Query psy1834
Match_columns 101
No_of_seqs 103 out of 187
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:34:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1834.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1834hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02939 UcrQ: UcrQ family; I 100.0 2.3E-45 5E-50 244.4 3.5 80 19-100 1-80 (80)
2 KOG4116|consensus 100.0 1.7E-42 3.7E-47 233.8 3.1 89 2-101 1-90 (90)
3 PF10890 DUF2741: Protein of u 99.1 8.2E-11 1.8E-15 77.2 2.7 60 27-88 5-65 (72)
4 COG0225 MsrA Peptide methionin 53.3 20 0.00044 27.1 3.6 74 16-98 86-159 (174)
5 PF15102 TMEM154: TMEM154 prot 27.2 23 0.0005 26.2 0.3 14 65-78 58-71 (146)
6 PF06374 NDUF_C2: NADH-ubiquin 25.9 29 0.00062 24.7 0.5 54 46-99 33-100 (117)
7 PF13049 DUF3910: Protein of u 25.0 47 0.001 22.6 1.4 20 29-48 51-70 (93)
8 PF15470 DUF4637: Domain of un 19.5 40 0.00087 25.4 0.2 47 29-82 63-109 (173)
9 KOG3887|consensus 14.5 97 0.0021 25.6 1.3 24 18-43 33-56 (347)
10 PF13269 DUF4060: Protein of u 13.9 1E+02 0.0022 20.4 1.1 15 23-39 26-40 (73)
No 1
>PF02939 UcrQ: UcrQ family; InterPro: IPR004205 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multi-enzyme complex [], which recognises a mitochondrial targeting presequence. The bc1 complex contains 11 subunits: 3 respiratory subunits (cytochrome b, cytochrome c1 and Rieske protein), 2 core proteins and 6 low molecular weight proteins. This family represents the 9.5 kDa subunit of the complex. This subunit together with cytochrome B binds to ubiquinone.; GO: 0008121 ubiquinol-cytochrome-c reductase activity; PDB: 1L0N_G 1SQQ_G 1PP9_G 1PPJ_T 2FYU_G 2BCC_G 1BCC_G 2A06_G 1NTZ_G 2YBB_g ....
Probab=100.00 E-value=2.3e-45 Score=244.37 Aligned_cols=80 Identities=41% Similarity=0.699 Sum_probs=73.1
Q ss_pred CCCCCCCCCceeeeEEEEEcCccchhhhccccchhhhhhHhhhhcccCeeehhhheehhhhhhcHHHHHHhhCCCCCCcc
Q psy1834 19 GHHGFGNLGPHIRNIVYHRISMFEQRAFAGLLNPGLQNTLRRITESAPRTVPYFLITYVIITQTNDYYAQLNRKNPKDYE 98 (101)
Q Consensus 19 G~~~fG~l~~k~rgivtYsLSP~eQra~aG~~~~~i~N~~RR~~~q~~~~~ppfi~~Y~iy~Wa~~~~~~~~rK~p~dye 98 (101)
|| +||+|. |||||+||+|||||||||+|++++||||++||+++|++||+||||++|+||+||+++||+++||||+|||
T Consensus 1 ~~-gfg~l~-k~kgi~tYslSP~eQr~~ag~~~~~i~N~~RR~~~q~~~v~ppfi~~y~i~~Wa~~~~~~~~rK~p~~~~ 78 (80)
T PF02939_consen 1 GW-GFGGLP-KQKGIITYSLSPFEQRPFAGAFSKGIFNTFRRFRSQVLYVAPPFIVGYLIYDWANEENEYLNRKNPADYE 78 (80)
T ss_dssp BT-TCTSS----EEEEEEEE-TTGB-SSTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCGCCSC
T ss_pred CC-cCCCCC-cccceEEEEeChhhhcccccchHhhHhHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHcCCCHHHHc
Confidence 45 788887 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q psy1834 99 HE 100 (101)
Q Consensus 99 nd 100 (101)
||
T Consensus 79 nd 80 (80)
T PF02939_consen 79 ND 80 (80)
T ss_dssp CH
T ss_pred cC
Confidence 98
No 2
>KOG4116|consensus
