Query psy16530
Match_columns 81
No_of_seqs 111 out of 337
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 23:39:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16530hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3382|consensus 100.0 4.6E-36 1E-40 205.7 3.1 79 3-81 65-147 (151)
2 PLN03095 NADH:ubiquinone oxido 100.0 4.9E-35 1.1E-39 195.6 6.5 79 2-81 27-115 (115)
3 PRK08183 NADH dehydrogenase; V 100.0 2.3E-34 4.9E-39 196.4 6.3 76 4-81 48-132 (133)
4 PLN02732 Probable NADH dehydro 100.0 2.1E-33 4.5E-38 196.3 6.5 80 2-81 67-156 (159)
5 COG3761 NADH:ubiquinone oxidor 100.0 9.6E-31 2.1E-35 173.2 5.0 77 3-81 32-118 (118)
6 PF05071 NDUFA12: NADH ubiquin 100.0 3.8E-30 8.3E-35 168.6 2.9 77 2-80 19-105 (105)
7 PRK06630 hypothetical protein; 99.9 2.4E-22 5.1E-27 131.3 3.9 47 5-55 35-81 (99)
8 PF11820 DUF3339: Protein of u 61.7 3.1 6.7E-05 25.7 0.3 16 3-18 24-39 (68)
9 KOG3731|consensus 38.5 17 0.00037 30.1 1.2 21 16-36 138-158 (541)
10 KOG3265|consensus 37.6 22 0.00048 26.9 1.6 19 6-25 68-86 (250)
11 PRK09177 xanthine-guanine phos 30.7 34 0.00074 23.3 1.6 17 8-25 135-151 (156)
12 PF10743 Phage_Cox: Regulatory 28.1 21 0.00045 23.0 0.1 12 21-32 71-86 (87)
13 PF04017 DUF366: Domain of unk 26.0 30 0.00065 25.1 0.6 13 16-28 10-22 (183)
14 KOG3879|consensus 25.6 58 0.0013 24.8 2.1 48 31-81 216-267 (267)
15 COG2029 Uncharacterized conser 24.2 23 0.0005 25.7 -0.2 13 16-28 13-25 (189)
No 1
>KOG3382|consensus
Probab=100.00 E-value=4.6e-36 Score=205.66 Aligned_cols=79 Identities=47% Similarity=0.879 Sum_probs=74.8
Q ss_pred CcCCccceEEcCC---cCCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCcCCCCC-CCCccccCCCCcCccccC
Q psy16530 3 ESWDQQRFCLESL---FTISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHTENFSG-SNKQYVPYSSTRTKIEAW 78 (81)
Q Consensus 3 e~~gr~RwV~y~~---~~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~~N~TG-T~~aY~P~~t~~~k~~~W 78 (81)
-++||||||+|+. +||||||||||||+|||+|+|+||++..+++.++|..+|.+|+|| |..+|+||+|++.||++|
T Consensus 65 ~fygRhRWVeya~kv~~Dyd~S~VP~EWh~WlH~iTD~~p~~~~~~~~~k~i~eHkeN~Sg~t~e~y~Pystt~tkiq~W 144 (151)
T KOG3382|consen 65 YFYGRHRWVEYASKVNWDYDASQVPAEWHGWLHFITDDPPDEKLPLPPKKWILEHKENFSGETGETYVPYSTTRTKIQSW 144 (151)
T ss_pred eecccceeEEecccccccccccCCCHHHHhHhHhhccCCccccCCCCHHHHhHhccccccccCCceeccCcCChhHhhee
Confidence 4789999999986 889999999999999999999999998658999999999999999 999999999999999999
Q ss_pred CCC
Q psy16530 79 KPK 81 (81)
Q Consensus 79 ~P~ 81 (81)
.|.
