Query 046046
Match_columns 177
No_of_seqs 129 out of 230
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 08:12:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046046.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046046hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2873 Ubiquinol cytochrome c 100.0 1.1E-29 2.3E-34 219.9 7.6 169 3-177 2-186 (284)
2 COG5452 Uncharacterized conser 99.9 4.1E-24 8.9E-29 173.6 9.5 88 90-177 3-91 (180)
3 PF03981 Ubiq_cyt_C_chap: Ubiq 99.8 1.2E-18 2.6E-23 134.7 6.8 57 121-177 1-57 (141)
4 PF10660 MitoNEET_N: Iron-cont 64.1 2.2 4.9E-05 30.2 0.0 22 116-137 12-33 (64)
5 PF11711 Tim54: Inner membrane 28.3 50 0.0011 30.7 2.7 43 73-115 287-329 (382)
6 PF04918 DltD_M: DltD central 22.4 85 0.0018 25.2 2.7 48 116-165 32-80 (163)
7 PF06812 ImpA-rel_N: ImpA-rela 19.8 1.2E+02 0.0025 20.5 2.6 33 137-169 21-57 (62)
8 TIGR03363 VI_chp_8 type VI sec 14.4 2E+02 0.0043 25.9 3.5 34 136-169 72-109 (353)
9 PF06761 IcmF-related: Intrace 14.0 7.3E+02 0.016 21.5 6.8 72 101-172 156-266 (312)
10 PF13268 DUF4059: Protein of u 13.7 5.3E+02 0.012 18.8 5.2 37 133-169 19-55 (72)
No 1
>KOG2873 consensus Ubiquinol cytochrome c reductase assembly protein CBP3 [Energy production and conversion]
Probab=99.96 E-value=1.1e-29 Score=219.91 Aligned_cols=169 Identities=41% Similarity=0.602 Sum_probs=134.6
Q ss_pred chHHHhhhhhccccccchhhhhhhhHHHHHHhhhcccCC----CC-CCCc-----c-----chhccchhhhccccccccC
Q 046046 3 PRWSRAVRSLNSITQRNDFHAISRQSYAMATAAAASVEP----AP-RPTK-----Q-----LVVSLDKMFWSKPASLALA 67 (177)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-~~~~-----~-----~~~~l~~~~~~kp~sl~~~ 67 (177)
+|..|.+....++.+ +.+...+......+. ..|.+++ .| .-+. . -.+++++++|+.|||++..
T Consensus 2 s~~~~v~~~~~~~~~-tp~~s~~~y~~~t~~-~~~~p~~~l~~spc~~~~~~pV~e~q~~~l~~~~d~~k~~~P~~~~~~ 79 (284)
T KOG2873|consen 2 SRLRRVLRLTPKLRR-TPVGSMKIYSHFTRY-FGASPSPLLNSSPCECSGLTPVFEPQNLPLSVNLDSMKWSPPCSLAAK 79 (284)
T ss_pred chhHHhhccCcceee-ccccccccccccccc-ccCCChhhhccCccccccCCcccccccccccccccccccCCCcchhhc
Confidence 567777888888887 555555554444344 2222210 01 0000 1 1247889999999999999
Q ss_pred CCCCCCCCCcchhhhHHHHHHHHhhhcccchhhhhHHHHHHHHHHhccchhhhhhcCCCCchhhHHHHHHHHHHHHHHHH
Q 046046 68 PDSPLRVDEPKYEGIKHFILKLMLFYSKQSKSIRGANVIYKRVVSQVDKPAIYDVFNLEKTFRMTFSLLVLHMWFCLRRL 147 (177)
Q Consensus 68 ~~S~~~~~ep~~~g~~~~i~kl~g~~~k~s~~~raa~~LY~~ivaqar~p~fY~~~glPDTF~gwF~m~~LHvWLllvRL 147 (177)
.+.+.+.-||...|++.++....-+|.. .+++..+|..|+++.+.+.||++|+|||||++||+||+||+|||++||
T Consensus 80 ~~~~~ri~~~d~~gf~~~~~~~s~~y~~----~~as~~~y~~~~~~~df~~fy~~f~Lp~TF~sWf~iT~LH~W~ll~Rl 155 (284)
T KOG2873|consen 80 GGLPLRIDEPDKVGFRRFILTGSMKYKI----QSASIQIYKDCIAQVDFEAFYEDFNLPDTFSSWFQITVLHVWLLLMRL 155 (284)
T ss_pred cCceeeeccccccceeeccchhHHHHHH----HHHHHHHHhhhhhhccHHHHHHHcCCchHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999987766665533 445557999999999999999999999999999999999999999999
Q ss_pred hhcCc-hhhHHHHHHHHHHHHHHHHHHHhcC
Q 046046 148 KEEGK-EGVELGQYLYGIYNHDVELRVSKAG 177 (177)
Q Consensus 148 Raeg~-~G~~l~Q~L~D~ff~DmE~RlRe~G 177 (177)
|+||. +|+.++|.|++.||+|||.|++++|
T Consensus 156 ~~eg~~~g~~l~q~lv~~mw~DvelR~~k~g 186 (284)
