Query psy15236
Match_columns 176
No_of_seqs 125 out of 148
Neff 4.8
Searched_HMMs 46136
Date Sat Aug 17 00:47:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05821 NDUF_B8: NADH-ubiquin 100.0 2.4E-69 5.2E-74 443.1 13.0 155 16-174 13-167 (179)
2 KOG4040|consensus 100.0 4.3E-61 9.4E-66 388.1 11.9 152 21-175 23-175 (186)
3 PF00446 GnRH: Gonadotropin-re 71.2 2.3 5E-05 20.0 0.8 9 29-37 2-10 (10)
4 PF05821 NDUF_B8: NADH-ubiquin 66.5 9.7 0.00021 31.7 4.2 46 124-173 121-179 (179)
5 PF06392 Asr: Acid shock prote 46.5 11 0.00025 20.6 0.9 12 41-52 8-19 (19)
6 PF13807 GNVR: G-rich domain o 38.3 61 0.0013 22.7 4.0 24 123-146 52-75 (82)
7 PHA02284 hypothetical protein 34.2 28 0.00061 29.9 1.9 43 10-60 89-133 (251)
8 PF14147 Spore_YhaL: Sporulati 29.7 65 0.0014 22.0 2.7 21 125-145 1-21 (52)
9 PF06166 DUF979: Protein of un 27.3 62 0.0014 29.3 3.0 24 32-55 67-91 (308)
10 PF01102 Glycophorin_A: Glycop 26.4 63 0.0014 25.4 2.6 15 129-143 65-79 (122)
11 smart00389 HOX Homeodomain. DN 26.2 74 0.0016 19.9 2.5 20 37-57 22-41 (56)
12 PF09098 Dehyd-heme_bind: Quin 26.2 48 0.001 27.6 2.0 24 40-63 50-77 (167)
13 PF14990 DUF4516: Domain of un 25.2 2.1E+02 0.0046 19.1 4.5 32 123-154 3-34 (47)
14 COG3817 Predicted membrane pro 24.4 71 0.0015 28.8 2.8 23 32-54 71-94 (313)
15 PF05920 Homeobox_KN: Homeobox 23.2 67 0.0015 20.2 1.8 21 36-57 7-27 (40)
16 cd00922 Cyt_c_Oxidase_IV Cytoc 22.3 1.5E+02 0.0033 23.4 4.1 35 126-163 73-107 (136)
17 COG5085 Predicted membrane pro 21.9 90 0.002 27.1 2.9 20 124-144 188-207 (230)
18 KOG4503|consensus 21.9 90 0.002 27.1 2.9 20 124-144 188-207 (230)
19 PF11821 DUF3341: Protein of u 21.1 1.3E+02 0.0028 24.8 3.6 34 102-143 37-70 (173)
20 PF11293 DUF3094: Protein of u 21.1 1.8E+02 0.0039 20.1 3.6 38 112-149 15-52 (55)
21 PF02936 COX4: Cytochrome c ox 20.8 98 0.0021 24.7 2.7 25 127-152 74-98 (142)
22 COG3765 WzzB Chain length dete 20.3 1.3E+02 0.0029 27.7 3.7 40 108-147 292-334 (347)
No 1
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 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 eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=100.00 E-value=2.4e-69 Score=443.05 Aligned_cols=155 Identities=35% Similarity=0.549 Sum_probs=147.2
Q ss_pred HHHhhhhhhccccCCCCCCCCCCCCCCHHHHHHHHHHcCCCCCCCccCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcCC
Q psy15236 16 VVSLQQNSVRTAFVYTPDWLPGERPKTEEERRKAAKKYNLLPEEYEVQPDDGFATGDYPHLPHTHYDSRDPFYPWDYPMF 95 (176)
Q Consensus 16 ~~~~~~~~~r~~~~~~~d~~P~~yP~t~eer~aaAkKY~~~~edY~p~~ddg~~~GDYP~lP~~s~q~RDPy~~WDdpq~ 95 (176)
