Query 019930
Match_columns 334
No_of_seqs 137 out of 356
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 05:40:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019930.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019930hhsearch_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 3.1E-38 6.7E-43 266.8 7.3 66 21-86 1-66 (138)
2 PLN03105 TCP24 transcription f 100.0 2.2E-33 4.7E-38 262.7 7.0 76 7-87 38-113 (324)
3 PLN03106 TCP2 Protein TCP2; Pr 100.0 6.1E-33 1.3E-37 269.6 9.8 70 19-88 69-138 (447)
4 PF13986 DUF4224: Domain of un 45.6 12 0.00026 27.4 1.3 21 54-74 7-27 (47)
5 PF10200 Ndufs5: NADH:ubiquino 34.5 28 0.0006 29.5 1.9 20 52-75 3-22 (96)
6 PF06303 MatP: Organiser of ma 31.7 37 0.00079 30.9 2.3 50 24-78 77-129 (148)
7 PRK02967 nickel responsive reg 26.9 77 0.0017 28.0 3.5 36 41-76 5-40 (139)
8 PHA02602 56 dCTP pyrophosphata 26.3 49 0.0011 30.8 2.2 30 55-84 42-83 (172)
9 cd07977 TFIIE_beta_winged_heli 24.1 49 0.0011 26.3 1.6 27 51-77 27-54 (75)
10 COG1689 Uncharacterized protei 23.8 72 0.0016 31.4 2.9 31 49-82 41-73 (274)
11 PF12614 RRF_GI: Ribosome recy 21.0 56 0.0012 29.1 1.5 43 48-91 49-102 (128)
12 KOG4682 Uncharacterized conser 20.7 47 0.001 35.0 1.1 33 43-75 169-202 (488)
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=3.1e-38 Score=266.76 Aligned_cols=66 Identities=53% Similarity=0.950 Sum_probs=63.7
Q ss_pred cCCCCCCccccccCCCCCcceeecCHHHHHHHhhhhhhhCCCCCCchHHHHHHhcHHHHHHHhcCC
Q 019930 21 STGRKDRHSKVYTSKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKSSIDKLAELP 86 (334)
Q Consensus 21 ~~~~kDRHsKv~ta~g~RdRRvRls~~~A~~ff~lqd~LG~dk~skTv~WLL~~ak~aI~~l~~~~ 86 (334)
.+++||||||||||+|+||||||||++||++|||||||||||||||||||||++||+||+||+...
T Consensus 1 ~~~~kdrhski~Ta~g~RdRRvRLs~~~Ar~FFdLQDmLGfDKaSKTveWLL~kSk~AIkeL~~~~ 66 (138)
T PF03634_consen 1 AAGKKDRHSKIHTAQGPRDRRVRLSLEIARKFFDLQDMLGFDKASKTVEWLLTKSKKAIKELTQSS 66 (138)
T ss_pred CCCCCCCCCccccccCCCCCceecCHHHHHHHHHHHHHhcCCCCCchHHHHHHhCHHHHHHHHHhh
Confidence 368999999999999999999999999999999999999999999999999999999999999873
No 2
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=99.98 E-value=2.2e-33 Score=262.66 Aligned_cols=76 Identities=63% Similarity=0.973 Sum_probs=71.6
Q ss_pred CCceEEeecceeeccCCCCCCccccccCCCCCcceeecCHHHHHHHhhhhhhhCCCCCCchHHHHHHhcHHHHHHHhcCC
Q 019930 7 EGEIVQVEGGHIVRSTGRKDRHSKVYTSKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKSSIDKLAELP 86 (334)
Q Consensus 7 ~g~iv~~~~~~~~r~~~~kDRHsKv~ta~g~RdRRvRls~~~A~~ff~lqd~LG~dk~skTv~WLL~~ak~aI~~l~~~~ 86 (334)
..+||.| .|+.++||||||||||+|+||||||||++||++|||||||||||||||||||||++||+||+||+.+.
