Query 035012
Match_columns 76
No_of_seqs 50 out of 52
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 08:28:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035012hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05839 Apc13p: Apc13p protei 99.7 2.3E-18 5E-23 111.6 0.4 61 5-65 10-82 (88)
2 cd04459 Rho_CSD Rho_CSD: Rho p 27.4 18 0.00039 22.5 -0.3 27 9-35 4-37 (68)
3 KOG3297 DNA-directed RNA polym 15.7 56 0.0012 24.7 0.2 15 24-38 104-118 (202)
4 PHA03297 envelope glycoprotein 14.4 37 0.0008 25.2 -1.0 26 7-32 122-147 (185)
5 PF08292 RNA_pol_Rbc25: RNA po 14.3 27 0.00059 23.6 -1.6 14 24-37 26-39 (122)
6 PF07497 Rho_RNA_bind: Rho ter 14.0 71 0.0015 20.4 0.4 28 9-36 6-40 (78)
7 KOG1708 Mitochondrial/chloropl 11.9 78 0.0017 24.4 0.1 19 3-22 166-184 (236)
8 PF04891 NifQ: NifQ; InterPro 11.8 81 0.0018 22.7 0.1 17 50-66 97-113 (167)
9 KOG3318 Predicted membrane pro 11.5 76 0.0016 23.6 -0.1 41 24-66 23-71 (178)
10 cd04469 S1_Hex1 S1_Hex1: Hex1, 10.0 2E+02 0.0043 18.3 1.5 23 8-31 6-32 (75)
No 1
>PF05839 Apc13p: Apc13p protein; InterPro: IPR008401 The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators. Members of this family are components of the anaphase-promoting complex homologous to Apc13p [].
Probab=99.70 E-value=2.3e-18 Score=111.60 Aligned_cols=61 Identities=38% Similarity=0.714 Sum_probs=50.4
Q ss_pred cCCcEEEeechhhhhcCCCCCCCCCC-CCCcCC-CCCCCC----------CCCCccccCcccccccccccccc
Q 035012 5 SQGILIDIVDEEWMRDTLPDDDLPLP-PVLVVR-PDDTED----------SNQEPQQVNEDTWHDLAMGTHET 65 (76)
Q Consensus 5 ~dGrLiDIVDe~W~~DtLP~DdI~vP-~~~~p~-pE~~d~----------~~qet~k~qe~kW~DLAL~~l~~ 65 (76)
.+|+++||||++|++|+||.|+|+|| +..+|. ||++++ ..+.+++.+|++|+||||.+|++
T Consensus 10 ~~~~~~~il~eeW~~D~LP~DdIeip~~~~~~~~pe~ed~~vp~~~~~~g~~~~~~~~~E~~W~Dl~l~~L~~ 82 (88)
T PF05839_consen 10 LDGSHHDILDEEWNQDKLPFDDIEIPLPQLQNVNPEDEDDVVPDQSAAFGNKKNRQKEKEKDWNDLGLEELMS 82 (88)
T ss_pred cccchHHHHHHHHHhCcCCcccccCcccccCCCCcccccCcCCCccccchhhhhchhcchhhhhhhchhHHhh
Confidence 46889999999999999999999999 666666 665555 12235789999999999999975
No 2
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=27.41 E-value=18 Score=22.48 Aligned_cols=27 Identities=22% Similarity=0.575 Sum_probs=19.9
Q ss_pred EEEeech--hhhhcC----C-CCCCCCCCCCCcC
Q 035012 9 LIDIVDE--EWMRDT----L-PDDDLPLPPVLVV 35 (76)
Q Consensus 9 LiDIVDe--~W~~Dt----L-P~DdI~vP~~~~p 35 (76)
++||.++ .|.+.. + ..+||+||+.+.-
T Consensus 4 iLdi~~~g~GFLR~~~~~y~~~~~DvyVs~~~Ir 37 (68)
T cd04459 4 VLEILPDGFGFLRSSGYNYLPGPDDIYVSPSQIR 37 (68)
T ss_pred EEEEcCCCceEEecCCcCCCCCCCCEEECHHHHH
Confidence 6889988 666766 3 4688999987643
No 3
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=15.73 E-value=56 Score=24.69 Aligned_cols=15 Identities=27% Similarity=0.432 Sum_probs=12.9
Q ss_pred CCCCCCCCCCcCCCC
Q 035012 24 DDDLPLPPVLVVRPD 38 (76)
Q Consensus 24 ~DdI~vP~~~~p~pE 38 (76)
+|||.||..++|.|-
T Consensus 104 FdDI~IP~~~L~~p~ 118 (202)
T KOG3297|consen 104 FDDIFIPKEMLPEPC 118 (202)
T ss_pred eeceeechhhCCCCc
Confidence 689999999999864
No 4
>PHA03297 envelope glycoprotein L; Provisional
Probab=14.36 E-value=37 Score=25.17 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.5
Q ss_pred CcEEEeechhhhhcCCCCCCCCCCCC
Q 035012 7 GILIDIVDEEWMRDTLPDDDLPLPPV 32 (76)
Q Consensus 7 GrLiDIVDe~W~~DtLP~DdI~vP~~ 32 (76)
++|+|..|+.|+++.+.-|.|.=||.