T Consensus 145 ~P~ 147 (151)
T KOG3382|consen 145 VPT 147 (151)
T ss_pred cCC
Confidence 984
No 2
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=100.00 E-value=4.9e-35 Score=195.62 Aligned_cols=79 Identities=23% Similarity=0.409 Sum_probs=71.5
Q ss_pred CCcCCccceEEcCC-cCCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCcCCCC--CCCCccccCCCC-------
Q psy16530 2 EESWDQQRFCLESL-FTISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHTENFS--GSNKQYVPYSST------- 71 (81)
Q Consensus 2 ~e~~gr~RwV~y~~-~~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~~N~T--GT~~aY~P~~t~------- 71 (81)
+++.||+|||+|++ .+||+|+||||||+||||++|+||+..+ +..+.|+++|++||| ||..||+|.|++
T Consensus 27 ~~~~~rrRWV~Y~~~~d~d~S~VPpeWH~WLh~~~d~pPt~~~-~~~~~w~~~H~~NlT~tGT~~aY~P~Gs~~~~~~~~ 105 (115)
T PLN03095 27 SYQSGRHRWVEYADKDDYNASNIPPEWHGWLHYVNDEPGELED-RTAPRYQLEFIAGGTTTGTQYMYHPKGHFLSKRPRN 105 (115)
T ss_pred CCCCCCeEEEEeCCCccCCccccCchHhHhhccCcCCCCCccc-cCCCccccCCCCCcCCCCCccceeCCCccccCCCCc
Confidence 34578999999998 5899999999999999999999999876 778899999999999 899999999987
Q ss_pred cCccccCCCC
Q psy16530 72 RTKIEAWKPK 81 (81)
Q Consensus 72 ~~k~~~W~P~ 81 (81)
..+|+||+|.
T Consensus 106 ~~dY~aW~P~ 115 (115)
T PLN03095 106 WKRYTPWSPP 115 (115)
T ss_pred ccCccCCCCC
Confidence 3489999995
No 3
>PRK08183 NADH dehydrogenase; Validated
Probab=100.00 E-value=2.3e-34 Score=196.39 Aligned_cols=76 Identities=30% Similarity=0.654 Sum_probs=69.7
Q ss_pred cCCccceEEcCCcCCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCcCCCCCCCCccccCCCC---------cCc
Q psy16530 4 SWDQQRFCLESLFTISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHTENFSGSNKQYVPYSST---------RTK 74 (81)
Q Consensus 4 ~~gr~RwV~y~~~~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~~N~TGT~~aY~P~~t~---------~~k 74 (81)
+.+|+|||+|++ ++|+|+||||||+||||++|+||++++ +..++|+++|++|||||++||+|+|++ +.+
T Consensus 48 ~~~~rRWV~Y~~-~~d~s~IPpeWh~WLh~~~d~pPt~~~-~~~~~w~~~H~~N~TGT~~aY~P~G~~~~~~~r~~~~~d 125 (133)
T PRK08183 48 DGRERRWVIYNG-YAEASRIPPEWHGWLHHTVDVPPTKEP-YPPREWEKPHQPNLTGTPLAYRPKGSILRGGERPRATGD 125 (133)
T ss_pred CCCceEEEEeCC-CCCccccCchHHhhhccCcCCCCCccc-cCCCccccCCCCCCCCCccceeCCCccccCCcCCcccCC
Confidence 456799999998 799999999999999999999999887 678899999999999999999999986 247
Q ss_pred cccCCCC
Q psy16530 75 IEAWKPK 81 (81)
Q Consensus 75 ~~~W~P~ 81 (81)
|+||+|+
T Consensus 126 Y~aW~P~ 132 (133)
T PRK08183 126 YDAWTPG 132 (133)
T ss_pred cccCCCC
Confidence 9999995
No 4
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=100.00 E-value=2.1e-33 Score=196.29 Aligned_cols=80 Identities=33% Similarity=0.543 Sum_probs=69.8
Q ss_pred CCcCCccceEEcCC-cCCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCcCCCCCCC--CccccCCCC-------
Q psy16530 2 EESWDQQRFCLESL-FTISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHTENFSGSN--KQYVPYSST------- 71 (81)
Q Consensus 2 ~e~~gr~RwV~y~~-~~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~~N~TGT~--~aY~P~~t~------- 71 (81)
