Query 033093
Match_columns 127
No_of_seqs 24 out of 26
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 09:43:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033093hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07347 CI-B14_5a: NADH:ubiqu 96.4 0.0047 1E-07 45.3 4.1 62 8-83 2-63 (97)
2 KOG4630 NADH:ubiquinone oxidor 93.5 0.14 3.1E-06 40.1 4.6 65 5-82 8-73 (142)
3 KOG0426 Ubiquitin-protein liga 35.6 87 0.0019 25.2 4.7 20 1-20 1-20 (165)
4 COG3211 PhoX Predicted phospha 20.3 32 0.00068 32.7 -0.2 27 11-37 542-570 (616)
5 KOG2406 MADS box transcription 19.0 38 0.00083 32.1 0.0 20 19-38 286-305 (635)
6 COG5078 Ubiquitin-protein liga 18.3 1.6E+02 0.0034 23.0 3.3 20 1-20 1-21 (153)
7 PRK13658 hypothetical protein; 17.5 47 0.001 22.9 0.2 7 17-23 53-59 (59)
8 PF11737 DUF3300: Protein of u 17.3 86 0.0019 26.4 1.7 22 44-66 135-156 (237)
9 cd01211 GAPCenA GAPCenA Phosph 17.1 1.4E+02 0.0031 23.1 2.7 14 63-76 68-84 (125)
10 PF10913 DUF2706: Protein of u 15.8 1.2E+02 0.0027 20.9 1.9 18 17-34 22-39 (60)
No 1
>PF07347 CI-B14_5a: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a); InterPro: IPR009947 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport, 0005743 mitochondrial inner membrane
Probab=96.43 E-value=0.0047 Score=45.31 Aligned_cols=62 Identities=29% Similarity=0.411 Sum_probs=45.6
Q ss_pred HHHHHHHHhhcCCceeeecCCCCccccccccccccccCCCCCCCceeecCCCCCcceeeeeeeecccccCCCccce
Q 033093 8 SLFQNLRRFIKKPWEITGVCSDPEYMGPLRKAAEYRVRCPATPEQQAIIPTSNPETVYDIKYYSRDQRRNRPPIRR 83 (127)
Q Consensus 8 sl~q~l~r~ik~PW~iTGP~S~pEy~~~~p~a~EYR~~sPAs~~~~~~VP~s~pe~VYDIkY~tRD~RRn~~pi~r 83 (127)
-++|.||.|+ .| =++...+--+. ..|+-|||. +.+|...-+...+.-||+||.||.-.|-.-
T Consensus 2 p~iq~lR~fl------~G----R~~~~~lRy~d---~~s~RTqPp-P~lP~Gp~hkls~NyYy~RD~RRev~PP~~ 63 (97)
T PF07347_consen 2 PFIQRLRNFL------LG----RKHKLQLRYAD---TISPRTQPP-PNLPGGPSHKLSANYYYTRDARREVQPPID 63 (97)
T ss_pred hHHHHHHHHH------cc----ccccccccccc---ccccCCCCC-CCCCCCCccccccccccccccccccCCCeE
Confidence 3678888876 12 24444333332 389999998 999999999999999999999998665443
No 2
>KOG4630 consensus NADH:ubiquinone oxidoreductase, NDUFA7/B14.5A subunit [Energy production and conversion]
Probab=93.50 E-value=0.14 Score=40.07 Aligned_cols=65 Identities=29% Similarity=0.416 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHhhcCCceeeecCCCCcccccccccccccc-CCCCCCCceeecCCCCCcceeeeeeeecccccCCCccc
Q 033093 5 AATSLFQNLRRFIKKPWEITGVCSDPEYMGPLRKAAEYRV-RCPATPEQQAIIPTSNPETVYDIKYYSRDQRRNRPPIR 82 (127)
Q Consensus 5 a~ksl~q~l~r~ik~PW~iTGP~S~pEy~~~~p~a~EYR~-~sPAs~~~~~~VP~s~pe~VYDIkY~tRD~RRn~~pi~ 82 (127)
++.-|+|.+|-|| +|+- |.+-+ +.-|-. .||-|||. +.||.......++--|+|||-||+-.|-.
T Consensus 8 vAt~ll~r~Rn~l------~g~~----~qhkl--a~rf~d~~sprTqpp-P~lP~GpshkL~aNYY~TRDgRR~v~pp~ 73 (142)
T KOG4630|consen 8 VATVLLQRDRNFL------LGRP----YQHKL--ALRFTDSASPRTQPP-PALPGGPSHKLSANYYCTRDGRREVDPPK 73 (142)
T ss_pred HHHHHHHHHhhhc------cCcc----ccCcc--cccchhccCcccCCC-CCCCCCcccccccceeeecCCccccCchH
Confidence 3444889999886 4432 43322 222322 68999998 88999999999999999999999876654
No 3
>KOG0426 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.60 E-value=87 Score=25.18 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=17.1
Q ss_pred ChhHHHHHHHHHHHHhhcCC
Q 033093 1 MAKAAATSLFQNLRRFIKKP 20 (127)
Q Consensus 1 ma~~a~ksl~q~l~r~ik~P 20 (127)
||+.|.+.|+..++..++.|
T Consensus 1 m~~~AlkRLm~EykqLt~~~ 20 (165)
T KOG0426|consen 1 MAGTALKRLMAEYKQLTLNP 20 (165)
T ss_pred CchhHHHHHHHHHHHHccCC
Confidence 88999999998888877655
No 4
>COG3211 PhoX Predicted phosphatase [General function prediction only]
Probab=20.32 E-value=32 Score=32.65 Aligned_cols=27 Identities=30% Similarity=0.580 Sum_probs=22.1
Q ss_pred HHHHHhhcCCc--eeeecCCCCccccccc
Q 033093 11 QNLRRFIKKPW--EITGVCSDPEYMGPLR 37 (127)
Q Consensus 11 q~l~r~ik~PW--~iTGP~S~pEy~~~~p 37 (127)
-+++||+-.|= ||||||-+|+.+-...