...++.++||+|++|+|||+|||||||+|||+||||||||+||||+|++|||+++||||+||.+|+|+||||++|||||+
T Consensus 13 ~~~~~~~~~r~~~~~~kd~~PgpyP~t~eer~aaAkKY~l~pedY~P~pDDg~~~GDYP~lp~~s~q~RDPy~~WDdpq~ 92 (179)
T PF05821_consen 13 NPAVLPLGARTASGWNKDWKPGPYPKTPEERAAAAKKYGLRPEDYEPYPDDGMGYGDYPKLPDISQQERDPYYDWDDPQE 92 (179)
T ss_pred hhhhhhhhhhhhccCCccCCCCCCCCCHHHHHHHHHHcCCCHHHcCCCCCCCcccCCCCCCCccchhhcCCCCCcCChhh
Confidence 33456899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCccCccccCCCCCCCccccCHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCCCCCCCccccccc
Q psy15236 96 RTNYGEPLPNDFAISHYGMGFNEQPVNQRISVWEQLAYMVGILGTISLVLKYFCWEKRYYYPKFDSPKYQKGVVHYGYH 174 (176)
Q Consensus 96 RRNfgEPvH~~~d~Dm~~~dr~d~~~~~~~s~~~~l~~~~g~l~g~~~~~~~l~~~y~~~~Pv~prqYP~~GL~Hytfe 174 (176)
|||||||||+ |+|||++||+|++ ++.++|.+++.+|++|+ ||+++++||++++++++||+|||||+|||.|+++.
T Consensus 93 RRNfgEPvH~--d~Dm~s~dr~d~~-~~~~~w~~~~~~l~~fl-g~~~~~~~~~~~~~~~~P~~pKqYP~~gL~~e~gg 167 (179)
T PF05821_consen 93 RRNFGEPVHE--DFDMYSPDRYDTS-PTPVSWQSMLKQLFGFL-GFMLFMFYLGEMYPPYRPVMPKQYPYNGLYLELGG 167 (179)
T ss_pred hcCCCCCCcc--cccceeecccccC-CCcccHHHHHHHHHHHH-HHHHHHHHHhhhccCCCCCCcccCCCCCeecccCC
Confidence 9999999999 9999999999988 56778999999999999 99999999998999999999999999999998875
No 2
>KOG4040|consensus
Probab=100.00 E-value=4.3e-61 Score=388.12 Aligned_cols=152 Identities=34% Similarity=0.535 Sum_probs=143.0
Q ss_pred hhhhccccCCCCCCCCCCCCCCHHHHHHHHHHcCCCCCCCccCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcCCCCCCC
Q psy15236 21 QNSVRTAFVYTPDWLPGERPKTEEERRKAAKKYNLLPEEYEVQPDDGFATGDYPHLPHTHYDSRDPFYPWDYPMFRTNYG 100 (176)
Q Consensus 21 ~~~~r~~~~~~~d~~P~~yP~t~eer~aaAkKY~~~~edY~p~~ddg~~~GDYP~lP~~s~q~RDPy~~WDdpq~RRNfg 100 (176)
..++|++++|+||++|||||+|||||+||||||||+|||||||+|||+++||||+|+.+++++||||+.||+||+|||||
T Consensus 23 ~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEdY~py~dDg~gyGDYPkLg~~~~~~kDpyy~Wd~p~~rrNwg 102 (186)
T KOG4040|consen 23 PRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPEDYQPYDDDGVGYGDYPKLGVITYDHKDPYYAWDDPQNRRNWG 102 (186)
T ss_pred ccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhhcCcCCcCCcccCCCCcCcccccccCCCccccCChhhhcccC
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccCccccCCCCCCC-ccccCHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCCCCCCCcccccccc
Q psy15236 101 EPLPNDFAISHYGMGFNEQPV-NQRISVWEQLAYMVGILGTISLVLKYFCWEKRYYYPKFDSPKYQKGVVHYGYHQ 175 (176)
Q Consensus 101 EPvH~~~d~Dm~~~dr~d~~~-~~~~s~~~~l~~~~g~l~g~~~~~~~l~~~y~~~~Pv~prqYP~~GL~Hytfe~ 175 (176)
||||+ |+|+|+.||++..+ ++.++|..+|.+|+|+| .++++++|+...++.|+||+|||||++|+.||+|+.
