Query psy17946
Match_columns 223
No_of_seqs 71 out of 73
Neff 1.9
Searched_HMMs 46136
Date Fri Aug 16 18:21:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17946.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17946hhsearch_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 100.0 5.6E-38 1.2E-42 242.1 6.3 75 87-170 2-76 (97)
2 KOG4630|consensus 100.0 1.9E-29 4.1E-34 206.2 3.0 73 87-166 11-83 (142)
3 PF13106 DUF3961: Domain of un 72.7 0.83 1.8E-05 31.6 -0.7 20 30-49 4-23 (40)
4 PF04037 DUF382: Domain of unk 45.8 9.6 0.00021 31.8 0.9 8 18-25 31-38 (129)
5 PF08101 DUF1708: Domain of un 44.7 22 0.00048 33.9 3.1 90 35-126 118-232 (420)
6 PF13671 AAA_33: AAA domain; P 35.0 39 0.00084 24.4 2.5 35 61-95 61-95 (143)
7 PF13478 XdhC_C: XdhC Rossmann 34.9 13 0.00028 29.6 -0.0 37 26-64 77-113 (136)
8 PF12257 DUF3608: Protein of u 32.6 49 0.0011 30.2 3.3 73 71-155 149-235 (281)
9 PRK11020 hypothetical protein; 25.6 17 0.00036 30.2 -0.8 18 189-206 95-112 (118)
10 PF09127 Leuk-A4-hydro_C: Leuk 25.5 42 0.0009 26.8 1.4 53 45-99 39-98 (143)
11 PF05456 eIF_4EBP: Eukaryotic 24.8 32 0.0007 27.9 0.7 28 87-129 47-76 (116)
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=100.00 E-value=5.6e-38 Score=242.09 Aligned_cols=75 Identities=47% Similarity=0.779 Sum_probs=71.6
Q ss_pred HHHHHHHHHhccccccccccCCCccCCCCCCCCCCCCCCCCCCCCCCCcccceeeccCCCCCCCCCeEEEeccchhhhhc
Q psy17946 87 RLIARLARLLGTKRRYKVVVDNPLRFQDYNIVPRTQPLPNLPEGPHHVLSANYYVNRDGSHEVKPPATLYLANAAQKQIG 166 (223)
Q Consensus 87 ~fI~~LRdFL~GRkh~ka~~kl~LRYaD~~IS~RTQPPPnLP~GPsHKLS~NYYYtRDaRREV~PPI~I~~~ns~qK~La 166 (223)
+|||+|||||+||+| +++|||+| +||+||||||+||+||+||+|+||||+||+||||+||++|| +++|+|.
T Consensus 2 p~iq~lR~fl~GR~~-----~~~lRy~d-~~s~RTqPpP~lP~Gp~hkls~NyYy~RD~RRev~PP~~i~---s~~k~L~ 72 (97)
T PF07347_consen 2 PFIQRLRNFLLGRKH-----KLQLRYAD-TISPRTQPPPNLPGGPSHKLSANYYYTRDARREVQPPIDIV---SSQKQLI 72 (97)
T ss_pred hHHHHHHHHHccccc-----cccccccc-ccccCCCCCCCCCCCCccccccccccccccccccCCCeEee---ccccccc
Confidence 799999999999988 99999999 99999999999999999999999999999999999999998 6789998
Q ss_pred cccc
Q psy17946 167 ESHT 170 (223)
Q Consensus 167 a~~~ 170 (223)
++++
T Consensus 73 a~~~ 76 (97)
T PF07347_consen 73 AGKA 76 (97)
T ss_pred cccc
Confidence 7763
No 2
>KOG4630|consensus
Probab=99.95 E-value=1.9e-29 Score=206.18 Aligned_cols=73 Identities=48% Similarity=0.751 Sum_probs=68.9
Q ss_pred HHHHHHHHHhccccccccccCCCccCCCCCCCCCCCCCCCCCCCCCCCcccceeeccCCCCCCCCCeEEEeccchhhhhc
Q psy17946 87 RLIARLARLLGTKRRYKVVVDNPLRFQDYNIVPRTQPLPNLPEGPHHVLSANYYVNRDGSHEVKPPATLYLANAAQKQIG 166 (223)
Q Consensus 87 ~fI~~LRdFL~GRkh~ka~~kl~LRYaD~~IS~RTQPPPnLP~GPsHKLS~NYYYtRDaRREV~PPI~I~~~ns~qK~La 166 (223)
.||+++|+||+|| ..+|++++||+| .+|+||||||+||+||+||||+||||||||||+|.||+||| +++|.+.
