Query 014360
Match_columns 426
No_of_seqs 160 out of 354
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 04:22:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014360.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014360hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03634 TCP: TCP family trans 100.0 1.2E-37 2.7E-42 269.9 6.8 65 34-98 1-65 (138)
2 PLN03105 TCP24 transcription f 100.0 6.6E-33 1.4E-37 265.7 7.3 75 20-99 38-112 (324)
3 PLN03106 TCP2 Protein TCP2; Pr 100.0 1.2E-32 2.7E-37 273.9 8.3 71 32-102 69-139 (447)
4 PF13986 DUF4224: Domain of un 43.9 14 0.0003 28.0 1.4 21 67-87 7-27 (47)
5 PF10200 Ndufs5: NADH:ubiquino 41.1 19 0.00041 31.4 1.9 20 65-88 3-22 (96)
6 PHA02602 56 dCTP pyrophosphata 29.3 41 0.00088 32.3 2.3 30 68-97 42-83 (172)
7 PRK02967 nickel responsive reg 27.9 70 0.0015 29.2 3.5 35 54-88 5-39 (139)
8 cd07977 TFIIE_beta_winged_heli 21.6 60 0.0013 26.7 1.7 27 64-90 27-54 (75)
9 COG1689 Uncharacterized protei 21.1 89 0.0019 31.7 3.0 32 61-95 40-73 (274)
10 KOG4705 Uncharacterized conser 20.2 59 0.0013 33.5 1.6 21 77-97 159-179 (303)
No 1
>PF03634 TCP: TCP family transcription factor; InterPro: IPR005333 The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [] and PCF in rice (Oryza sativa) [, ]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits []. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event []. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [].
Probab=100.00 E-value=1.2e-37 Score=269.87 Aligned_cols=65 Identities=58% Similarity=0.990 Sum_probs=63.2
Q ss_pred cCCCCCCccccccCCCCCCceeecCHHHHHHHhhhhhhhCCCCCChhHHHHHHhcHHHHHHHhcC
Q 014360 34 STGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKAAIDELAEL 98 (426)
Q Consensus 34 ~~~~kDRHsKv~ta~g~RdRRvRls~~~A~~ff~Lqd~LG~dk~skTveWLL~~ak~AI~~l~~~ 98 (426)
+++|||||||||||+|+||||||||++||++|||||||||||||||||||||++||+||+||+..
T Consensus 1 ~~~~kdrhski~Ta~g~RdRRvRLs~~~Ar~FFdLQDmLGfDKaSKTveWLL~kSk~AIkeL~~~ 65 (138)
T PF03634_consen 1 AAGKKDRHSKIHTAQGPRDRRVRLSLEIARKFFDLQDMLGFDKASKTVEWLLTKSKKAIKELTQS 65 (138)
T ss_pred CCCCCCCCCccccccCCCCCceecCHHHHHHHHHHHHHhcCCCCCchHHHHHHhCHHHHHHHHHh
Confidence 36899999999999999999999999999999999999999999999999999999999999986
No 2
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=99.97 E-value=6.6e-33 Score=265.69 Aligned_cols=75 Identities=61% Similarity=0.971 Sum_probs=71.6
Q ss_pred CCceEEeecccccccCCCCCCccccccCCCCCCceeecCHHHHHHHhhhhhhhCCCCCChhHHHHHHhcHHHHHHHhcCC
Q 014360 20 GGEIVEVQGGHIVRSTGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKAAIDELAELP 99 (426)
Q Consensus 20 ~~~iv~v~~~~~~r~~~~kDRHsKv~ta~g~RdRRvRls~~~A~~ff~Lqd~LG~dk~skTveWLL~~ak~AI~~l~~~~ 99 (426)
..+||.| .|+.++||||||||||+|+||||||||++||++||+||||||||||||||||||++||+||+||+.+.