+++.||+|||+|++ .++|||+||||||+||||++|+||++.....++.|+++|++|||||+ .||+|.|++
T Consensus 67 ~~~~grrRWV~Y~~~~~~daS~VPpeWH~WLH~~~D~pP~~~~~~~~~~w~~~H~pNlTGT~~~~ay~p~Gs~~~~g~~~ 146 (159)
T PLN02732 67 DTQYGRHRWVEYAEKSRYNASQVPAEWHGWLHFITDHTGDELLMLKPKRYGLEHKENFSGEGEEYIYHSKGHTLNPGQKD 146 (159)
T ss_pred CCCCCceeEEEeCCCccCCcCcCCchhhhhhccccCCCCccccccCCCccccCCCCCcCCCCCCceECCCcccccCCCCc
Confidence 35689999999998 57999999999999999999999987442567889999999999997 788888876
Q ss_pred cCccccCCCC
Q psy16530 72 RTKIEAWKPK 81 (81)
Q Consensus 72 ~~k~~~W~P~ 81 (81)
+.+|+||+|+
T Consensus 147 ~~dYeaW~P~ 156 (159)
T PLN02732 147 WTRYQSWQPT 156 (159)
T ss_pred ccCccCCCCC
Confidence 2479999995
No 5
>COG3761 NADH:ubiquinone oxidoreductase 17.2 kD subunit [Energy production and conversion]
Probab=99.96 E-value=9.6e-31 Score=173.21 Aligned_cols=77 Identities=29% Similarity=0.598 Sum_probs=70.4
Q ss_pred CcCCc-cceEEcCCcCCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCcCCCCCCCCccccCCCC-----cC---
Q psy16530 3 ESWDQ-QRFCLESLFTISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHTENFSGSNKQYVPYSST-----RT--- 73 (81)
Q Consensus 3 e~~gr-~RwV~y~~~~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~~N~TGT~~aY~P~~t~-----~~--- 73 (81)
.+.|| +|||+|++ ..+||+|||+|||||||.+|++|.... +.++.|||+|.+|+|||..||+|.|++ ||
T Consensus 32 ds~gr~RRwVIYng-yaEas~IPp~WhgWlHh~vd~~P~~~~-~~~reWqKph~pn~tgt~~a~rPkgs~~~~gerp~~t 109 (118)
T COG3761 32 DSEGRTRRWVIYNG-YAEASKIPPGWHGWLHHRVDEPPKSEQ-LFPREWQKPHLPNLTGTPHAYRPKGSLARAGERPRVT 109 (118)
T ss_pred ccCCCeeeEEEEcC-cchhccCCCchhhhhhhhccCCccccc-cchhhhccccccCCCCCcceeccCccccccCcCcccc
Confidence 35676 89999999 489999999999999999999999988 889999999999999999999999997 33
Q ss_pred -ccccCCCC
Q psy16530 74 -KIEAWKPK 81 (81)
Q Consensus 74 -k~~~W~P~ 81 (81)
||.+|+|.
T Consensus 110 ~dYdaWtP~ 118 (118)
T COG3761 110 GDYDAWTPG 118 (118)
T ss_pred ccccccCCC
Confidence 89999995
No 6
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 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 entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=99.96 E-value=3.8e-30 Score=168.60 Aligned_cols=77 Identities=30% Similarity=0.630 Sum_probs=70.0
Q ss_pred CCcCCccceEEcCCc-CCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCcCCCCCCCCccccCCCCcC-------
Q psy16530 2 EESWDQQRFCLESLF-TISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHTENFSGSNKQYVPYSSTRT------- 73 (81)
Q Consensus 2 ~e~~gr~RwV~y~~~-~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~~N~TGT~~aY~P~~t~~~------- 73 (81)
.+..+++|||+|++. +||+|+||||||+||||++|+||+.+. +....|+++|++|+|||.+||+|+++ ++
T Consensus 19 ~~~~~~rRwV~y~~~~~~~~s~IPpeWh~WL~~~r~~pPt~~~-~~~~~~~~~~~~n~t~~~~ay~p~~~-~~~~~~~~~ 96 (105)
T PF05071_consen 19 DEQGRRRRWVEYAGKSDYDPSQIPPEWHAWLHHTRDEPPTEEE-LARRQWQKPHKPNLTGTEEAYRPKGT-KSKEREQRN 96 (105)
T ss_pred CCcCCCcEEEEcCCccccCcCccCcchHHHhccCcCCCCCccc-cchHHHHHHhhhhhhcChHhhcCCCc-ccccccccc
Confidence 355689999999984 789999999999999999999999777 67889999999999999999999998 55
Q ss_pred --ccccCCC