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 3467777 79999999999999999999999999999999999999999999999999999999999999998776
Q ss_pred C
Q 019930 87 P 87 (334)
Q Consensus 87 ~ 87 (334)
.
T Consensus 113 ~ 113 (324)
T PLN03105 113 T 113 (324)
T ss_pred c
Confidence 4
No 3
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=99.98 E-value=6.1e-33 Score=269.59 Aligned_cols=70 Identities=70% Similarity=1.028 Sum_probs=66.7
Q ss_pred eccCCCCCCccccccCCCCCcceeecCHHHHHHHhhhhhhhCCCCCCchHHHHHHhcHHHHHHHhcCCCC
Q 019930 19 VRSTGRKDRHSKVYTSKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKSSIDKLAELPPW 88 (334)
Q Consensus 19 ~r~~~~kDRHsKv~ta~g~RdRRvRls~~~A~~ff~lqd~LG~dk~skTv~WLL~~ak~aI~~l~~~~~~ 88 (334)
.|+.++||||||||||+|+||||||||++|||||||||||||||||||||||||++||+||+||+.++..
T Consensus 69 sRasg~KDRHSKI~Ta~G~RDRRvRLS~~~ArkFFdLQD~LGfDkaSKTvEWLL~~Sk~AI~EL~~l~~s 138 (447)
T PLN03106 69 SRASGGKDRHSKVLTSKGLRDRRVRLSVSTAIQFYDLQDRLGYDQPSKAVEWLIKAAEDSISELPSLNNS 138 (447)
T ss_pred ecccCCCCcccceecccCCcccceeccHHHHHHHHhHHHHhCCCCcchHHHHHHHHhHHHHHHhhccccc
Confidence 3678999999999999999999999999999999999999999999999999999999999999988753
No 4
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=45.63 E-value=12 Score=27.39 Aligned_cols=21 Identities=43% Similarity=0.966 Sum_probs=19.0
Q ss_pred hhhhhhCCCCCCchHHHHHHh
Q 019930 54 DVQDRLGYDRPSKAVDWLIKK 74 (334)
Q Consensus 54 ~lqd~LG~dk~skTv~WLL~~ 74 (334)
+|++.-||+++++=++||-++
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=34.48 E-value=28 Score=29.46 Aligned_cols=20 Identities=35% Similarity=0.823 Sum_probs=16.1
Q ss_pred HhhhhhhhCCCCCCchHHHHHHhc
Q 019930 52 FYDVQDRLGYDRPSKAVDWLIKKA 75 (334)
Q Consensus 52 ff~lqd~LG~dk~skTv~WLL~~a 75 (334)
|||||.+||.+ .-.||+-+|
T Consensus 3 ~~~~~~~~~~~----~d~~~~~~s 22 (96)
T PF10200_consen 3 FLDLQKRLGIN----LDRWMLIQS 22 (96)
T ss_pred hhhHHHHhCcC----HHHHHHHhc
Confidence 89999999995 446887655
No 6
>PF06303 MatP: Organiser of macrodomain of Terminus of chromosome; InterPro: IPR009390 Many bacteria have circular genomes that are large in comparison to their cellular dimensions; this imposes the necessity for compaction of the chromosome during cellular growth, replication, transcription, and segregation. Compaction of chromosomes results in the formation of structures called nucleoids. Nucleoids can be generated by a number of different processes: they include unrestrained DNA supercoiling, formation of a chromatin-like structure through the interaction of DNA binding proteins, condensation by structural maintenance of chromosomes (SMC)-like proteins, and macromolecular crowding []. Chromosome replication and segregation are intimately linked and tightly controlled to ensure that daughter cells each receive a complete copy of the genome. Chromosomes have replication origin (Ori) and termination (Ter) regions that are diametrically opposed. During the process of chromosome replication and cell division the Ori and Ter regions form two macrodomains (MDs), the Ori MD is centred on migS, a 25 bp sequence, that acts as the cis-acting site for the bipolar positioning of oriC []. The Ter MD is centred on dif (deletion-induced filamentation), which is a resolvase site that reduces chromosome multimers to monomers []. The Ori and Ter MDs are insulated from one and other by non-structural regions and other nucleoids. Chromosome replication initiates bidirectionally from oriC. Within the Ori MD with sister chromatids being located in separate cell halves and with the Ter macrodomain anchored to the cell pole. Cell division occurs with the completion of replication of the Ter region and the subsequent separation of the two sister chromatids [, ]. This entry contains MatP (YcbG), which is a component of the MatP/MatS site-specific system that organises the Ter macrodomain (MD) in Escherichia coli (strain K12) and related enterobacteria during replication of the chromosome. In E. coli there are 23 matS sequences, located in the Ter region which is centred on dif. The matS consensus is a palindromic sequence 5'-GTGAC[AG][CT]GTCAC, which is the recognition sequence for MatP. MatP binds to the matS sequences; and is critical for Ter MD formation. Inactivation of matP causes severe defects in chromosome segregation and cell division revealing its role as a major organiser of the Ter MD [].