Probab=100.00 E-value=1.7e-42 Score=233.78 Aligned_cols=89 Identities=36% Similarity=0.643 Sum_probs=82.6
Q ss_pred CccccccccCCCCCcccCCCCCCCCCceeeeEEEEEcCccchhhhccccchhhhhhHhhhhcc-cCeeehhhheehhhhh
Q psy1834 2 MMTTAILIPIGKESSTMGHHGFGNLGPHIRNIVYHRISMFEQRAFAGLLNPGLQNTLRRITES-APRTVPYFLITYVIIT 80 (101)
Q Consensus 2 m~~t~~~~p~~k~~~~mG~~~fG~l~~k~rgivtYsLSP~eQra~aG~~~~~i~N~~RR~~~q-~~~~~ppfi~~Y~iy~ 80 (101)
||+|.+. ||. |||||+ ||+||++|+||||||||++|+|++|+||++||++++ +++++|+||++|+||+
T Consensus 1 ~~~t~~~---------~g~-hfGnl~-K~~giisYaLSPfeQra~~g~F~~~~~n~fRr~~~~~~y~~iP~~Iv~yliy~ 69 (90)
T KOG4116|consen 1 MRKTYVG---------MGG-HFGNLG-KMKGIISYALSPFEQRAYAGFFDKAFPNMFRRFRSDQLYVVIPQFIVAYLIYD 69 (90)
T ss_pred CCcceee---------hhh-hcCCch-hccceEEEecCchhhccccchhhhhhHHHHHHhhhccEEEEeccceEEEEEEe
Confidence 5666665 777 899999 999999999999999999999999999999999777 7888999999999999
Q ss_pred hcHHHHHHhhCCCCCCcccCC
Q psy1834 81 QTNDYYAQLNRKNPKDYEHEV 101 (101)
Q Consensus 81 Wa~~~~~~~~rK~p~dyend~ 101 (101)
|++++||.++||||+|+.||+
T Consensus 70 wg~e~ne~l~rK~p~~~~n~~ 90 (90)
T KOG4116|consen 70 WGKETNEALNRKNPADFANDQ 90 (90)
T ss_pred cchhHhHHHhccCchhhhccC
Confidence 999999999999999999996
No 3
>PF10890 DUF2741: Protein of unknown function (DUF2741); InterPro: IPR020101 This entry represents subunit 8 of the Cytochrome b-c1 complex. The ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) is part of the mitochondrial respiratory chain. This subunit, together with cytochrome b, binds to ubiquinone. In plants, the b-c1 complex contains 10 subunits: 3 respiratory subunits, 2 core proteins and 5 low-molecular weight proteins.
Probab=99.07 E-value=8.2e-11 Score=77.24 Aligned_cols=60 Identities=17% Similarity=0.268 Sum_probs=46.8
Q ss_pred CceeeeEEEEEcCccchhhhccccchhhhhhH-hhhhcccCeeehhhheehhhhhhcHHHHHH
Q psy1834 27 GPHIRNIVYHRISMFEQRAFAGLLNPGLQNTL-RRITESAPRTVPYFLITYVIITQTNDYYAQ 88 (101)
Q Consensus 27 ~~k~rgivtYsLSP~eQra~aG~~~~~i~N~~-RR~~~q~~~~~ppfi~~Y~iy~Wa~~~~~~ 88 (101)
.++.|- |+|+||||+|+.|.|.| +.+|..+ ++++++|...+.-++..+++|.+|.++-|+
T Consensus 5 pvrlke-VvY~LSP~qq~Vm~GLw-KDlp~ki~hk~~enwv~a~~~~~p~~Gt~~Ya~~y~e~ 65 (72)
T PF10890_consen 5 PVRLKE-VVYALSPFQQKVMPGLW-KDLPKKIHHKFSENWVSATLFLVPLVGTYWYAENYKEQ 65 (72)
T ss_pred ccchhH-heeeeChhhhhhhhhhh-hhcHHHHHHHHhhcceeeEEEeeeehhhHHHHHHHHHH
Confidence 357777 89999999999999955 5555555 558999998887777888888888766543
No 4
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=53.32 E-value=20 Score=27.12 Aligned_cols=74 Identities=18% Similarity=0.071 Sum_probs=50.9
Q ss_pred cccCCCCCCCCCceeeeEEEEEcCccchhhhccccchhhhhhHhhhhcccCeeehhhheehhhhhhcHHHHHHhhCCCCC
Q psy1834 16 STMGHHGFGNLGPHIRNIVYHRISMFEQRAFAGLLNPGLQNTLRRITESAPRTVPYFLITYVIITQTNDYYAQLNRKNPK 95 (101)
Q Consensus 16 ~~mG~~~fG~l~~k~rgivtYsLSP~eQra~aG~~~~~i~N~~RR~~~q~~~~~ppfi~~Y~iy~Wa~~~~~~~~rK~p~ 95 (101)
.-++. +.+.| .|.+-.-|..++ +|+..+......+-. -..+...+..-+-|+--+ .-|+++|.....|||.