T Consensus 38 ssrivrv-----sRa~g~KDRHSKI~TAqGpRDRRvRLSv~iArkFFdLQDmLGFDKaSKTVEWLL~kSk~AI~ELp~l~ 112 (324)
T PLN03105 38 SSRIIRV-----SRASGGKDRHSKVLTSKGLRDRRIRLSVATAIQFYDLQDRLGFDQPSKAVEWLINAASDSITDLPLLN 112 (324)
T ss_pred cceEEEe-----eccCCCCCcccceecccCCcccceecCHHHHHHHhhHHHHhCCCCcchHHHHHHHHhHHHHHhcccCc
Confidence 4588888 89999999999999999999999999999999999999999999999999999999999999988765
No 3
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=99.97 E-value=1.2e-32 Score=273.90 Aligned_cols=71 Identities=68% Similarity=0.989 Sum_probs=67.8
Q ss_pred cccCCCCCCccccccCCCCCCceeecCHHHHHHHhhhhhhhCCCCCChhHHHHHHhcHHHHHHHhcCCCCC
Q 014360 32 VRSTGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKAAIDELAELPPWN 102 (426)
Q Consensus 32 ~r~~~~kDRHsKv~ta~g~RdRRvRls~~~A~~ff~Lqd~LG~dk~skTveWLL~~ak~AI~~l~~~~~~~ 102 (426)
.|+.++||||||||||+|+||||||||++|||+||+||||||||||||||||||++||+||+||+.|....
T Consensus 69 sRasg~KDRHSKI~Ta~G~RDRRvRLS~~~ArkFFdLQD~LGfDkaSKTvEWLL~~Sk~AI~EL~~l~~sf 139 (447)
T PLN03106 69 SRASGGKDRHSKVLTSKGLRDRRVRLSVSTAIQFYDLQDRLGYDQPSKAVEWLIKAAEDSISELPSLNNSF 139 (447)
T ss_pred ecccCCCCcccceecccCCcccceeccHHHHHHHHhHHHHhCCCCcchHHHHHHHHhHHHHHHhhcccccC
Confidence 67889999999999999999999999999999999999999999999999999999999999999887543
No 4
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=43.90 E-value=14 Score=27.97 Aligned_cols=21 Identities=43% Similarity=0.966 Sum_probs=19.0
Q ss_pred hhhhhhCCCCCChhHHHHHHh
Q 014360 67 DVQDRLGYDRPSKAVDWLIKK 87 (426)
Q Consensus 67 ~Lqd~LG~dk~skTveWLL~~ 87 (426)
+|+++-||++++|=++||-++
T Consensus 7 El~elTG~k~~~~Q~~~L~~~ 27 (47)
T PF13986_consen 7 ELQELTGYKRPSKQIRWLRRN 27 (47)
T ss_pred HHHHHHCCCCHHHHHHHHHHC
Confidence 588899999999999999875
No 5
>PF10200 Ndufs5: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa; InterPro: IPR019342 Proteins in this entry form part of the NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The mammalian complex I is composed of 45 different subunits. The proteins in this entry represent a component of the iron-sulphur (IP) fragment of the enzyme, that is not involved in catalysis. These proteins carry four highly conserved cysteine residues, but these do not appear to be in a configuration which would favour metal binding, so the exact function of the protein is uncertain [].