T Consensus 11 ~ll~r~Rn~l~g~---~~qhkla~rf~d-~~sprTqppP~lP~GpshkL~aNYY~TRDgRR~v~pp~~lv---ss~k~l~ 83 (142)
T KOG4630|consen 11 VLLQRDRNFLLGR---PYQHKLALRFTD-SASPRTQPPPALPGGPSHKLSANYYCTRDGRREVDPPKDLV---SSQKFLG 83 (142)
T ss_pred HHHHHHhhhccCc---cccCcccccchh-ccCcccCCCCCCCCCcccccccceeeecCCccccCchHHHH---HHHHHhh
Confidence 3999999999999 456799999999 99999999999999999999999999999999999999999 6788876
No 3
>PF13106 DUF3961: Domain of unknown function (DUF3961)
Probab=72.74 E-value=0.83 Score=31.64 Aligned_cols=20 Identities=35% Similarity=1.079 Sum_probs=17.4
Q ss_pred ceeeeeeeeccccchhhhhh
Q psy17946 30 IEYFGLVQCEEKQNWFFDLL 49 (223)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~~ 49 (223)
-||||+-+|.+.|-||+-.+
T Consensus 4 n~~FGie~~~sdqIWFYG~~ 23 (40)
T PF13106_consen 4 NEWFGIEECKSDQIWFYGFF 23 (40)
T ss_pred hhhcCccccccccEEEeeHH
Confidence 48999999999999998644
No 4
>PF04037 DUF382: Domain of unknown function (DUF382) ; InterPro: IPR007180 This domain is specific to the human splicing factor 3b subunit 2 and its orthologs.; GO: 0005634 nucleus
Probab=45.84 E-value=9.6 Score=31.83 Aligned_cols=8 Identities=50% Similarity=1.273 Sum_probs=6.8
Q ss_pred eecccccc
Q psy17946 18 MVPQHWCS 25 (223)
Q Consensus 18 ~~~~~~~~ 25 (223)
-||+|||+
T Consensus 31 PVP~HW~~ 38 (129)
T PF04037_consen 31 PVPRHWSQ 38 (129)
T ss_pred CCCcchhh
Confidence 48999996
No 5
>PF08101 DUF1708: Domain of unknown function (DUF1708); InterPro: IPR012965 This is a fungal domain of unknown function, though the yeast protein MSB1(P21339 from SWISSPROT) which contains this domain is thought to play a role in bud formation [].
Probab=44.66 E-value=22 Score=33.89 Aligned_cols=90 Identities=28% Similarity=0.377 Sum_probs=63.5
Q ss_pred eeeeccccc------hhhhhhh------hccCCcccchhhhhhhhccCcceee----cc---chhhhhh------HHHHH
Q psy17946 35 LVQCEEKQN------WFFDLLK------TKRGISKTKIERIDTLQNAGARTVV----DN---ELIGRWY------WHRLI 89 (223)
Q Consensus 35 ~~~~~~~~~------~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~----~~---~~~~~~~------~~~fI 89 (223)
+.||-+.++ =|||||- .+.|+|-.||-|++-+=..|..... +| +.+..|. -|=|+
T Consensus 118 lp~~l~s~a~~~Iv~dFfdLL~sIaa~s~~NglsgrKlsrm~g~WaF~~~~~~~~~~~~~f~~gy~~W~~aadA~~HLfl 197 (420)
T PF08101_consen 118 LPQCLPSPAHASIVYDFFDLLSSIAAHSKKNGLSGRKLSRMAGIWAFGHPDFGKDSGFNSFEEGYKAWIRAADALEHLFL 197 (420)
T ss_pred ccccCCChhHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHCCCCCcccCCCcccHHHHHHHHHHHHHHHHHHHH
Confidence 456765444 4788873 3589999999999999888887776 22 3344565 58999
Q ss_pred HHHHHHhccccccccccCCCccCCCCCCCCCCCCCCC
Q psy17946 90 ARLARLLGTKRRYKVVVDNPLRFQDYNIVPRTQPLPN 126 (223)
Q Consensus 90 ~~LRdFL~GRkh~ka~~kl~LRYaD~~IS~RTQPPPn 126 (223)
+-||.++-..+.+...-+++.|-++ +-..++=||.
