Query 030495
Match_columns 176
No_of_seqs 55 out of 57
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 14:35:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030495.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030495hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12077 DUF3556: Transmembran 72.1 2.3 5E-05 41.2 1.8 49 80-128 118-167 (574)
2 PF12270 Cyt_c_ox_IV: Cytochro 36.7 29 0.00062 28.1 2.2 22 115-136 113-134 (137)
3 PF12955 DUF3844: Domain of un 27.3 2.3E+02 0.005 22.0 5.7 39 76-129 48-86 (103)
4 KOG0593 Predicted protein kina 23.2 20 0.00044 33.6 -0.8 18 122-139 184-202 (396)
5 PF12301 CD99L2: CD99 antigen 21.0 23 0.0005 29.2 -0.8 10 46-55 133-142 (169)
6 TIGR00752 slp outer membrane l 18.6 72 0.0016 26.6 1.5 10 3-12 11-20 (182)
7 KOG1614 Exosomal 3'-5' exoribo 17.7 1E+02 0.0022 28.1 2.3 42 114-160 145-200 (291)
8 PF04120 Iron_permease: Low af 16.9 1.2E+02 0.0026 24.2 2.4 40 108-147 13-52 (132)
9 PF03941 INCENP_ARK-bind: Inne 14.6 54 0.0012 22.0 -0.1 8 90-97 18-25 (57)
10 PF08122 NDUF_B12: NADH-ubiqui 14.3 1.1E+02 0.0023 21.0 1.3 11 91-101 3-13 (57)
No 1
>PF12077 DUF3556: Transmembrane protein of unknown function (DUF3556); InterPro: IPR021941 This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 amino acids in length.
Probab=72.09 E-value=2.3 Score=41.22 Aligned_cols=49 Identities=24% Similarity=0.529 Sum_probs=40.7
Q ss_pred CCCCCCCCCCCCCc-ccccCCCcCCCCccCchHHHHHHHHHHHHHHHhcc
Q 030495 80 PSWAKPDSDEPPPW-ATDEGKGLTSQGSFEIPFYVYLLTSTITAIAAIGS 128 (176)
Q Consensus 80 pswAkp~sde~PPW-aR~E~~~~~a~~~~~lPfgvyLl~ScItAIAAVGS 128 (176)
=-|.+|+.-.+||| .|--.-+......+|+=.|+-|+.+.+.|++.=|.
T Consensus 118 lyWlRpgTIRLpPWP~~VP~T~Gd~Rt~~DV~LYaalL~~lv~aL~~pG~ 167 (574)
T PF12077_consen 118 LYWLRPGTIRLPPWPGRVPLTAGDRRTPFDVALYAALLASLVVALLSPGT 167 (574)
T ss_pred eEEecCCceeCCCCCCCCCCCCCCcCchHHHHHHHHHHHHHHHHHcCCCC
Confidence 45999999999999 55555555556788999999999999999998777
No 2
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=36.70 E-value=29 Score=28.10 Aligned_cols=22 Identities=27% Similarity=0.579 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHhcceeEeecCC
Q 030495 115 LLTSTITAIAAIGSIFEYVNKN 136 (176)
Q Consensus 115 Ll~ScItAIAAVGSIFElssg~ 136 (176)
+++..++.++++|=+|||..|+
T Consensus 113 ~iG~~~~i~~~~G~vfEy~rg~ 134 (137)
T PF12270_consen 113 LIGAVLLIVAVVGWVFEYYRGP 134 (137)
T ss_pred HHHHHHHHHHHHHHhheeccCc
Confidence 3445567788999999998875
No 3
>PF12955 DUF3844: Domain of unknown function (DUF3844); InterPro: IPR024382 This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins thought to be located in the endoplasmic reticulum.
Probab=27.29 E-value=2.3e+02 Score=22.03 Aligned_cols=39 Identities=15% Similarity=0.476 Sum_probs=25.2
Q ss_pred ccCCCCCCCCCCCCCCCcccccCCCcCCCCccCchHHHHHHHHHHHHHHHhcce
Q 030495 76 EETIPSWAKPDSDEPPPWATDEGKGLTSQGSFEIPFYVYLLTSTITAIAAIGSI 129 (176)
Q Consensus 76 ~e~~pswAkp~sde~PPWaR~E~~~~~a~~~~~lPfgvyLl~ScItAIAAVGSI 129 (176)
..|...|+-+.=+ .+..-.||-+|+..+.+..++.+++|
T Consensus 48 ~~ktt~W~G~aCq---------------KkDvS~~F~L~~~~ti~lv~~~~~~I 86 (103)
T PF12955_consen 48 KGKTTHWGGPACQ---------------KKDVSVPFWLFAGFTIALVVLVAGAI 86 (103)
T ss_pred cCceeeecccccc---------------cccccchhhHHHHHHHHHHHHHHHHH
Confidence 3477788765421 23445899998888777666655555
No 4
>KOG0593 consensus Predicted protein kinase KKIAMRE [General function prediction only]
Probab=23.18 E-value=20 Score=33.60 Aligned_cols=18 Identities=39% Similarity=0.778 Sum_probs=14.6
Q ss_pred HHHHhccee-EeecCCCcc
Q 030495 122 AIAAIGSIF-EYVNKNPVF 139 (176)
Q Consensus 122 AIAAVGSIF-Elssg~P~f 139 (176)
-|-|||||| |++.|+|-|
T Consensus 184 DiWAiGCv~aEl~~G~pL~ 202 (396)
T KOG0593|consen 184 DIWAIGCVFAELLTGEPLW 202 (396)
T ss_pred cchhhhHHHHHHhcCCcCC
Confidence 356888887 999999965
No 5
>PF12301 CD99L2: CD99 antigen like protein 2; InterPro: IPR022078 This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.