T Consensus 86 ~~nrQ--GnD~G-tqYRs~Iy~~~~-~q~~~a~~~~~~~q~-~~~~~~~IvteI~p~~~F----y~AEeYHQ~Yl~KNP~ 156 (174)
T COG0225 86 SLNRQ--GNDRG-TQYRSAIYYTNE-EQKAIAEASIEELQA-SGYFKKPIVTEIEPAKNF----YPAEEYHQDYLKKNPN 156 (174)
T ss_pred CCCcc--CCccc-ccceeEEEEcCH-HHHHHHHHHHHHHHH-hccCCCCeEEEeeccccC----cccHHHHHHHHHhCCC
Confidence 33555 89999 888888999988 677776644444433 222333444445555444 4799999999999999
Q ss_pred Ccc
Q psy1834 96 DYE 98 (101)
Q Consensus 96 dye 98 (101)
.|-
T Consensus 157 gY~ 159 (174)
T COG0225 157 GYC 159 (174)
T ss_pred Cce
Confidence 885
No 5
>PF15102 TMEM154: TMEM154 protein family
Probab=27.24 E-value=23 Score=26.15 Aligned_cols=14 Identities=0% Similarity=-0.010 Sum_probs=9.6
Q ss_pred cCeeehhhheehhh
Q psy1834 65 APRTVPYFLITYVI 78 (101)
Q Consensus 65 ~~~~~ppfi~~Y~i 78 (101)
++++++|.|++.++
T Consensus 58 iLmIlIP~VLLvlL 71 (146)
T PF15102_consen 58 ILMILIPLVLLVLL 71 (146)
T ss_pred EEEEeHHHHHHHHH
Confidence 78899996555443
No 6
>PF06374 NDUF_C2: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2); InterPro: IPR009423 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 consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport, NADH to ubiquinone, 0005743 mitochondrial inner membrane
Probab=25.86 E-value=29 Score=24.70 Aligned_cols=54 Identities=26% Similarity=0.468 Sum_probs=38.2
Q ss_pred hccccchhhhhhHhh---h----hcccCeeehhhheehhhhhhcHHHHHHhh-------CCCCCCccc
Q psy1834 46 FAGLLNPGLQNTLRR---I----TESAPRTVPYFLITYVIITQTNDYYAQLN-------RKNPKDYEH 99 (101)
Q Consensus 46 ~aG~~~~~i~N~~RR---~----~~q~~~~~ppfi~~Y~iy~Wa~~~~~~~~-------rK~p~dyen 99 (101)
+.|+.+.-+-|.++| + ..|+++++....++|.+-.+-+...+..- +-+|+||..
