Query 008187
Match_columns 574
No_of_seqs 147 out of 286
Neff 2.2
Searched_HMMs 46136
Date Thu Mar 28 20:35:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008187.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008187hhsearch_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 3.9E-32 8.4E-37 238.1 6.6 66 174-239 3-72 (138)
2 PLN03105 TCP24 transcription f 99.9 1.2E-25 2.5E-30 220.5 6.7 84 174-260 49-136 (324)
3 PLN03106 TCP2 Protein TCP2; Pr 99.9 2.1E-24 4.5E-29 219.5 7.2 60 174-233 73-136 (447)
4 KOG1819 FYVE finger-containing 62.6 3.4 7.3E-05 46.4 1.0 25 29-53 572-597 (990)
5 PHA03308 transcriptional regul 39.9 19 0.0004 42.4 2.2 13 77-89 1243-1255(1463)
6 KOG1819 FYVE finger-containing 34.4 13 0.00027 42.1 -0.1 16 27-42 574-589 (990)
7 PF10200 Ndufs5: NADH:ubiquino 31.8 22 0.00048 31.9 1.0 21 199-223 3-23 (96)
8 PF11593 Med3: Mediator comple 30.7 95 0.002 33.9 5.5 12 520-533 366-377 (379)
9 PF06303 MatP: Organiser of ma 30.4 29 0.00063 33.5 1.5 51 175-226 77-130 (148)
10 PRK02967 nickel responsive reg 29.8 58 0.0013 30.4 3.4 36 189-224 6-41 (139)
11 PHA02570 dexA exonuclease; Pro 28.1 51 0.0011 33.4 2.9 31 200-230 49-80 (220)
12 KOG3915 Transcription regulato 27.6 76 0.0017 35.9 4.3 15 78-92 118-132 (641)
13 PRK05097 Ter macrodomain organ 26.2 72 0.0016 30.9 3.3 50 176-226 78-130 (150)
14 COG3120 Uncharacterized protei 24.0 75 0.0016 30.6 3.0 51 176-227 78-131 (149)
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=99.97 E-value=3.9e-32 Score=238.13 Aligned_cols=66 Identities=33% Similarity=0.578 Sum_probs=61.6
Q ss_pred CCCCcccccC----CCCcccccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHHHHHHhhCCCCCCCCc
Q 008187 174 STKDRHTKVD----GRGRRIRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEPAIIAATGTGTIPANF 239 (574)
Q Consensus 174 s~KDRHSKV~----~RDRRmRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskpAI~aaTgtgtiP~nf 239 (574)
.+||||+||| +||||||||++||++||+||||||||||||||||||.+||+||++++.....|.+.
T Consensus 3 ~~kdrhski~Ta~g~RdRRvRLs~~~Ar~FFdLQDmLGfDKaSKTveWLL~kSk~AIkeL~~~~~~~~s~ 72 (138)
T PF03634_consen 3 GKKDRHSKIHTAQGPRDRRVRLSLEIARKFFDLQDMLGFDKASKTVEWLLTKSKKAIKELTQSSSSSSSE 72 (138)
T ss_pred CCCCCCCccccccCCCCCceecCHHHHHHHHHHHHHhcCCCCCchHHHHHHhCHHHHHHHHHhhcccccc
Confidence 4799999999 79999999999999999999999999999999999999999999999987776643
No 2
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=99.92 E-value=1.2e-25 Score=220.51 Aligned_cols=84 Identities=33% Similarity=0.497 Sum_probs=72.2
Q ss_pred CCCCcccccC----CCCcccccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHHHHHHhhCCCCCCCCccccccccccC
Q 008187 174 STKDRHTKVD----GRGRRIRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEPAIIAATGTGTIPANFSTLNVSLRSS 249 (574)
Q Consensus 174 s~KDRHSKV~----~RDRRmRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskpAI~aaTgtgtiP~nfstln~slr~s 249 (574)
.+||||+||+ +||||||||++||++||+|||||||||+||||||||.+||+||++++...+ .|..++.++...