Probab=41.10 E-value=19 Score=31.45 Aligned_cols=20 Identities=35% Similarity=0.823 Sum_probs=16.4
Q ss_pred HhhhhhhhCCCCCChhHHHHHHhc
Q 014360 65 FYDVQDRLGYDRPSKAVDWLIKKA 88 (426)
Q Consensus 65 ff~Lqd~LG~dk~skTveWLL~~a 88 (426)
|||||.+||.+ .-.||+-+|
T Consensus 3 ~~~~~~~~~~~----~d~~~~~~s 22 (96)
T PF10200_consen 3 FLDLQKRLGIN----LDRWMLIQS 22 (96)
T ss_pred hhhHHHHhCcC----HHHHHHHhc
Confidence 89999999998 446887665
No 6
>PHA02602 56 dCTP pyrophosphatase; Provisional
Probab=29.33 E-value=41 Score=32.26 Aligned_cols=30 Identities=33% Similarity=0.506 Sum_probs=21.3
Q ss_pred hhhhhCCCC------------CChhHHHHHHhcHHHHHHHhc
Q 014360 68 VQDRLGYDR------------PSKAVDWLIKKAKAAIDELAE 97 (426)
Q Consensus 68 Lqd~LG~dk------------~skTveWLL~~ak~AI~~l~~ 97 (426)
||.+|+-++ .+|+++||.+....-.+|+.+
T Consensus 42 lq~~l~~~~p~~~~~p~~l~t~ge~l~W~~~~~~ai~dE~rE 83 (172)
T PHA02602 42 LQVRLANDKPEYNPHPDELKTCGEILDWLRNQDDYIADETRE 83 (172)
T ss_pred HHHHHcccccccCCCchhHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 455677666 688899999987665555543
No 7
>PRK02967 nickel responsive regulator; Provisional
Probab=27.89 E-value=70 Score=29.19 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=32.0
Q ss_pred eeecCHHHHHHHhhhhhhhCCCCCChhHHHHHHhc
Q 014360 54 RVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKA 88 (426)
Q Consensus 54 RvRls~~~A~~ff~Lqd~LG~dk~skTveWLL~~a 88 (426)
-|+|+-+...+|=.+..+.||..-|++|+.|++..
T Consensus 5 svslp~~ll~~lD~~~~~~gy~sRSeaIrd~iR~~ 39 (139)
T PRK02967 5 TITLDDDLLETLDSLIARRGYQNRSEAIRDLLRAA 39 (139)
T ss_pred EEEcCHHHHHHHHHHHHHcCCCCHhHHHHHHHHHH
Confidence 37899999999999999999999999999998754
No 8
>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=21.60 E-value=60 Score=26.67 Aligned_cols=27 Identities=26% Similarity=0.404 Sum_probs=22.9
Q ss_pred HHhhhhhhhC-CCCCChhHHHHHHhcHH
Q 014360 64 QFYDVQDRLG-YDRPSKAVDWLIKKAKA 90 (426)
Q Consensus 64 ~ff~Lqd~LG-~dk~skTveWLL~~ak~ 90 (426)
.|=++.|.|. +|...+.++||.+.++.
T Consensus 27 t~~EIl~~ls~~d~~~~~~~~L~~~~~~ 54 (75)
T cd07977 27 TLDEILDYLSLLDIGPKLKEWLKSEALV 54 (75)
T ss_pred cHHHHHHHHhccCccHHHHHHHHhhhhc
Confidence 3558899999 99999999999987765
No 9
>COG1689 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.10 E-value=89 Score=31.69 Aligned_cols=32 Identities=28% Similarity=0.520 Sum_probs=23.7
Q ss_pred HHHHHhhhhhhhCCCCC--ChhHHHHHHhcHHHHHHH
Q 014360 61 TAIQFYDVQDRLGYDRP--SKAVDWLIKKAKAAIDEL 95 (426)
Q Consensus 61 ~A~~ff~Lqd~LG~dk~--skTveWLL~~ak~AI~~l 95 (426)
.|+++|.| ||.+-| -||||||-.+-..||.-+
T Consensus 40 YAi~i~s~---lg~evPr~EktiefL~d~~qt~~~~~ 73 (274)
T COG1689 40 YAIKIYSL---LGHEVPRKEKTIEFLYDQMQTAGVGV 73 (274)
T ss_pred hhhhhhhh---cCCcCchHHHHHHHHHHHHHHhhhHH
Confidence 46777765 888876 589999999777666554
No 10
>KOG4705 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.22 E-value=59 Score=33.52 Aligned_cols=21 Identities=38% Similarity=0.684 Sum_probs=18.3
Q ss_pred CChhHHHHHHhcHHHHHHHhc
Q 014360 77 PSKAVDWLIKKAKAAIDELAE 97 (426)
Q Consensus 77 ~skTveWLL~~ak~AI~~l~~ 97 (426)
..||+.||++|++.+-+.|..
T Consensus 159 ~ektLkwL~rK~~q~~k~Lk~ 179 (303)
T KOG4705|consen 159 EEKTLKWLLRKAKQAQKNLKP 179 (303)
T ss_pred HHHHHHHHHHHHHHHHHhcCc
Confidence 579999999999999888753
Done!