Query 034437
Match_columns 95
No_of_seqs 23 out of 25
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 02:52:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034437.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034437hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02935 COX7C: Cytochrome c o 98.0 3.4E-07 7.4E-12 59.0 -3.0 55 22-92 11-65 (65)
2 KOG4527 Cytochrome c oxidase, 96.7 0.00082 1.8E-08 46.0 1.7 31 63-93 45-75 (76)
3 cd00929 Cyt_c_Oxidase_VIIc Cyt 95.7 0.0011 2.3E-08 41.0 -1.9 42 38-91 5-46 (46)
4 KOG4632 NADH:ubiquinone oxidor 49.2 11 0.00023 29.6 1.5 31 12-42 12-43 (187)
5 PF08693 SKG6: Transmembrane a 35.1 3.2 6.9E-05 25.3 -2.6 16 70-85 9-24 (40)
6 cd06854 GT_WbpL_WbcO_like The 34.8 19 0.00042 27.3 0.9 19 21-39 2-20 (253)
7 PF00880 Nebulin: Nebulin repe 34.0 12 0.00026 19.8 -0.2 14 43-56 1-14 (29)
8 PF13786 DUF4179: Domain of un 33.3 14 0.00031 23.1 0.0 20 68-87 14-33 (94)
9 PF14143 YrhC: YrhC-like prote 28.0 24 0.00052 23.6 0.4 19 66-84 16-34 (72)
10 PLN03165 chaperone protein dna 25.7 37 0.00081 24.0 1.1 14 74-87 18-31 (111)
11 TIGR02184 Myco_arth_vir_N Myco 24.1 45 0.00098 19.8 1.0 31 53-83 1-31 (33)
12 KOG4631 NADH:ubiquinone oxidor 23.4 42 0.00091 24.2 1.0 7 39-45 2-8 (100)
13 COG4615 PvdE ABC-type sideroph 23.4 27 0.00058 31.2 -0.0 32 26-57 484-522 (546)
No 1
>PF02935 COX7C: Cytochrome c oxidase subunit VIIc; InterPro: IPR004202 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. This entry represents cytochrome C subunit 7C. The yeast member of this family is called cytochrome C subunit 8P.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABL_Y 3ABM_L 2EIM_L 3ASO_L 3AG3_Y 3AG1_Y 1OCC_Y 2DYS_Y 2OCC_L 1V54_L ....
Probab=97.97 E-value=3.4e-07 Score=58.99 Aligned_cols=55 Identities=25% Similarity=0.393 Sum_probs=34.6
Q ss_pred ccccccceeccccccccCCCCCCccchhhhhhcccccccccchhhhhhhhhhhhcccccceEEEEEeeecc
Q 034437 22 PSSVNRAFHSTGVKRMGGHGHDEPYYLHAKHMYNLDRMKHQGLKMSLAVFSAFSIGVGVPIYAVIFQQRKT 92 (95)
Q Consensus 22 ~~~~sR~fhsTg~krmggHgHdeP~YiHAkhMYnl~~mK~qklk~~lav~~a~~iGv~vPv~Av~FQqkKT 92 (95)
..+..|++|+ --+|-+++.| +|. ++ |..+++..++++++|+++|+++|.+|.+|+
T Consensus 11 ~~~~~R~~~~----~~~gp~~NLP--------F~~---~n-K~~~~~~~~~f~g~GF~~PF~~~~~Ql~Ks 65 (65)
T PF02935_consen 11 FTSAVRSSHS----YPEGPYSNLP--------FNV---KN-KWPFAVKFWGFFGSGFAAPFLIVRWQLKKS 65 (65)
T ss_dssp --------------S--STTTSSS--------S-----SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHccCC----CCCCCCCccc--------ccC---cc-hhHHHHHHHHHHHHHHHhHHHHHHHHHhcC
Confidence 3345566655 1136668888 665 44 788889999999999999999999999985
No 2
>KOG4527 consensus Cytochrome c oxidase, subunit VIIc/COX8 [Energy production and conversion]
Probab=96.73 E-value=0.00082 Score=46.04 Aligned_cols=31 Identities=29% Similarity=0.400 Sum_probs=27.6
Q ss_pred chhhhhhhhhhhhcccccceEEEEEeeeccc
Q 034437 63 GLKMSLAVFSAFSIGVGVPIYAVIFQQRKTA 93 (95)
Q Consensus 63 klk~~lav~~a~~iGv~vPv~Av~FQqkKT~ 93 (95)
|..++..-+++++||+++|+++|-.|.+|++
T Consensus 45 Kw~~aak~~~ffaigFa~PFlvv~~QL~K~~ 75 (76)
T KOG4527|consen 45 KWTYAAKHFGFFAIGFAVPFLVVRHQLLKSG 75 (76)
T ss_pred hHHHHHHHHHHHHHhccCcceeehhhhhhcc
Confidence 4447888899999999999999999999985
No 3
>cd00929 Cyt_c_Oxidase_VIIc Cytochrome c oxidase subunit VIIc. 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. The VIIc subunit is found only in eukaryotes and its specific function remains unclear. Peroxide inactivation of bovine CcO coincides with the direct oxidation of tryptophan (W19) within subunit VIIc, along with other structural changes in other subunits.