T Consensus 49 g~KDRHSKI~TAqGpRDRRvRLSv~iArkFFdLQDmLGFDKaSKTVEWLL~kSk~AI~ELp~l~~---~~~~~~qnq~~~ 125 (324)
T PLN03105 49 GGKDRHSKVLTSKGLRDRRIRLSVATAIQFYDLQDRLGFDQPSKAVEWLINAASDSITDLPLLNT---NFDHLDQNQNQT 125 (324)
T ss_pred CCCCcccceecccCCcccceecCHHHHHHHhhHHHHhCCCCcchHHHHHHHHhHHHHHhcccCcc---cchhHHHHhhcc
Confidence 5899999999 799999999999999999999999999999999999999999999987654 488888777665
Q ss_pred CCcccCCCCCC
Q 008187 250 GSTLSAPPSKS 260 (574)
Q Consensus 250 ~s~~s~p~~~~ 260 (574)
-|.-+.-.++.
T Consensus 126 kS~cSS~Tskg 136 (324)
T PLN03105 126 KSACSSGTSES 136 (324)
T ss_pred cccccCCCCCC
Confidence 55544444443
No 3
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=99.90 E-value=2.1e-24 Score=219.53 Aligned_cols=60 Identities=33% Similarity=0.577 Sum_probs=57.6
Q ss_pred CCCCcccccC----CCCcccccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHHHHHHhhCCC
Q 008187 174 STKDRHTKVD----GRGRRIRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEPAIIAATGTG 233 (574)
Q Consensus 174 s~KDRHSKV~----~RDRRmRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskpAI~aaTgtg 233 (574)
.+||||+||+ +||||||||++||+|||+|||||||||+||||||||++||+||++++.+.
T Consensus 73 g~KDRHSKI~Ta~G~RDRRvRLS~~~ArkFFdLQD~LGfDkaSKTvEWLL~~Sk~AI~EL~~l~ 136 (447)
T PLN03106 73 GGKDRHSKVLTSKGLRDRRVRLSVSTAIQFYDLQDRLGYDQPSKAVEWLIKAAEDSISELPSLN 136 (447)
T ss_pred CCCCcccceecccCCcccceeccHHHHHHHHhHHHHhCCCCcchHHHHHHHHhHHHHHHhhccc
Confidence 5799999999 89999999999999999999999999999999999999999999998754
No 4
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=62.57 E-value=3.4 Score=46.40 Aligned_cols=25 Identities=32% Similarity=0.503 Sum_probs=12.1
Q ss_pred HHHhhhhcccCCCCCCCCCCC-CCce
Q 008187 29 QRQQQHHRHLHLPQQQFDGRS-VPFI 53 (574)
Q Consensus 29 h~~~~hh~hhh~~q~~~~gr~-~p~m 53 (574)
|||-|||||||-|+-+-.-|+ +|--
T Consensus 572 hhqrhhhhhhhrhphqhqhrqphphr 597 (990)
T KOG1819|consen 572 HHQRHHHHHHHRHPHQHQHRQPHPHR 597 (990)
T ss_pred hhhhccccccccCcchhcccCCCCcc
Confidence 344444455554444444555 5543
No 5
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=39.92 E-value=19 Score=42.40 Aligned_cols=13 Identities=54% Similarity=0.409 Sum_probs=9.0
Q ss_pred eeecCCcccccCC
Q 008187 77 VITSSSSTTASSS 89 (574)
Q Consensus 77 ~l~sst~t~~~ss 89 (574)
.|+-|++|-|+||
T Consensus 1243 dlsessstmhsss 1255 (1463)
T PHA03308 1243 DLSESSSTMHSSS 1255 (1463)
T ss_pred Ccccccccccccc
Confidence 4677778887743
No 6
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=34.45 E-value=13 Score=42.13 Aligned_cols=16 Identities=38% Similarity=0.652 Sum_probs=9.4