Probab=31.67 E-value=37 Score=30.93 Aligned_cols=50 Identities=24% Similarity=0.426 Sum_probs=43.8
Q ss_pred CCCCc---cccccCCCCCcceeecCHHHHHHHhhhhhhhCCCCCCchHHHHHHhcHHH
Q 019930 24 RKDRH---SKVYTSKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKSS 78 (334)
Q Consensus 24 ~kDRH---sKv~ta~g~RdRRvRls~~~A~~ff~lqd~LG~dk~skTv~WLL~~ak~a 78 (334)
||+|| -+++| |-.-|=|...+=.++=.|..+.|. +=|+||+.||..++.-
T Consensus 77 rRkR~fnae~~~t----~kKSIDLey~vW~rLS~lA~~~g~-TLSEtI~~li~e~e~k 129 (148)
T PF06303_consen 77 RRKRHFNAEHQHT----RKKSIDLEYRVWQRLSALAQRRGM-TLSETIEYLIEEAERK 129 (148)
T ss_pred HHHhhccccccCC----CcceeeecHHHHHHHHHHHHHcCC-cHHHHHHHHHHhHHHH
Confidence 56777 56778 888999999999999999999999 8999999999988654
No 7
>PRK02967 nickel responsive regulator; Provisional
Probab=26.95 E-value=77 Score=28.02 Aligned_cols=36 Identities=22% Similarity=0.292 Sum_probs=32.5
Q ss_pred eeecCHHHHHHHhhhhhhhCCCCCCchHHHHHHhcH
Q 019930 41 RVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAK 76 (334)
Q Consensus 41 RvRls~~~A~~ff~lqd~LG~dk~skTv~WLL~~ak 76 (334)
-|+|+-+.+.+|=.+..+.||..-|++|..|++..-
T Consensus 5 svslp~~ll~~lD~~~~~~gy~sRSeaIrd~iR~~l 40 (139)
T PRK02967 5 TITLDDDLLETLDSLIARRGYQNRSEAIRDLLRAAL 40 (139)
T ss_pred EEEcCHHHHHHHHHHHHHcCCCCHhHHHHHHHHHHH
Confidence 378999999999999999999999999999987543
No 8
>PHA02602 56 dCTP pyrophosphatase; Provisional
Probab=26.26 E-value=49 Score=30.76 Aligned_cols=30 Identities=30% Similarity=0.472 Sum_probs=21.2
Q ss_pred hhhhhCCCC------------CCchHHHHHHhcHHHHHHHhc
Q 019930 55 VQDRLGYDR------------PSKAVDWLIKKAKSSIDKLAE 84 (334)
Q Consensus 55 lqd~LG~dk------------~skTv~WLL~~ak~aI~~l~~ 84 (334)
||.+|+-++ .+++++||......-.+|+.+
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 456777666 678899999887665555544
No 9
>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=24.10 E-value=49 Score=26.28 Aligned_cols=27 Identities=26% Similarity=0.390 Sum_probs=23.1
Q ss_pred HHhhhhhhhC-CCCCCchHHHHHHhcHH
Q 019930 51 QFYDVQDRLG-YDRPSKAVDWLIKKAKS 77 (334)
Q Consensus 51 ~ff~lqd~LG-~dk~skTv~WLL~~ak~ 77 (334)
.|=++.|.|+ +|...+.++||.+.++.