Q psy16530 74 --KIEAWKP 80 (81)
Q Consensus 74 --k~~~W~P 80 (81)
||+||+|
T Consensus 97 ~~~y~~W~P 105 (105)
T PF05071_consen 97 WKKYEAWTP 105 (105)
T ss_pred cCCccCCCC
Confidence 5999998
No 7
>PRK06630 hypothetical protein; Provisional
Probab=99.86 E-value=2.4e-22 Score=131.30 Aligned_cols=47 Identities=19% Similarity=0.504 Sum_probs=41.7
Q ss_pred CCccceEEcCCcCCCCCccCccchhhhccccCCCCCCCCCCCCCCcccCCc
Q psy16530 5 WDQQRFCLESLFTISGSLVPAEWYGWLHYKTDYLPHEDPGRPKYKWMAEHT 55 (81)
Q Consensus 5 ~gr~RwV~y~~~~~daS~IPPeWH~WLH~~~D~~P~~~~~~~~~~w~~~h~ 55 (81)
.+++|||+|++ .+|||+|||||||||||++|++|++ ...+.||++..
T Consensus 35 gr~rRWViY~g-~~daS~VPpeWHgWLHh~~D~pPt~---~~~k~WqKp~~ 81 (99)
T PRK06630 35 GRPRRFVIYKN-VNEPTKIPPSWHAWLHHLVNEIPKN---IQLFPWQKNNK 81 (99)
T ss_pred CCceEEEEeCC-CCccccCCcchhhhhccccCCCCCC---CCCccccCcch
Confidence 44589999999 7999999999999999999999984 56999998754
No 8
>PF11820 DUF3339: Protein of unknown function (DUF3339); InterPro: IPR021775 This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length.
Probab=61.71 E-value=3.1 Score=25.72 Aligned_cols=16 Identities=6% Similarity=-0.168 Sum_probs=13.2
Q ss_pred CcCCccceEEcCCcCC
Q psy16530 3 ESWDQQRFCLESLFTI 18 (81)
Q Consensus 3 e~~gr~RwV~y~~~~~ 18 (81)
+++|++|.||+.+..-
T Consensus 24 qlPG~~r~veFgn~~T 39 (68)
T PF11820_consen 24 QLPGRGRVVEFGNMKT 39 (68)
T ss_pred EecCCCceEEEcCCcc
Confidence 5789999999998543
No 9
>KOG3731|consensus
Probab=38.46 E-value=17 Score=30.10 Aligned_cols=21 Identities=24% Similarity=0.624 Sum_probs=17.5
Q ss_pred cCCCCCccCccchhhhccccC
Q psy16530 16 FTISGSLVPAEWYGWLHYKTD 36 (81)
Q Consensus 16 ~~~daS~IPPeWH~WLH~~~D 36 (81)
..|++|-|||+|-.|..-+.+
T Consensus 138 ney~gsyiPpgW~ew~~l~kn 158 (541)
T KOG3731|consen 138 NEYNGSYIPPGWSEWAGLIKN 158 (541)
T ss_pred cccCcccCCCCchhhhccccc
Confidence 579999999999999875543
No 10
>KOG3265|consensus
Probab=37.63 E-value=22 Score=26.86 Aligned_cols=19 Identities=16% Similarity=0.370 Sum_probs=16.5
Q ss_pred CccceEEcCCcCCCCCccCc
Q psy16530 6 DQQRFCLESLFTISGSLVPA 25 (81)
Q Consensus 6 gr~RwV~y~~~~~daS~IPP 25 (81)
||++||.=++ -.|+|+||-
T Consensus 68 G~~~FVf~AD-~Pd~~kIP~ 86 (250)
T KOG3265|consen 68 GRHKFVFQAD-APDPSKIPE 86 (250)
T ss_pred cceEEEEecC-CCCcccCcc
Confidence 8999999888 599999984
No 11
>PRK09177 xanthine-guanine phosphoribosyltransferase; Validated
Probab=30.68 E-value=34 Score=23.27 Aligned_cols=17 Identities=12% Similarity=0.272 Sum_probs=13.9
Q ss_pred cceEEcCCcCCCCCccCc
Q psy16530 8 QRFCLESLFTISGSLVPA 25 (81)
Q Consensus 8 ~RwV~y~~~~~daS~IPP 25 (81)
-|||+|. |+.+.++|+|
T Consensus 135 ~~Wi~fp-we~~~~~~~~ 151 (156)
T PRK09177 135 DTWIEFP-WDMGLTFVPP 151 (156)
T ss_pred CCeEEeC-CCCCccccCc
Confidence 5899994 5788899887
No 12
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=28.07 E-value=21 Score=23.03 Aligned_cols=12 Identities=42% Similarity=0.905 Sum_probs=9.9
Q ss_pred CccCcc----chhhhc
Q psy16530 21 SLVPAE----WYGWLH 32 (81)
Q Consensus 21 S~IPPe----WH~WLH 32 (81)
-+-|+| ||.||.