T Consensus 103 Epv~~--d~d~Y~~dR~t~~e~p~y~~w~~~~mcl~g~~-~~~l~~~y~~d~~p~ykPv~pKQYpy~~~~~y~f~d 175 (186)
T KOG4040|consen 103 EPVPI--DMDRYRGDRFTGLEAPDYTTWNSIVMCLRGLV-PMALLAWYFTDEHPRYKPVMPKQYPYDFYRAYPFDD 175 (186)
T ss_pred CCcch--hHhhhccccccccCCCCcccHHHHHHHHHHHH-HHHHHHHHHcccccccccCCcccCCCCCeeeccCCC
Confidence 99999 99999999987643 66789999999999999 666667788889999999999999999999999984
No 3
>PF00446 GnRH: Gonadotropin-releasing hormone; InterPro: IPR002012 The gonadotropin-releasing hormones (GnRH) (gonadoliberin) [] are a family of peptides that play a pivotal role in reproduction. The main function of GnRH is to act on the pituitary to stimulate the synthesis and secretion of luteinizing and follicle-stimulating hormones, but GnRH also acts on the brain, retina, sympathetic nervous system, gonads and placenta in certain species. There seems to be at least three forms of GnRH. The second form is expressed in midbrain and seems to be widespread. The third form has only been found so far in fish. GnRH is a C-terminal amidated decapeptide processed from a larger precursor protein. Four of the ten residues are perfectly conserved in all species where GnRH has been sequenced.; GO: 0005179 hormone activity, 0007275 multicellular organismal development, 0005576 extracellular region
Probab=71.24 E-value=2.3 Score=19.98 Aligned_cols=9 Identities=33% Similarity=1.069 Sum_probs=8.0
Q ss_pred CCCCCCCCC
Q psy15236 29 VYTPDWLPG 37 (176)
Q Consensus 29 ~~~~d~~P~ 37 (176)
+|+.+|+||
T Consensus 2 HwS~~w~PG 10 (10)
T PF00446_consen 2 HWSHGWKPG 10 (10)
T ss_pred ccccccCCC
Confidence 699999997
No 4
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 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 eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=66.46 E-value=9.7 Score=31.68 Aligned_cols=46 Identities=22% Similarity=0.116 Sum_probs=28.1
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhhccccc-------------CCCCCCCCCCCCCcccccc
Q psy15236 124 RISVWEQLAYMVGILGTISLVLKYFCWEKRY-------------YYPKFDSPKYQKGVVHYGY 173 (176)
Q Consensus 124 ~~s~~~~l~~~~g~l~g~~~~~~~l~~~y~~-------------~~Pv~prqYP~~GL~Hytf 173 (176)
..+...+++.|+||+++++.++-... .+.+ +.-=-|+..| ++||+|
T Consensus 121 w~~~~~~l~~flg~~~~~~~~~~~~~-~~~P~~pKqYP~~gL~~e~ggdp~k~p---~~~y~~ 179 (179)
T PF05821_consen 121 WQSMLKQLFGFLGFMLFMFYLGEMYP-PYRPVMPKQYPYNGLYLELGGDPSKEP---VVHYEI 179 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcc-CCCCCCcccCCCCCeecccCCCCccCC---cCCccC
Confidence 33566689999999977666653322 1111 1223355666 899997
No 5