Q ss_pred HHHHHhhhhcccCCCC
Q 008187 27 ELQRQQQHHRHLHLPQ 42 (574)
Q Consensus 27 ~~h~~~~hh~hhh~~q 42 (574)
.-||+||||+|-|+||
T Consensus 574 qrhhhhhhhrhphqhq 589 (990)
T KOG1819|consen 574 QRHHHHHHHRHPHQHQ 589 (990)
T ss_pred hhccccccccCcchhc
Confidence 4466666666666555
No 7
>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=31.83 E-value=22 Score=31.91 Aligned_cols=21 Identities=33% Similarity=0.718 Sum_probs=17.4
Q ss_pred HhhhhhhhCCCCCchHHHHHHhhcH
Q 008187 199 VFQLTRELGHKSDGETIEWLLQQAE 223 (574)
Q Consensus 199 fF~LQdeLGfdk~skTIeWLL~qsk 223 (574)
||+||.+||++-| .||+-+|-
T Consensus 3 ~~~~~~~~~~~~d----~~~~~~s~ 23 (96)
T PF10200_consen 3 FLDLQKRLGINLD----RWMLIQSA 23 (96)
T ss_pred hhhHHHHhCcCHH----HHHHHhcc
Confidence 8999999999855 69887753
No 8
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=30.69 E-value=95 Score=33.85 Aligned_cols=12 Identities=50% Similarity=0.753 Sum_probs=6.7
Q ss_pred hhhhhccCCCCCCC
Q 008187 520 LNAVYSRAGGLNMN 533 (574)
Q Consensus 520 lNa~ySR~~gl~Mn 533 (574)
||+ .-- |||||+
T Consensus 366 lNn-Ldl-~~LNMD 377 (379)
T PF11593_consen 366 LNN-LDL-GSLNMD 377 (379)
T ss_pred ccc-ccc-CccCcc
Confidence 444 344 667775
No 9
>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=30.38 E-value=29 Score=33.47 Aligned_cols=51 Identities=27% Similarity=0.386 Sum_probs=42.6
Q ss_pred CCCcc---cccCCCCcccccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHHHH
Q 008187 175 TKDRH---TKVDGRGRRIRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEPAI 226 (574)
Q Consensus 175 ~KDRH---SKV~~RDRRmRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskpAI 226 (574)
+|+|| -+++.|-+-|=|...+=.++=.|..+.| -.=|+||+.||..++.--
T Consensus 77 rRkR~fnae~~~t~kKSIDLey~vW~rLS~lA~~~g-~TLSEtI~~li~e~e~k~ 130 (148)
T PF06303_consen 77 RRKRHFNAEHQHTRKKSIDLEYRVWQRLSALAQRRG-MTLSETIEYLIEEAERKE 130 (148)
T ss_pred HHHhhccccccCCCcceeeecHHHHHHHHHHHHHcC-CcHHHHHHHHHHhHHHHH
Confidence 34555 4567899999999999999999999999 678999999999887543
No 10
>PRK02967 nickel responsive regulator; Provisional
Probab=29.84 E-value=58 Score=30.40 Aligned_cols=36 Identities=22% Similarity=0.194 Sum_probs=32.8
Q ss_pred cccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHH
Q 008187 189 IRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEP 224 (574)
Q Consensus 189 mRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskp 224 (574)
|+||-+...+|=.+-.+.||..-||.|..|++..-.