Probab=20.98 E-value=23 Score=29.22 Aligned_cols=10 Identities=60% Similarity=0.853 Sum_probs=9.1
Q ss_pred CCcccccccc
Q 030495 46 PSYHAFQNKK 55 (176)
Q Consensus 46 ~~~~~~~~~k 55 (176)
.||++|||||
T Consensus 133 sSyiaYqkKK 142 (169)
T PF12301_consen 133 SSYIAYQKKK 142 (169)
T ss_pred HHHHHHHhhc
Confidence 5899999999
No 6
>TIGR00752 slp outer membrane lipoprotein, Slp family. Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.
Probab=18.64 E-value=72 Score=26.57 Aligned_cols=10 Identities=10% Similarity=-0.117 Sum_probs=7.8
Q ss_pred cceeeccCCc
Q 030495 3 SATILSSSSC 12 (176)
Q Consensus 3 ~a~~~~~~~~ 12 (176)
+|++|+.|.+
T Consensus 11 ~~l~LsgCas 20 (182)
T TIGR00752 11 LCFGLTGCIA 20 (182)
T ss_pred HHHHHhcccC
Confidence 4677888988
No 7
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=17.67 E-value=1e+02 Score=28.13 Aligned_cols=42 Identities=24% Similarity=0.209 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhcceeEeecCCCccccccC--------------Cceehhhhccceeeec
Q 030495 114 YLLTSTITAIAAIGSIFEYVNKNPVFGILNS--------------DSIFYAPLLGFFAFTG 160 (176)
Q Consensus 114 yLl~ScItAIAAVGSIFElssg~P~fGv~~t--------------d~iLYaPiLgFF~~Tg 160 (176)
++=++||++|||.= .-++|+.-+.+- -+|+|.||-.+|.|.+
T Consensus 145 lvDaA~iAviaaL~-----hFrrPdvTv~g~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffn 200 (291)
T KOG1614|consen 145 LVDAACIAVIAALM-----HFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFN 200 (291)
T ss_pred eehhHHHHHHHHHH-----hcCCCCcccccceeEecChhccCCcceeeeeccceEEEEEec
Confidence 45689999999973 357888777654 4677888988888765
No 8
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=16.85 E-value=1.2e+02 Score=24.17 Aligned_cols=40 Identities=15% Similarity=0.212 Sum_probs=29.5
Q ss_pred CchHHHHHHHHHHHHHHHhcceeEeecCCCccccccCCce
Q 030495 108 EIPFYVYLLTSTITAIAAIGSIFEYVNKNPVFGILNSDSI 147 (176)
Q Consensus 108 ~lPfgvyLl~ScItAIAAVGSIFElssg~P~fGv~~td~i 147 (176)
+-|+...+.+.+|.+-++.|.+|.++.-==-+=+.+|.++
T Consensus 13 gs~~~f~~~~~~Ii~W~i~Gp~~~~sdtWQLviNt~ttIi 52 (132)
T PF04120_consen 13 GSPWAFVIAVAVIIVWAISGPVFGFSDTWQLVINTATTII 52 (132)
T ss_pred CCHHHHHHHHHHHHHHHHHhccccCcchHHHHHccHHHHH
Confidence 4689999999999999999999998754333333444443
No 9
>PF03941 INCENP_ARK-bind: Inner centromere protein, ARK binding region; InterPro: IPR005635 This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast [].; PDB: 2BFX_C 2BFY_C 3ZTX_D 2VGO_D 2VGP_D 2VRX_D 4AF3_D.
Probab=14.62 E-value=54 Score=22.05 Aligned_cols=8 Identities=38% Similarity=0.916 Sum_probs=2.8
Q ss_pred CCCccccc
Q 030495 90 PPPWATDE 97 (176)
Q Consensus 90 ~PPWaR~E 97 (176)
.|.||+.+
T Consensus 18 iP~WA~~~ 25 (57)
T PF03941_consen 18 IPSWAQSP 25 (57)
T ss_dssp --GGGSHH
T ss_pred CCCCcCcH
Confidence 44555443
No 10
>PF08122 NDUF_B12: NADH-ubiquinone oxidoreductase B12 subunit family; InterPro: IPR012576 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 the B12 subunit of NADH:ubiquinone oxidoreductase proteins. The function of this subunit is unclear [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=14.27 E-value=1.1e+02 Score=21.04 Aligned_cols=11 Identities=36% Similarity=0.761 Sum_probs=8.6
Q ss_pred CCcccccCCCc
Q 030495 91 PPWATDEGKGL 101 (176)
Q Consensus 91 PPWaR~E~~~~ 101 (176)
-||+|+|.=|-
T Consensus 3 DPW~RneaWRy 13 (57)
T PF08122_consen 3 DPWARNEAWRY 13 (57)
T ss_pred ChHhhhHHHhC
Confidence 38999997664
Done!