T Consensus 71 ~~~P~E~rd~Wl~Wlg 86 (87)
T PF10743_consen 71 ENRPKEQRDAWLLWLG 86 (87)
T ss_pred HhCChHHHHHHHHhcc
Confidence 467999 999984
No 13
>PF04017 DUF366: Domain of unknown function (DUF366); InterPro: IPR007162 This is an archaeal family of unknown function.; PDB: 2DDZ_E.
Probab=25.96 E-value=30 Score=25.08 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=10.1
Q ss_pred cCCCCCccCccch
Q psy16530 16 FTISGSLVPAEWY 28 (81)
Q Consensus 16 ~~~daS~IPPeWH 28 (81)
.+||+|||.|-|-
T Consensus 10 i~YDGsqi~slWA 22 (183)
T PF04017_consen 10 IDYDGSQISSLWA 22 (183)
T ss_dssp --BSSGGGSTTHH
T ss_pred cCcChhhhhHHHH
Confidence 6899999999985
No 14
>KOG3879|consensus
Probab=25.56 E-value=58 Score=24.79 Aligned_cols=48 Identities=17% Similarity=0.171 Sum_probs=30.7
Q ss_pred hccccCCCCCCCCCCCC----CCcccCCcCCCCCCCCccccCCCCcCccccCCCC
Q psy16530 31 LHYKTDYLPHEDPGRPK----YKWMAEHTENFSGSNKQYVPYSSTRTKIEAWKPK 81 (81)
Q Consensus 31 LH~~~D~~P~~~~~~~~----~~w~~~h~~N~TGT~~aY~P~~t~~~k~~~W~P~ 81 (81)
+||-.+++-.+++.... ..+.+....-.||+++.|.+.- ||.+-|.|+
T Consensus 216 th~~d~e~~ee~~~~~~~~iaa~f~k~~r~~~~~s~g~~~~p~---p~~~i~~pd 267 (267)
T KOG3879|consen 216 THHEDNEPEEETEVPEEPKIAAEFRKKARVVITGSPGKYVSPP---PKLNIDMPD 267 (267)
T ss_pred cccccCCCCcccCCCCCcchhHHHhhhhhhhccCCCCCccCCC---CcccCCCCC
Confidence 67766665444442222 2344666678899999998765 777777663
No 15
>COG2029 Uncharacterized conserved protein [Function unknown]
Probab=24.17 E-value=23 Score=25.69 Aligned_cols=13 Identities=23% Similarity=0.624 Sum_probs=11.5
Q ss_pred cCCCCCccCccch
Q psy16530 16 FTISGSLVPAEWY 28 (81)
Q Consensus 16 ~~~daS~IPPeWH 28 (81)
.+||+|||.|-|-
T Consensus 13 ldYdGSqI~~~wA 25 (189)
T COG2029 13 LDYDGSQIRSAWA 25 (189)
T ss_pred ccCchhhhhhhHh
Confidence 6899999999884
Done!