T Consensus 6 vslp~~ll~~lD~~~~~~gy~sRSeaIrd~iR~~l~ 41 (139)
T PRK02967 6 ITLDDDLLETLDSLIARRGYQNRSEAIRDLLRAALA 41 (139)
T ss_pred EEcCHHHHHHHHHHHHHcCCCCHhHHHHHHHHHHHH
Confidence 789999999999999999999999999999986443
No 11
>PHA02570 dexA exonuclease; Provisional
Probab=28.11 E-value=51 Score=33.36 Aligned_cols=31 Identities=32% Similarity=0.421 Sum_probs=24.2
Q ss_pred hhhhhhhC-CCCCchHHHHHHhhcHHHHHHhh
Q 008187 200 FQLTRELG-HKSDGETIEWLLQQAEPAIIAAT 230 (574)
Q Consensus 200 F~LQdeLG-fdk~skTIeWLL~qskpAI~aaT 230 (574)
|++....| ...+..||+|-++|+..|=.++.
T Consensus 49 ~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~ 80 (220)
T PHA02570 49 FDLKSQKGKRLFDKSTIEWWKNQSPEARKNLK 80 (220)
T ss_pred cchhhccCCCccCchHHHHHHhCCHHHHHhcc
Confidence 34445567 78899999999999999866653
No 12
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=27.56 E-value=76 Score=35.87 Aligned_cols=15 Identities=27% Similarity=0.275 Sum_probs=9.7
Q ss_pred eecCCcccccCCCCC
Q 008187 78 ITSSSSTTASSSTTG 92 (574)
Q Consensus 78 l~sst~t~~~ss~~~ 92 (574)
|.++++-|++..+++
T Consensus 118 l~~s~p~~~~~g~~p 132 (641)
T KOG3915|consen 118 LFSSTPIYASTGSSP 132 (641)
T ss_pred ccCCCCCcCCCCCCC
Confidence 566777887744444
No 13
>PRK05097 Ter macrodomain organizer matS-binding protein; Provisional
Probab=26.24 E-value=72 Score=30.93 Aligned_cols=50 Identities=28% Similarity=0.336 Sum_probs=42.8
Q ss_pred CCcc---cccCCCCcccccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHHHH
Q 008187 176 KDRH---TKVDGRGRRIRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEPAI 226 (574)
Q Consensus 176 KDRH---SKV~~RDRRmRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskpAI 226 (574)
+.|| -|+|+|-.-|-|...+=.|+-.|.+++| -.=|+||++||..++.--
T Consensus 78 RKRhFNAE~qhTrKKSIDLey~vW~rLs~~a~~~~-~TLSetI~~li~eae~ke 130 (150)
T PRK05097 78 RKRHFNAEHQHTRKKSIDLEYRVWQRLAGLAQRRG-KTLSETIVQLIEDAERKE 130 (150)
T ss_pred HHccCCcccccccccCccccHHHHHHHHHHHHHcC-CcHHHHHHHHHHHHHHHH
Confidence 4455 4677999999999999999999999999 678999999999887543
No 14
>COG3120 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.97 E-value=75 Score=30.56 Aligned_cols=51 Identities=29% Similarity=0.388 Sum_probs=42.8
Q ss_pred CCcc---cccCCCCcccccCHHHHHHHhhhhhhhCCCCCchHHHHHHhhcHHHHH
Q 008187 176 KDRH---TKVDGRGRRIRMPATCAARVFQLTRELGHKSDGETIEWLLQQAEPAII 227 (574)
Q Consensus 176 KDRH---SKV~~RDRRmRLs~~~A~rfF~LQdeLGfdk~skTIeWLL~qskpAI~ 227 (574)
+.|| -++|+|..-|-|-..|=-|+-.|.+++| ..=|+||.+|+..++.--+
T Consensus 78 RKRhFNaE~qhTrKKSIDLey~VW~rLs~~a~~~g-~TLSetI~~li~eae~kek 131 (149)
T COG3120 78 RKRHFNAEHQHTRKKSIDLEYAVWQRLSGLARRRG-KTLSETIVYLIEEAERKEK 131 (149)
T ss_pred HHhhccHhhhhhhhccccHHHHHHHHHHHHHHHhc-CcHHHHHHHHHHHHHHHHH
Confidence 4455 3567899999999999999999999999 8899999999998876443
Done!