0.466 Sum_probs=20.9
Q ss_pred hhccchhhhhHhhHHHHHHHHhhc
Q psy17810 9 TSQLDKASIIRLTISYLKLRDFSG 32 (62)
Q Consensus 9 ~s~LDKaSImRLtisyLr~r~~~~ 32 (62)
.++|+||=|+=+|+-|||..+-.+
T Consensus 69 ~sklEKAdILEltV~hL~~l~~~~ 92 (250)
T KOG4304|consen 69 HSKLEKADILELTVNHLRQLQRSQ 92 (250)
T ss_pred hhhhHHHHHHHHHHHHHHHHhccc
Confidence 489999999999999999877654
No 10
>TIGR03331 SAM_DCase_Eco S-adenosylmethionine decarboxylase proenzyme, Escherichia coli form. Members of this protein family are the single chain precursor of the S-adenosylmethionine decarboxylase as found in Escherichia coli. This form shows a substantially different architecture from the form shared by the Archaea, Bacillus, and many other species (TIGR03330). It shows little or no similarity to the form found in eukaryotes (TIGR00535).
Probab=36.03 E-value=13 Score=27.92 Aligned_cols=13 Identities=54% Similarity=1.017 Sum_probs=12.1
Q ss_pred CCchHHhhccchh
Q psy17810 3 PLPAAITSQLDKA 15 (62)
Q Consensus 3 Plp~~v~s~LDKa 15 (62)
|+|..|.+||||.
T Consensus 98 p~~~~vvahLdkS 110 (259)
T TIGR03331 98 PLPDAVVAHLDKS 110 (259)
T ss_pred CCccchhcccccC
Confidence 8899999999996
No 11
>PRK05462 S-adenosylmethionine decarboxylase; Provisional
Probab=33.82 E-value=15 Score=27.74 Aligned_cols=13 Identities=46% Similarity=0.979 Sum_probs=12.2
Q ss_pred CCchHHhhccchh
Q psy17810 3 PLPAAITSQLDKA 15 (62)
Q Consensus 3 Plp~~v~s~LDKa 15 (62)
|+|..|.+||||.
T Consensus 102 p~~~~vvahLdkS 114 (266)
T PRK05462 102 PLPETVVAHLDKS 114 (266)
T ss_pred CCccchhcccccc
Confidence 8999999999996
No 12
>COG5485 Predicted ester cyclase [General function prediction only]
Probab=31.70 E-value=15 Score=25.19 Aligned_cols=13 Identities=38% Similarity=0.447 Sum_probs=11.2
Q ss_pred HHhhccchhhhhH
Q psy17810 7 AITSQLDKASIIR 19 (62)
Q Consensus 7 ~v~s~LDKaSImR 19 (62)
++-+++||++|+|
T Consensus 116 ~vwsv~Dk~ai~r 128 (131)
T COG5485 116 EVWSVIDKMAIER 128 (131)
T ss_pred eeehhccHHHHHH
Confidence 4568999999998
Done!