T KOG2873|consen 156 KAEGQGEGVDLQQYLVERMWEDVELRLSKAG 186 (284)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99998 8999999999999999999999987
No 2
>COG5452 Uncharacterized conserved protein [Function unknown]
Probab=99.91 E-value=4.1e-24 Score=173.65 Aligned_cols=88 Identities=25% Similarity=0.437 Sum_probs=81.6
Q ss_pred Hhhhcccc-hhhhhHHHHHHHHHHhccchhhhhhcCCCCchhhHHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHH
Q 046046 90 MLFYSKQS-KSIRGANVIYKRVVSQVDKPAIYDVFNLEKTFRMTFSLLVLHMWFCLRRLKEEGKEGVELGQYLYGIYNHD 168 (177)
Q Consensus 90 ~g~~~k~s-~~~raa~~LY~~ivaqar~p~fY~~~glPDTF~gwF~m~~LHvWLllvRLRaeg~~G~~l~Q~L~D~ff~D 168 (177)
++.|.|++ .+..++.+||..+|+++|+|.||.++|||||..|||+|+.|||.++++|+|.+|+.+.+++|+|+|.||.|
T Consensus 3 ~~lf~k~~~an~Ai~krlYa~~vaaARq~~fY~d~~VpDt~~GRfEmlSlh~il~~~R~kg~g~a~qeiaQei~Daff~d 82 (180)
T COG5452 3 LDLFLKKRPANLAIVKRLYASIVAAARQPAFYRDLGVPDTPLGRFEMLSLHMILYFHRLKGEGEAAQEIAQEIVDAFFKD 82 (180)
T ss_pred hHHhcCCCchhHHHHHHHHHHHHHHHhchhHHHhcCCCCCcchHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhh
Confidence 45555666 45567788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcC
Q 046046 169 VELRVSKAG 177 (177)
Q Consensus 169 mE~RlRe~G 177 (177)
+|+.+||+|
T Consensus 83 vDhs~RElG 91 (180)
T COG5452 83 VDHSLRELG 91 (180)
T ss_pred hhHHHHHhC
Confidence 999999998
No 3
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=99.76 E-value=1.2e-18 Score=134.73 Aligned_cols=57 Identities=44% Similarity=0.775 Sum_probs=55.4
Q ss_pred hhcCCCCchhhHHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHHHHHhcC
Q 046046 121 DVFNLEKTFRMTFSLLVLHMWFCLRRLKEEGKEGVELGQYLYGIYNHDVELRVSKAG 177 (177)
Q Consensus 121 ~~~glPDTF~gwF~m~~LHvWLllvRLRaeg~~G~~l~Q~L~D~ff~DmE~RlRe~G 177 (177)
++||+||||++||+++.||+||+++|||+++++|+.+.|.|+|.||+|+|.|||++|
T Consensus 1 ~~~~~~dt~~~~f~~~~lh~~l~~~RLk~~~~~~~~~~q~l~~~~~~d~~~~l~~~g 57 (141)
T PF03981_consen 1 EHFGVPDTFAGRFQMLGLHVWLVLRRLKAEGKEGKELEQALFDKFFEDMDERLREMG 57 (141)
T ss_pred CCCCCccCHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 579999999999999999999999999999988999999999999999999999987
No 4
>PF10660 MitoNEET_N: Iron-containing outer mitochondrial membrane protein N-terminus ; InterPro: IPR019610 The CDGSH iron sulphur domain are a group of iron-sulphur (Fe-S) clusters and a unique 39 amino acid CDGSH domain [C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H]. The CDGSH iron sulphur domain protein (also referred to as mitoNEET) is an integral membrane protein located in the outer mitochondrial membrane and whose function may be to transport iron into the mitochondria []. Iron in turn is essential for the function of several mitochondrial enzymes. This entry represents the N-terminal of the mitoNEET and Miner-type proteins that carry a CDGSH-type cluster-binding domain (IPR018967 from INTERPRO) that coordinate a redox-active 2Fe-2S cluster. In the outer mitochondrian membrane (OMM), the CDGSH 2Fe-2S-containing domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by the N-terminal domain found in higher vertebrates [, , ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM.; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 2R13_A 3REE_A 2QD0_B.