T Consensus 33 ~~G~~~~ll~N~~~rRP~~~sGihr~ll~~t~g~~~Gy~~~k~~n~~~A~rD~~m~~YI~lHPEDFp~ 100 (117)
T PF06374_consen 33 FLGFCTALLDNAINRRPPLKSGIHRQLLLATIGWFIGYYITKYRNYYYAERDADMRHYIKLHPEDFPE 100 (117)
T ss_pred HHHHHHHHHHHHHhcCCchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhCcccCCC
Confidence 556666677787777 3 46788888888899988887776655433 346777764
No 7
>PF13049 DUF3910: Protein of unknown function (DUF3910)
Probab=25.03 E-value=47 Score=22.59 Aligned_cols=20 Identities=20% Similarity=0.022 Sum_probs=17.2
Q ss_pred eeeeEEEEEcCccchhhhcc
Q psy1834 29 HIRNIVYHRISMFEQRAFAG 48 (101)
Q Consensus 29 k~rgivtYsLSP~eQra~aG 48 (101)
.+..+|+|++-|=.||||+=
T Consensus 51 ~hyk~vqyg~kpgsqkpfpi 70 (93)
T PF13049_consen 51 THYKFVQYGIKPGSQKPFPI 70 (93)
T ss_pred ceeEEEEeccCcCCCCCccc
Confidence 45678999999999999974
No 8
>PF15470 DUF4637: Domain of unknown function (DUF4637)
Probab=19.51 E-value=40 Score=25.37 Aligned_cols=47 Identities=15% Similarity=0.005 Sum_probs=36.1
Q ss_pred eeeeEEEEEcCccchhhhccccchhhhhhHhhhhcccCeeehhhheehhhhhhc
Q psy1834 29 HIRNIVYHRISMFEQRAFAGLLNPGLQNTLRRITESAPRTVPYFLITYVIITQT 82 (101)
Q Consensus 29 k~rgivtYsLSP~eQra~aG~~~~~i~N~~RR~~~q~~~~~ppfi~~Y~iy~Wa 82 (101)
+.+|-|.| ||.+|..-+- ---.+||.-+.++-|+.||.+.-++..=|
T Consensus 63 rergSVSY--~PLRQEsStq-----qValLRRadsgFWgwlsPfaLl~gl~aPa 109 (173)
T PF15470_consen 63 RERGSVSY--CPLRQESSTQ-----QVALLRRADSGFWGWLSPFALLGGLAAPA 109 (173)
T ss_pred ccCCceec--ccccccchhh-----HHHHhhcccCCchhhhcHHHHhccccCcc
Confidence 67887877 7999986443 34578999999999999999877665444
No 9
>KOG3887|consensus
Probab=14.53 E-value=97 Score=25.59 Aligned_cols=24 Identities=33% Similarity=0.595 Sum_probs=17.6
Q ss_pred cCCCCCCCCCceeeeEEEEEcCccch
Q psy1834 18 MGHHGFGNLGPHIRNIVYHRISMFEQ 43 (101)
Q Consensus 18 mG~~~fG~l~~k~rgivtYsLSP~eQ 43 (101)
||.+.=|. ..++.+|-+..||+|.
T Consensus 33 MG~rRsGK--sSI~KVVFhkMsPneT 56 (347)
T KOG3887|consen 33 MGLRRSGK--SSIQKVVFHKMSPNET 56 (347)
T ss_pred EeecccCc--chhhheeeeccCCCce
Confidence 77644443 3577889999999986
No 10
>PF13269 DUF4060: Protein of unknown function (DUF4060)
Probab=13.86 E-value=1e+02 Score=20.38 Aligned_cols=15 Identities=20% Similarity=0.304 Sum_probs=13.1
Q ss_pred CCCCCceeeeEEEEEcC
Q psy1834 23 FGNLGPHIRNIVYHRIS 39 (101)
Q Consensus 23 fG~l~~k~rgivtYsLS 39 (101)
+|+ | +++..+||++-
T Consensus 26 yG~-g-r~~~~~tY~i~ 40 (73)
T PF13269_consen 26 YGD-G-RQKWPETYTIK 40 (73)
T ss_pred hCc-c-ccCCcEEEEEE
Confidence 788 8 89999999984
Done!