T Consensus 542 g~~~rf~t~P~g~E~tG~~FspD~~TlFV 570 (616)
T COG3211 542 GTIKRFLTGPIGCEFTGPCFSPDGKTLFV 570 (616)
T ss_pred ceeeeeccCCCcceeecceeCCCCceEEE
Confidence 35788999998 9999999999775543
No 5
>KOG2406 consensus MADS box transcription factor [Transcription]
Probab=19.04 E-value=38 Score=32.10 Aligned_cols=20 Identities=20% Similarity=0.393 Sum_probs=17.9
Q ss_pred CCceeeecCCCCcccccccc
Q 033093 19 KPWEITGVCSDPEYMGPLRK 38 (127)
Q Consensus 19 ~PW~iTGP~S~pEy~~~~p~ 38 (127)
++|.++-|+|||+|+++..+
T Consensus 286 r~yhlps~vsd~dy~ea~LG 305 (635)
T KOG2406|consen 286 RGYHLPSPVSDPDYEEAELG 305 (635)
T ss_pred CCcCCCCCCCChhHHHHHhc
Confidence 49999999999999998765
No 6
>COG5078 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=18.33 E-value=1.6e+02 Score=23.00 Aligned_cols=20 Identities=30% Similarity=0.602 Sum_probs=16.2
Q ss_pred ChhH-HHHHHHHHHHHhhcCC
Q 033093 1 MAKA-AATSLFQNLRRFIKKP 20 (127)
Q Consensus 1 ma~~-a~ksl~q~l~r~ik~P 20 (127)
|+.+ |.+-|.+-++++.+-|
T Consensus 1 ~~s~~a~~RL~kE~~~l~~~~ 21 (153)
T COG5078 1 MSSPSALKRLLKELKKLQKDP 21 (153)
T ss_pred CCchhHHHHHHHHHHHHhcCC
Confidence 4555 8888999999988888
No 7
>PRK13658 hypothetical protein; Provisional
Probab=17.49 E-value=47 Score=22.91 Aligned_cols=7 Identities=71% Similarity=1.407 Sum_probs=5.7
Q ss_pred hcCCcee
Q 033093 17 IKKPWEI 23 (127)
Q Consensus 17 ik~PW~i 23 (127)
-|+||+|
T Consensus 53 pkaPwei 59 (59)
T PRK13658 53 PKAPWEI 59 (59)
T ss_pred CCCCCCC
Confidence 5889986
No 8
>PF11737 DUF3300: Protein of unknown function (DUF3300); InterPro: IPR021728 This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
Probab=17.30 E-value=86 Score=26.36 Aligned_cols=22 Identities=41% Similarity=0.683 Sum_probs=18.0
Q ss_pred cCCCCCCCceeecCCCCCcceee
Q 033093 44 VRCPATPEQQAIIPTSNPETVYD 66 (127)
Q Consensus 44 ~~sPAs~~~~~~VP~s~pe~VYD 66 (127)
.+-||.+.+ +.||..+|..||-
T Consensus 135 ~IePa~p~v-VYVP~YdP~vVYg 156 (237)
T PF11737_consen 135 VIEPAQPEV-VYVPYYDPAVVYG 156 (237)
T ss_pred EEecCCCCe-EEecCCCCceeeC
Confidence 456776666 9999999999998
No 9
>cd01211 GAPCenA GAPCenA Phosphotyrosine-binding (PTB) domain. GAPCenA Phosphotyrosine-binding (PTB) domain. GAPCenA is a centrosome-associated GTPase activating protein (GAP) for rab 6. It consists of an N-terminal PTB domain and a C-terminal TBC domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=17.07 E-value=1.4e+02 Score=23.09 Aligned_cols=14 Identities=14% Similarity=0.491 Sum_probs=11.4
Q ss_pred ceeeeeeeec---cccc
Q 033093 63 TVYDIKYYSR---DQRR 76 (127)
Q Consensus 63 ~VYDIkY~tR---D~RR 76 (127)
.||.|.|+.| |+.-
T Consensus 68 ~I~rI~fC~rG~~~t~e 84 (125)
T cd01211 68 SIVNIRFCIRGESSTSE 84 (125)
T ss_pred EEEEEEEEEecCCCCcc
Confidence 4899999999 7654
No 10
>PF10913 DUF2706: Protein of unknown function (DUF2706); InterPro: IPR024444 This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Probab=15.76 E-value=1.2e+02 Score=20.85 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=15.1
Q ss_pred hcCCceeeecCCCCcccc
Q 033093 17 IKKPWEITGVCSDPEYMG 34 (127)
Q Consensus 17 ik~PW~iTGP~S~pEy~~ 34 (127)
=.+|+||..||-++|--+
T Consensus 22 psapyeikspcvs~didd 39 (60)
T PF10913_consen 22 PSAPYEIKSPCVSADIDD 39 (60)
T ss_pred CCCCccccCCccccccCC
Confidence 368999999999998654
Done!