>PF06392 Asr: Acid shock protein repeat ; InterPro: IPR009435 The Asr protein is synthesised as a precursor and the cleavage is essential for moderate to high acid tolerance []. Enterobacteria have developed numerous constitutive and inducible strategies to sense and adapt to external acidity. These molecular responses require many specific acid shock proteins (ASPs) [].; GO: 0010447 response to acidity, 0042597 periplasmic space
Probab=46.53 E-value=11 Score=20.60 Aligned_cols=12 Identities=50% Similarity=0.661 Sum_probs=10.1
Q ss_pred CCHHHHHHHHHH
Q psy15236 41 KTEEERRKAAKK 52 (176)
Q Consensus 41 ~t~eer~aaAkK 52 (176)
+|.|.++.||||
T Consensus 8 ~~~eqkaqaakk 19 (19)
T PF06392_consen 8 KATEQKAQAAKK 19 (19)
T ss_pred ccHHHHHHHhcC
Confidence 578999999986
No 6
>PF13807 GNVR: G-rich domain on putative tyrosine kinase
Probab=38.27 E-value=61 Score=22.74 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=16.4
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHH
Q psy15236 123 QRISVWEQLAYMVGILGTISLVLK 146 (176)
Q Consensus 123 ~~~s~~~~l~~~~g~l~g~~~~~~ 146 (176)
.++++.+.+...+|+++|+++.+.
T Consensus 52 ~P~~P~~~lil~l~~~~Gl~lgi~ 75 (82)
T PF13807_consen 52 KPVSPKRALILALGLFLGLILGIG 75 (82)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 367777777777777777776443
No 7
>PHA02284 hypothetical protein
Probab=34.21 E-value=28 Score=29.93 Aligned_cols=43 Identities=30% Similarity=0.308 Sum_probs=30.8
Q ss_pred cchhhHHHHhhhhhhccccCCCCCCCCCCCCC-CHHHHHHHHHHcCCCC-CCC
Q psy15236 10 VKSLGKVVSLQQNSVRTAFVYTPDWLPGERPK-TEEERRKAAKKYNLLP-EEY 60 (176)
Q Consensus 10 ~~~~~~~~~~~~~~~r~~~~~~~d~~P~~yP~-t~eer~aaAkKY~~~~-edY 60 (176)
|.+-||+-||++.++- -.|.|||+ |+++.+.|.+-||..- |||
T Consensus 89 VDs~~K~~SLL~Q~~E--------L~~~~~~~~~~~~~K~~T~YYNF~~f~D~ 133 (251)
T PHA02284 89 VDSDRKYYSLLQQITE--------LSKDPFPKWVEDDAKGLTKYYNFQDFEDV 133 (251)
T ss_pred eccchhHHHHHHHHHH--------hCcccchhhhHHHHhhhhhhcccccHHHh
Confidence 4566899999988886 46789998 5556666666677654 444
No 8
>PF14147 Spore_YhaL: Sporulation protein YhaL
Probab=29.70 E-value=65 Score=21.99 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=13.8
Q ss_pred cCHHHHHHHHHHHHHHHHHHH
Q psy15236 125 ISVWEQLAYMVGILGTISLVL 145 (176)
Q Consensus 125 ~s~~~~l~~~~g~l~g~~~~~ 145 (176)
++||..+..++.++.|+|++-
T Consensus 1 ~PwWvY~vi~gI~~S~ym~v~ 21 (52)
T PF14147_consen 1 IPWWVYFVIAGIIFSGYMAVK 21 (52)
T ss_pred CcchHHHHHHHHHHHHHHHHH
Confidence 468877776666666666643
No 9
>PF06166 DUF979: Protein of unknown function (DUF979); InterPro: IPR009323 This family consists of several putative bacterial membrane proteins. The function of this family is unclear.
Probab=27.31 E-value=62 Score=29.33 Aligned_cols=24 Identities=29% Similarity=0.267 Sum_probs=19.0
Q ss_pred CCCCCCCCCC-CHHHHHHHHHHcCC
Q psy15236 32 PDWLPGERPK-TEEERRKAAKKYNL 55 (176)
Q Consensus 32 ~d~~P~~yP~-t~eer~aaAkKY~~ 55 (176)
+.-+.|.++. |+|||++.|||+|.