T Consensus 27 t~~EIl~~ls~~d~~~~~~~~L~~~~~~ 54 (75)
T cd07977 27 TLDEILDYLSLLDIGPKLKEWLKSEALV 54 (75)
T ss_pred cHHHHHHHHhccCccHHHHHHHHhhhhc
Confidence 3558999999 99999999999987765
No 10
>COG1689 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.83 E-value=72 Score=31.37 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=22.8
Q ss_pred HHHHhhhhhhhCCCCC--CchHHHHHHhcHHHHHHH
Q 019930 49 AIQFYDVQDRLGYDRP--SKAVDWLIKKAKSSIDKL 82 (334)
Q Consensus 49 A~~ff~lqd~LG~dk~--skTv~WLL~~ak~aI~~l 82 (334)
|+++|.| ||.+-| -||||||-.+-..|+.-+
T Consensus 41 Ai~i~s~---lg~evPr~EktiefL~d~~qt~~~~~ 73 (274)
T COG1689 41 AIKIYSL---LGHEVPRKEKTIEFLYDQMQTAGVGV 73 (274)
T ss_pred hhhhhhh---cCCcCchHHHHHHHHHHHHHHhhhHH
Confidence 6677765 888877 489999999766665544
No 11
>PF12614 RRF_GI: Ribosome recycling factor ; InterPro: IPR022253 This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Probab=20.95 E-value=56 Score=29.05 Aligned_cols=43 Identities=35% Similarity=0.474 Sum_probs=31.1
Q ss_pred HHHHHhhhhhhhCCCCCCchHHHHHHhcHHHH-----------HHHhcCCCCCCC
Q 019930 48 TAIQFYDVQDRLGYDRPSKAVDWLIKKAKSSI-----------DKLAELPPWQPS 91 (334)
Q Consensus 48 ~A~~ff~lqd~LG~dk~skTv~WLL~~ak~aI-----------~~l~~~~~~~p~ 91 (334)
.|.++-.+-+.|-- .+++.++||++|.+.++ ++|..+-..+|.
T Consensus 49 e~~~l~~~~~~lk~-~~~~~~~~li~kie~~L~~~~dkle~l~~~L~~Li~~nP~ 102 (128)
T PF12614_consen 49 EADQLQSFLDQLKA-EDYEEFQFLIKKIEAALLQHSDKLEPLEDKLARLIPQNPN 102 (128)
T ss_pred hHHHHHHHHHHHHh-cchHHHHHHHHHHHHHhcccccccchHHHHHHHHHHhCCc
Confidence 56666666777744 47789999999999988 555666555554
No 12
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=20.65 E-value=47 Score=34.99 Aligned_cols=33 Identities=27% Similarity=0.624 Sum_probs=28.8
Q ss_pred ecCHHHHHHHhhhhhhhCCCCC-CchHHHHHHhc
Q 019930 43 RLSAHTAIQFYDVQDRLGYDRP-SKAVDWLIKKA 75 (334)
Q Consensus 43 Rls~~~A~~ff~lqd~LG~dk~-skTv~WLL~~a 75 (334)
||+..+|.+||+.--..|.++- -|+.+||+.+-
T Consensus 169 ~lspkta~~yYea~ckYgle~vk~kc~ewl~~nl 202 (488)
T KOG4682|consen 169 TLSPKTACGYYEAACKYGLESVKKKCLEWLLNNL 202 (488)
T ss_pred hcChhhhhHhhhhhhhhhhHHHHHHHHHHHHHhh
Confidence 7999999999999999998764 57899999763
Done!