T Consensus 198 AyLRs~~pe~~~~~~~~~LP~sLq~--Ll~~~~YPP~ 232 (420)
T PF08101_consen 198 AYLRSLAPEGKSSTLISKLPRSLQS--LLQNTEYPPK 232 (420)
T ss_pred HHHHhcCcccccccccccCCHHHHH--hccccCCCCC
Confidence 9999998888764433466666666 5556665655
No 6
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=34.95 E-value=39 Score=24.43 Aligned_cols=35 Identities=26% Similarity=0.195 Sum_probs=25.8
Q ss_pred hhhhhhhccCcceeeccchhhhhhHHHHHHHHHHH
Q psy17946 61 ERIDTLQNAGARTVVDNELIGRWYWHRLIARLARL 95 (223)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~fI~~LRdF 95 (223)
+.+......|...|||+....+|++-++++.++.+
T Consensus 61 ~~~~~~l~~g~~~vvd~~~~~~~~r~~~~~~~~~~ 95 (143)
T PF13671_consen 61 AAIRKALRNGNSVVVDNTNLSREERARLRELARKH 95 (143)
T ss_dssp HHHHHHHHTT-EEEEESS--SHHHHHHHHHHHHHC
T ss_pred HHHHHHHHcCCCceeccCcCCHHHHHHHHHHHHHc
Confidence 34555667899999999999999998888888765
No 7
>PF13478 XdhC_C: XdhC Rossmann domain; PDB: 3ON5_A 2WE8_B 2WE7_A.
Probab=34.85 E-value=13 Score=29.56 Aligned_cols=37 Identities=27% Similarity=0.531 Sum_probs=29.1
Q ss_pred ccccceeeeeeeeccccchhhhhhhhccCCcccchhhhh
Q psy17946 26 FESSIEYFGLVQCEEKQNWFFDLLKTKRGISKTKIERID 64 (223)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (223)
.++...|.|++-...|...+++.|+ .|+|...++||-
T Consensus 77 l~~~~~YiG~lGS~~k~~~~~~~L~--~G~~~~~l~ri~ 113 (136)
T PF13478_consen 77 LASPARYIGLLGSRRKAARRLERLR--EGVSEEELARIH 113 (136)
T ss_dssp TTSS-SEEEESS-HHHHHHHCCCHH--TT--CHHHTTEE
T ss_pred HcCCCCEEEeecCchHHHHHHHHhh--cccchHHHhcEE
Confidence 3567889999999999999999999 599999999874
No 8
>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with PF00610 from PFAM.
Probab=32.61 E-value=49 Score=30.23 Aligned_cols=73 Identities=21% Similarity=0.258 Sum_probs=41.4
Q ss_pred cceeeccchhhhhhHHHHHHHHHHHhccccccccccCCCccCCCCCCCCCCCCCCCCCCC--CCCC------------cc
Q psy17946 71 ARTVVDNELIGRWYWHRLIARLARLLGTKRRYKVVVDNPLRFQDYNIVPRTQPLPNLPEG--PHHV------------LS 136 (223)
Q Consensus 71 ~~~~~~~~~~~~~~~~~fI~~LRdFL~GRkh~ka~~kl~LRYaD~~IS~RTQPPPnLP~G--PsHK------------LS 136 (223)
.|.|||++-++.| .+++..|++-+.--++ ...+.-+. ... ....+.+. |+++ .+
T Consensus 149 YrVVv~~~~~~~W--~~il~~Lk~eF~~f~r-----di~~~~~~----~~~-~~~~i~g~~s~A~~gNiLEaINlaln~~ 216 (281)
T PF12257_consen 149 YRVVVDEENSQDW--TSILVTLKKEFNQFQR-----DILLYHQS----DED-GTTRIKGRFSPAIKGNILEAINLALNQF 216 (281)
T ss_pred eEEEEeccccccH--HHHHHHHHHHHHHHHH-----Hhhccccc----ccC-CCccccceEeecccccHHHHHHHHhhhc
Confidence 4789999998855 7888888776654433 11111100 000 11122222 2222 36
Q ss_pred cceeeccCCCCCCCCCeEE
Q psy17946 137 ANYYVNRDGSHEVKPPATL 155 (223)
Q Consensus 137 ~NYYYtRDaRREV~PPI~I 155 (223)
+++|-+||-+|.-+--++|
T Consensus 217 ~~~~idRdl~rTG~~iivI 235 (281)
T PF12257_consen 217 DKHYIDRDLRRTGQSIIVI 235 (281)
T ss_pred ccccccCcccccCceEEEE
Confidence 6899999999987765544
No 9
>PRK11020 hypothetical protein; Provisional
Probab=25.58 E-value=17 Score=30.15 Aligned_cols=18 Identities=39% Similarity=0.573 Sum_probs=16.0