Probab=64.06 E-value=2.2 Score=30.24 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=0.0
Q ss_pred chhhhhhcCCCCchhhHHHHHH
Q 046046 116 KPAIYDVFNLEKTFRMTFSLLV 137 (177)
Q Consensus 116 ~p~fY~~~glPDTF~gwF~m~~ 137 (177)
-|.+-+.+-+||||.|||.+..
T Consensus 12 lP~YL~~lPiP~s~gg~f~Ls~ 33 (64)
T PF10660_consen 12 LPNYLKSLPIPDSFGGFFKLSV 33 (64)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccH
Confidence 4788889999999999999654
No 5
>PF11711 Tim54: Inner membrane protein import complex subunit Tim54; InterPro: IPR021056 Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targeting information, into the inner membrane [].
Probab=28.29 E-value=50 Score=30.68 Aligned_cols=43 Identities=12% Similarity=0.140 Sum_probs=36.2
Q ss_pred CCCCcchhhhHHHHHHHHhhhcccchhhhhHHHHHHHHHHhcc
Q 046046 73 RVDEPKYEGIKHFILKLMLFYSKQSKSIRGANVIYKRVVSQVD 115 (177)
Q Consensus 73 ~~~ep~~~g~~~~i~kl~g~~~k~s~~~raa~~LY~~ivaqar 115 (177)
.+.-|...||.++=.+|..||+++......++..+..|.+++|
T Consensus 287 ~ipfp~llGF~n~P~RiyRFfnrR~~ad~~g~~~aaiVl~~~R 329 (382)
T PF11711_consen 287 PIPFPHLLGFLNTPRRIYRFFNRRYLADDIGEEVAAIVLAQTR 329 (382)
T ss_pred EecCcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhhCCc
Confidence 5566667899999999999999988888889888888888844
No 6
>PF04918 DltD_M: DltD central region; InterPro: IPR007002 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the central region of DltD.; PDB: 3BMA_C.
Probab=22.36 E-value=85 Score=25.18 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=27.5
Q ss_pred chhhhhhcCCC-CchhhHHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHH
Q 046046 116 KPAIYDVFNLE-KTFRMTFSLLVLHMWFCLRRLKEEGKEGVELGQYLYGIY 165 (177)
Q Consensus 116 ~p~fY~~~glP-DTF~gwF~m~~LHvWLllvRLRaeg~~G~~l~Q~L~D~f 165 (177)
.|.||..-|+. +.|.++|.-+.+--||.--.+..+ .-+.+++.|.+.-
T Consensus 32 SPQWF~k~G~~~~aF~~~fS~~q~~~fl~n~~is~~--~k~~~AkRlL~~~ 80 (163)
T PF04918_consen 32 SPQWFTKKGVDPDAFQSYFSPLQAYNFLFNPKISDE--TKRYAAKRLLELP 80 (163)
T ss_dssp -GGG--TT-S-HHHHHHH--HHHHHHHHHH---SSH--HHHHHHHHHHHH-
T ss_pred CCcccCCCCcCHHHHHHhcCHHHHHHHHHCCCCCcH--HHHHHHHHHHhhc
Confidence 48999999975 899999999888888876554443 2356676666544
No 7
>PF06812 ImpA-rel_N: ImpA-related N-terminal; InterPro: IPR010657 This entry represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans []. Note that many members are hypothetical proteins.