T Consensus 67 ~~v~~g~~~~~s~e~r~~~a~rlGn 91 (308)
T PF06166_consen 67 GQVGIGSYKEPSEEEREASAKRLGN 91 (308)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHhcC
Confidence 4466788877 67889999999994
No 10
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=26.36 E-value=63 Score=25.35 Aligned_cols=15 Identities=7% Similarity=0.270 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHH
Q psy15236 129 EQLAYMVGILGTISL 143 (176)
Q Consensus 129 ~~l~~~~g~l~g~~~ 143 (176)
.+..++||+|+|+.+
T Consensus 65 ~i~~Ii~gv~aGvIg 79 (122)
T PF01102_consen 65 AIIGIIFGVMAGVIG 79 (122)
T ss_dssp CHHHHHHHHHHHHHH
T ss_pred ceeehhHHHHHHHHH
Confidence 346666777766665
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=26.25 E-value=74 Score=19.90 Aligned_cols=20 Identities=35% Similarity=0.449 Sum_probs=16.4
Q ss_pred CCCCCCHHHHHHHHHHcCCCC
Q psy15236 37 GERPKTEEERRKAAKKYNLLP 57 (176)
Q Consensus 37 ~~yP~t~eer~aaAkKY~~~~ 57 (176)
.+|| |.+++..+|+..||..
T Consensus 22 ~~~P-~~~~~~~la~~~~l~~ 41 (56)
T smart00389 22 NPYP-SREEREELAAKLGLSE 41 (56)
T ss_pred CCCC-CHHHHHHHHHHHCcCH
Confidence 4477 8899999999999863
No 12
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=26.16 E-value=48 Score=27.56 Aligned_cols=24 Identities=38% Similarity=0.466 Sum_probs=13.8
Q ss_pred CCCHHHHHHH----HHHcCCCCCCCccC
Q psy15236 40 PKTEEERRKA----AKKYNLLPEEYEVQ 63 (176)
Q Consensus 40 P~t~eer~aa----AkKY~~~~edY~p~ 63 (176)
+-|++||+|+ |++|||-|+|-+++
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et~~~ 77 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSETAPV 77 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGCTT-
T ss_pred CCCHHHHHHHHHHHHHccCCCchhhcch
Confidence 5588999886 78999999886543
No 13
>PF14990 DUF4516: Domain of unknown function (DUF4516)
Probab=25.23 E-value=2.1e+02 Score=19.07 Aligned_cols=32 Identities=13% Similarity=-0.139 Sum_probs=17.5
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHhhccccc
Q psy15236 123 QRISVWEQLAYMVGILGTISLVLKYFCWEKRY 154 (176)
Q Consensus 123 ~~~s~~~~l~~~~g~l~g~~~~~~~l~~~y~~ 154 (176)
..++|.+.++.+.+.+++.++..-.+-..|++
T Consensus 3 ~Gv~~~~yl~~~~~s~~sM~aGA~vVH~~ykP 34 (47)
T PF14990_consen 3 AGVSWPSYLKSLVASLLSMLAGASVVHNIYKP 34 (47)
T ss_pred CCCcHHHHHHHHHHHHHHHHhhhHHHHHHhCc
Confidence 35788877776666664444433333324444
No 14
>COG3817 Predicted membrane protein [Function unknown]
Probab=24.39 E-value=71 Score=28.77 Aligned_cols=23 Identities=30% Similarity=0.423 Sum_probs=19.4
Q ss_pred CCCCCCCCCC-CHHHHHHHHHHcC
Q psy15236 32 PDWLPGERPK-TEEERRKAAKKYN 54 (176)
Q Consensus 32 ~d~~P~~yP~-t~eer~aaAkKY~ 54 (176)
+.-++|.+|+ ++|||++-|++||
T Consensus 71 ~~v~~G~~~~~~~e~re~~A~rlg 94 (313)
T COG3817 71 GQVKIGALPELSPEEREKSANRLG 94 (313)
T ss_pred CCcccCCCCCCCHHHHHHHHHHhc
Confidence 4468899988 6789999999998
No 15
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=23.18 E-value=67 Score=20.18 Aligned_cols=21 Identities=29% Similarity=0.385 Sum_probs=14.6
Q ss_pred CCCCCCCHHHHHHHHHHcCCCC
Q psy15236 36 PGERPKTEEERRKAAKKYNLLP 57 (176)
Q Consensus 36 P~~yP~t~eer~aaAkKY~~~~ 57 (176)
--||| |++|++.+|++-||..