Q ss_pred hhheeeccceEEEEEEEe
Q psy17946 189 SHVMTRVGREVKISVVTE 206 (223)
Q Consensus 189 ~~~~~~~~~~~~~~~~~~ 206 (223)
-|-||..|||..+.+||-
T Consensus 95 VHPMTaLGrEmgLk~mTG 112 (118)
T PRK11020 95 VHPMTALGREMGLKEMTG 112 (118)
T ss_pred ecCchHHHHHcCcceecc
Confidence 388999999999999984
No 10
>PF09127 Leuk-A4-hydro_C: Leukotriene A4 hydrolase, C-terminal; InterPro: IPR015211 This C-terminal domain is found in peptidases belonging to MEROPS peptidase family M1, particularly: aminopeptidase-1 of Caenorhabditis elegans, aminopeptidase O, aminopeptidase B and the bifunctional leukotriene A4 hydrolase/aminopeptidase. The domain adopts a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. It is required for the formation of a deep cleft harbouring the catalytic Zn2+ site in leukotriene A4 hydrolase []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0019370 leukotriene biosynthetic process; PDB: 3FUJ_A 3FU3_A 3FTX_A 3FTS_A 3B7R_L 2VJ8_A 3FTW_A 3FUF_A 3FU0_A 3CHO_A ....
Probab=25.52 E-value=42 Score=26.81 Aligned_cols=53 Identities=21% Similarity=0.473 Sum_probs=38.2
Q ss_pred hhhhhhhccCCcccchhhhhhhhccCcceeeccchhhhhh-------HHHHHHHHHHHhccc
Q psy17946 45 FFDLLKTKRGISKTKIERIDTLQNAGARTVVDNELIGRWY-------WHRLIARLARLLGTK 99 (223)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~fI~~LRdFL~GR 99 (223)
|.|-|-.+.-++..+++.+|..=+ -...-+.|+.=||| |.+.+..+.+||...
T Consensus 39 FL~~L~~~~~l~~~~l~~Ld~~y~--l~~s~NaEI~~rW~~l~i~~~~~~~~~~v~~fL~~~ 98 (143)
T PF09127_consen 39 FLDQLLEPKPLSPEKLQALDKVYK--LSNSKNAEIRFRWLRLAIKAKYEPALPQVEEFLGSQ 98 (143)
T ss_dssp HHHHHHTCCG-CHHHHHHHHHHHC--HCT-SSHHHHHHHHHHHHHTT-GGGHHHHHHHHHHS
T ss_pred HHHHhccCCCCCHHHHHHHHHHhC--CCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHc
Confidence 667774444599999999998763 33445789999998 678889999999644
No 11
>PF05456 eIF_4EBP: Eukaryotic translation initiation factor 4E binding protein (EIF4EBP); InterPro: IPR008606 This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1, -2 and -3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F [].; GO: 0008190 eukaryotic initiation factor 4E binding, 0045947 negative regulation of translational initiation; PDB: 2JGB_B 2V8Y_F 1WKW_B 3HXG_C 3U7X_D 3M94_C 3M93_C 2V8X_B 3HXI_C 2V8W_B ....
Probab=24.83 E-value=32 Score=27.94 Aligned_cols=28 Identities=36% Similarity=0.555 Sum_probs=7.4
Q ss_pred HHHHHHHHHhccccccccccCCCccCCCCCCCCCCCCC--CCCCC
Q psy17946 87 RLIARLARLLGTKRRYKVVVDNPLRFQDYNIVPRTQPL--PNLPE 129 (223)
Q Consensus 87 ~fI~~LRdFL~GRkh~ka~~kl~LRYaD~~IS~RTQPP--PnLP~ 129 (223)
|+| -=|+||+-.|+ .+ .+||+|. |+||+
T Consensus 47 RII-YdR~FLL~~Rn-----------SP---lSrTPP~~Lp~IPg 76 (116)
T PF05456_consen 47 RII-YDRKFLLECRN-----------SP---LSRTPPRNLPNIPG 76 (116)
T ss_dssp ------HHHHHCTCG------------------------------
T ss_pred EEE-EeHHHHHHhcC-----------CC---cccCCCCccCCCCc
Confidence 444 34889988876 23 5677775 66664
Done!