T Consensus 122 ~~LldaLd~al~~~q~spD~st~pP~ 147 (185)
T PHA03297 122 EKLLFALDDSLSQSQSSPDEILGPPP 147 (185)
T ss_pred HHHHHHHHHHHhhcccCCccccCCCC
Confidence 57889999999999999999866664
No 5
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=14.26 E-value=27 Score=23.64 Aligned_cols=14 Identities=43% Similarity=0.783 Sum_probs=10.8
Q ss_pred CCCCCCCCCCcCCC
Q 035012 24 DDDLPLPPVLVVRP 37 (76)
Q Consensus 24 ~DdI~vP~~~~p~p 37 (76)
+|||.||+..+|.|
T Consensus 26 FddI~IP~~~L~~p 39 (122)
T PF08292_consen 26 FDDIFIPPSLLPEP 39 (122)
T ss_dssp EEEEEEECCCC-TT
T ss_pred cccEEECHHHCCCC
Confidence 46799999999964
No 6
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=14.04 E-value=71 Score=20.37 Aligned_cols=28 Identities=29% Similarity=0.691 Sum_probs=17.2
Q ss_pred EEEeech--hhhhcC----CC-CCCCCCCCCCcCC
Q 035012 9 LIDIVDE--EWMRDT----LP-DDDLPLPPVLVVR 36 (76)
Q Consensus 9 LiDIVDe--~W~~Dt----LP-~DdI~vP~~~~p~ 36 (76)
++||.++ .|.|.. +| .+||+||+.+.-.
T Consensus 6 vLei~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr 40 (78)
T PF07497_consen 6 VLEILPDGYGFLRSPDNNYLPSPDDVYVSPSQIRR 40 (78)
T ss_dssp EEEE-TTS-EEEE-GGGTTS-STTSEEE-CCCCCC
T ss_pred EEEECCCCcEEeECCCcCCCCCCCCEEECHHHHHH
Confidence 5678877 466665 44 5899999987644
No 7
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=11.92 E-value=78 Score=24.41 Aligned_cols=19 Identities=32% Similarity=0.611 Sum_probs=15.1
Q ss_pred cccCCcEEEeechhhhhcCC
Q 035012 3 ELSQGILIDIVDEEWMRDTL 22 (76)
Q Consensus 3 ~l~dGrLiDIVDe~W~~DtL 22 (76)
..|.||+|+|. |.|+.|-+
T Consensus 166 strSG~iIpip-e~~t~dy~ 184 (236)
T KOG1708|consen 166 STRSGRIIPIP-EKWTADYI 184 (236)
T ss_pred EecccccccCc-cccccccc
Confidence 36899999999 89966644
No 8
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=11.83 E-value=81 Score=22.68 Aligned_cols=17 Identities=24% Similarity=0.589 Sum_probs=11.7
Q ss_pred cCccccccccccccccc
Q 035012 50 VNEDTWHDLAMGTHETL 66 (76)
Q Consensus 50 ~qe~kW~DLAL~~l~~~ 66 (76)
...-=|.||||.+=..|
T Consensus 97 ~~~HLWqDLGL~~R~eL 113 (167)
T PF04891_consen 97 GPDHLWQDLGLRSRAEL 113 (167)
T ss_pred CCCccHHhcCCCCHHHH
Confidence 34456999999875544
No 9
>KOG3318 consensus Predicted membrane protein [Function unknown]
Probab=11.47 E-value=76 Score=23.59 Aligned_cols=41 Identities=22% Similarity=0.550 Sum_probs=23.3
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCccc--cC------ccccccccccccccc
Q 035012 24 DDDLPLPPVLVVRPDDTEDSNQEPQQ--VN------EDTWHDLAMGTHETL 66 (76)
Q Consensus 24 ~DdI~vP~~~~p~pE~~d~~~qet~k--~q------e~kW~DLAL~~l~~~ 66 (76)
-|.|+-||+....--..+ ...++++ +| .++| |+||+.++++
T Consensus 23 sd~~~~PpGf~~~s~~~~-~s~~a~r~~d~~~~L~~kkaW-diAl~P~K~i 71 (178)
T KOG3318|consen 23 SDSIPSPPGFSRKSLVQQ-TSAEADRKKDQEATLVLKKAW-DIALGPLKNI 71 (178)
T ss_pred ccCCCCCCCccccccccc-hHHHHhhhhhHHHHHHHHHHH-HHhhChHhhc
Confidence 466788998887622111 1111111 22 3445 8999999876
No 10
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=10.03 E-value=2e+02 Score=18.25 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=14.6
Q ss_pred cEEEeechhhhh---cCC-CCCCCCCCC
Q 035012 8 ILIDIVDEEWMR---DTL-PDDDLPLPP 31 (76)
Q Consensus 8 rLiDIVDe~W~~---DtL-P~DdI~vP~ 31 (76)
+|||| |+.+.. |.= --||++||+
T Consensus 6 qLidI-~DG~lsLM~e~G~~kdDl~lP~ 32 (75)
T cd04469 6 RVLDI-QDGSIVAMTETGDVKQGLPVID 32 (75)
T ss_pred EEEEe-cCCeEEEEcCCCCcccCccCCC
Confidence 57888 765443 332 267888886
Done!