T Consensus 7 ~nPYP-s~~ek~~L~~~tgls~ 27 (40)
T PF05920_consen 7 HNPYP-SKEEKEELAKQTGLSR 27 (40)
T ss_dssp TSGS---HHHHHHHHHHHTS-H
T ss_pred CCCCC-CHHHHHHHHHHcCCCH
Confidence 35786 6788999999998753
No 16
>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.
Probab=22.31 E-value=1.5e+02 Score=23.39 Aligned_cols=35 Identities=9% Similarity=-0.107 Sum_probs=18.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCCC
Q psy15236 126 SVWEQLAYMVGILGTISLVLKYFCWEKRYYYPKFDSPK 163 (176)
Q Consensus 126 s~~~~l~~~~g~l~g~~~~~~~l~~~y~~~~Pv~prqY 163 (176)
.|.+.+...+.++ |+.++++++...+. -+-.|+++
T Consensus 73 ewk~v~~~~~~~i-~~s~~~~~~~r~~~--~~~~P~T~ 107 (136)
T cd00922 73 EWKTVFGGVLAFI-GITGVIFGLQRAFV--YGPKPHTF 107 (136)
T ss_pred cHHHHHHHHHHHH-HHHHHHHHHHHHhc--cCCCCCCc
Confidence 4555555555555 66666666664443 13344544
No 17
>COG5085 Predicted membrane protein [Function unknown]
Probab=21.89 E-value=90 Score=27.11 Aligned_cols=20 Identities=15% Similarity=0.262 Sum_probs=15.4
Q ss_pred ccCHHHHHHHHHHHHHHHHHH
Q psy15236 124 RISVWEQLAYMVGILGTISLV 144 (176)
Q Consensus 124 ~~s~~~~l~~~~g~l~g~~~~ 144 (176)
++||.+++.++++++ |++++
T Consensus 188 ~~s~rs~lfili~vi-g~lf~ 207 (230)
T COG5085 188 KFSVRSSLFILIFVI-GFLFF 207 (230)
T ss_pred hhhHHHHHHHHHHHH-HHHHh
Confidence 688988888888777 66653
No 18
>KOG4503|consensus
Probab=21.89 E-value=90 Score=27.11 Aligned_cols=20 Identities=15% Similarity=0.262 Sum_probs=15.4
Q ss_pred ccCHHHHHHHHHHHHHHHHHH
Q psy15236 124 RISVWEQLAYMVGILGTISLV 144 (176)
Q Consensus 124 ~~s~~~~l~~~~g~l~g~~~~ 144 (176)
++||.+++.++++++ |++++
T Consensus 188 ~~s~rs~lfili~vi-g~lf~ 207 (230)
T KOG4503|consen 188 KFSVRSSLFILIFVI-GFLFF 207 (230)
T ss_pred hhhHHHHHHHHHHHH-HHHHh
Confidence 688988888888777 66653
No 19
>PF11821 DUF3341: Protein of unknown function (DUF3341); InterPro: IPR021776 This family of proteins are functionally uncharacterised. This family is found in bacteria. Proteins in this family are about 170 amino acids in length.