Probab=19.76 E-value=1.2e+02 Score=20.45 Aligned_cols=33 Identities=27% Similarity=0.391 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhhcCch----hhHHHHHHHHHHHHHH
Q 046046 137 VLHMWFCLRRLKEEGKE----GVELGQYLYGIYNHDV 169 (177)
Q Consensus 137 ~LHvWLllvRLRaeg~~----G~~l~Q~L~D~ff~Dm 169 (177)
.+=+|++.-+++.+|-+ |-.+-..+++.||+++
T Consensus 21 rv~~~l~~a~~~~~g~~gl~~gl~ll~~ll~~~W~~l 57 (62)
T PF06812_consen 21 RVAVWLTEALLRLEGLAGLAEGLELLADLLENYWDSL 57 (62)
T ss_pred HHHHHHHHHHHHccChhHHHHHHHHHHHHHHHCCccc
Confidence 45578888888888754 5567788888888764
No 8
>TIGR03363 VI_chp_8 type VI secretion-associated protein, ImpA family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
Probab=14.41 E-value=2e+02 Score=25.91 Aligned_cols=34 Identities=32% Similarity=0.432 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhhcCc----hhhHHHHHHHHHHHHHH
Q 046046 136 LVLHMWFCLRRLKEEGK----EGVELGQYLYGIYNHDV 169 (177)
Q Consensus 136 ~~LHvWLllvRLRaeg~----~G~~l~Q~L~D~ff~Dm 169 (177)
+.+=+|++.-+++.+|- .|-.+-..+++.||+++
T Consensus 72 Lrv~~~l~~a~~~~~Gl~Gl~~gl~ll~~ll~~~Wd~l 109 (353)
T TIGR03363 72 LRLAAWLTEAWLQLRGLPGLADGLALVAGLLERYWDDV 109 (353)
T ss_pred HHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHcchhc
Confidence 45667888888888874 46778899999999654
No 9
>PF06761 IcmF-related: Intracellular multiplication and human macrophage-killing; InterPro: IPR009612 This entry represents a conserved region within several bacterial proteins that resemble ImcF, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation, resulting in increased adherence to epithelial cells and increased conjugation frequency. Note that many entry members are hypothetical proteins.
Probab=14.01 E-value=7.3e+02 Score=21.45 Aligned_cols=72 Identities=15% Similarity=0.100 Sum_probs=51.2
Q ss_pred hhHHHHHHHHHHhc--c-ch--------------hhhhhcC------CC--CchhhHHHHHHHHHHHHHHHHhhcC----
Q 046046 101 RGANVIYKRVVSQV--D-KP--------------AIYDVFN------LE--KTFRMTFSLLVLHMWFCLRRLKEEG---- 151 (177)
Q Consensus 101 raa~~LY~~ivaqa--r-~p--------------~fY~~~g------lP--DTF~gwF~m~~LHvWLllvRLRaeg---- 151 (177)
..++++|..+..++ . .| .|...-| || =|.+||.+++.=.+=-+...+..|.
T Consensus 156 ~~~~rvY~~l~~~~~~~~~~~~~L~~~~G~~~~~vf~~~s~~~l~~~Ipg~yT~~G~~~~~~~~~~~~~~~~~~e~~WVl 235 (312)
T PF06761_consen 156 PLAERVYQRLKAEAEAERLPPFTLADALGPSAAQVFTRKSGKPLSDGIPGLYTRQGFEDYFLPALPKLAEALRSEDDWVL 235 (312)
T ss_pred CchhHHHHHHHHHHhhcccCCCcHHHHhChhhhheeecCCCcccccCCChhhhHHHHHHHHHHHHHHHHHHHhhccCccc
Confidence 45678999998875 2 11 3333333 77 4669999999888888888887776
Q ss_pred ----------chhhHHHHHHHHHHHHHHHHH
Q 046046 152 ----------KEGVELGQYLYGIYNHDVELR 172 (177)
Q Consensus 152 ----------~~G~~l~Q~L~D~ff~DmE~R 172 (177)
.+...+.++|-..++.|--..
T Consensus 236 g~~~~~~~~~~~~~~L~~~v~~~Y~~DY~~~ 266 (312)
T PF06761_consen 236 GDSEDSDASEADLEQLRQDVRKLYFQDYIAA 266 (312)
T ss_pred CCCCCCCcccccHHHHHHHHHHHHHHHHHHH
Confidence 124568899999998886543
No 10
>PF13268 DUF4059: Protein of unknown function (DUF4059)
Probab=13.65 E-value=5.3e+02 Score=18.79 Aligned_cols=37 Identities=27% Similarity=0.521 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHH
Q 046046 133 FSLLVLHMWFCLRRLKEEGKEGVELGQYLYGIYNHDV 169 (177)
Q Consensus 133 F~m~~LHvWLllvRLRaeg~~G~~l~Q~L~D~ff~Dm 169 (177)
+-++..-+|...+.+|.-++..++=+..|||..--|+
T Consensus 19 ~V~~~~~~wi~~Ra~~~~DKT~~eRQa~LyD~lmi~I 55 (72)
T PF13268_consen 19 LVLLVSGIWILWRALRKKDKTAKERQAFLYDMLMIAI 55 (72)
T ss_pred HHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHH
Confidence 3455667899999999998888888889999876553
Done!