Probab=21.13 E-value=1.3e+02 Score=24.82 Aligned_cols=34 Identities=15% Similarity=0.228 Sum_probs=20.6
Q ss_pred CCCCCCccCccccCCCCCCCccccCHHHHHHHHHHHHHHHHH
Q psy15236 102 PLPNDFAISHYGMGFNEQPVNQRISVWEQLAYMVGILGTISL 143 (176)
Q Consensus 102 PvH~~~d~Dm~~~dr~d~~~~~~~s~~~~l~~~~g~l~g~~~ 143 (176)
|||. =.+.++. .+++++|..-+.-++|+++|+++
T Consensus 37 Pvhg--ld~alg~------~~s~l~~~~l~~Gl~G~~~~~~l 70 (173)
T PF11821_consen 37 PVHG--LDEALGL------KRSRLPWIALVGGLTGFATAFLL 70 (173)
T ss_pred cCcC--HHHHhCC------CCCchHHHHHHHHHHHHHHHHHH
Confidence 6776 4445543 25688887666666666655554
No 20
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=21.09 E-value=1.8e+02 Score=20.08 Aligned_cols=38 Identities=13% Similarity=0.212 Sum_probs=25.1
Q ss_pred cccCCCCCCCccccCHHHHHHHHHHHHHHHHHHHHHhh
Q psy15236 112 YGMGFNEQPVNQRISVWEQLAYMVGILGTISLVLKYFC 149 (176)
Q Consensus 112 ~~~dr~d~~~~~~~s~~~~l~~~~g~l~g~~~~~~~l~ 149 (176)
|..-..+..+..++-++..+..+++++.|+.++..+++
T Consensus 15 yL~a~~~~VER~PFrP~~Ll~~li~Vv~gl~llS~ll~ 52 (55)
T PF11293_consen 15 YLQAGVNQVERKPFRPWRLLIVLIVVVIGLGLLSRLLS 52 (55)
T ss_pred HHhCCCCccccCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444446677777777778888878888776665
No 21
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=20.83 E-value=98 Score=24.67 Aligned_cols=25 Identities=8% Similarity=-0.044 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccc
Q psy15236 127 VWEQLAYMVGILGTISLVLKYFCWEK 152 (176)
Q Consensus 127 ~~~~l~~~~g~l~g~~~~~~~l~~~y 152 (176)
|.+.+...+.++ |+.++++++...|
T Consensus 74 wk~v~~~~~~~i-~~s~~l~~~~r~~ 98 (142)
T PF02936_consen 74 WKKVFGGVFIFI-GFSVLLFIWQRSY 98 (142)
T ss_dssp HHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 445555555555 5666666665433
No 22
>COG3765 WzzB Chain length determinant protein [Cell envelope biogenesis, outer membrane]
Probab=20.28 E-value=1.3e+02 Score=27.71 Aligned_cols=40 Identities=15% Similarity=-0.034 Sum_probs=24.3
Q ss_pred ccCccccCCCCCC--Cc-cccCHHHHHHHHHHHHHHHHHHHHH
Q psy15236 108 AISHYGMGFNEQP--VN-QRISVWEQLAYMVGILGTISLVLKY 147 (176)
Q Consensus 108 d~Dm~~~dr~d~~--~~-~~~s~~~~l~~~~g~l~g~~~~~~~ 147 (176)
..+-.+.-|++-+ .| .+.++.++|..++|+++|+|+.++.
T Consensus 292 ~d~~~~~yRYl~~P~~Pvkrd~PrrA~ilil~~LiGgm~g~g~ 334 (347)
T COG3765 292 LDERFSTYRYLQKPTLPVKRDSPRRAIILILGALIGGMLGAGV 334 (347)
T ss_pred cccceeEEEecCCCCCCCcCCCcchHHHHHHHHHHHHHHHHHH
Confidence 4445555566643 12 2567778887777777777765544
Done!