Probab=95.69 E-value=0.0011 Score=41.04 Aligned_cols=42 Identities=21% Similarity=0.387 Sum_probs=30.5
Q ss_pred cCCCCCCccchhhhhhcccccccccchhhhhhhhhhhhcccccceEEEEEeeec
Q 034437 38 GGHGHDEPYYLHAKHMYNLDRMKHQGLKMSLAVFSAFSIGVGVPIYAVIFQQRK 91 (95)
Q Consensus 38 ggHgHdeP~YiHAkhMYnl~~mK~qklk~~lav~~a~~iGv~vPv~Av~FQqkK 91 (95)
+|-|++.| ++++ +++ .+.+-.+.++++|+++|+++|..|++|
T Consensus 5 egp~sNLP--------F~~~---nk~-~~~~~~~~ffg~GF~~PF~i~~~Ql~K 46 (46)
T cd00929 5 EGPGSNLP--------FSVT---NKW-RLTALFHLFFGSGFSAPFIVVRHQLLK 46 (46)
T ss_pred CCCCCCCC--------cccC---ccc-hHHHHHHHHHHHHHhhhHHHHHHHhhC
Confidence 46677889 5544 333 233334459999999999999999987
No 4
>KOG4632 consensus NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit [Energy production and conversion]
Probab=49.20 E-value=11 Score=29.61 Aligned_cols=31 Identities=23% Similarity=0.302 Sum_probs=24.0
Q ss_pred hhhhccccccccccccceecccccccc-CCCC
Q 034437 12 KLLASSQSLVPSSVNRAFHSTGVKRMG-GHGH 42 (95)
Q Consensus 12 ~l~~~~~~~~~~~~sR~fhsTg~krmg-gHgH 42 (95)
--.++.+++.-+|..+||=--+.+||+ .|||
T Consensus 12 aa~as~R~~~~~p~~~~~l~~~~rr~~gdHg~ 43 (187)
T KOG4632|consen 12 AACASGRSAFLKPSTSGFLIPAIRRHSGDHGA 43 (187)
T ss_pred HHHhccchhhcCcCcccchhhhhhhcCCcccc
Confidence 345666778889999999777888995 6876
No 5
>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]. This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].
Probab=35.12 E-value=3.2 Score=25.27 Aligned_cols=16 Identities=31% Similarity=0.463 Sum_probs=11.0
Q ss_pred hhhhhhcccccceEEE
Q 034437 70 VFSAFSIGVGVPIYAV 85 (95)
Q Consensus 70 v~~a~~iGv~vPv~Av 85 (95)
-..++++||+|||..+
T Consensus 9 ~~vaIa~~VvVPV~vI 24 (40)
T PF08693_consen 9 NTVAIAVGVVVPVGVI 24 (40)
T ss_pred ceEEEEEEEEechHHH
Confidence 3456778888887644
No 6
>cd06854 GT_WbpL_WbcO_like The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor. The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic end products implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The subgroup of bacterial UDP-HexNAc:polyprenol-P HexNAc-1-P transferases includes the WbcO protein from Yersinia enterocolitica and the WbpL protein from Pseudomonas aeruginosa. These transferases initiate LPS O-antigen biosynthesis. Similar to other GlcNAc/MurNAc-1-P transferase family members, WbpL is a highly hydrophobic protein possessing 11 predicted transmembrane segments.
Probab=34.77 E-value=19 Score=27.27 Aligned_cols=19 Identities=26% Similarity=0.373 Sum_probs=16.8
Q ss_pred cccccccceeccccccccC
Q 034437 21 VPSSVNRAFHSTGVKRMGG 39 (95)
Q Consensus 21 ~~~~~sR~fhsTg~krmgg 39 (95)
+-+|-.|.-|.+..|++||
T Consensus 2 ~D~P~~Rk~H~~~~P~~GG 20 (253)
T cd06854 2 LDIPNERSSHTKPTPRGGG 20 (253)
T ss_pred CCCCCCCCCCCCCcCCcCh
Confidence 3578899999999999997
No 7
>PF00880 Nebulin: Nebulin repeat; InterPro: IPR000900 Nebulin is a 600-800kDa protein found in the thin filaments of striated vertebrate muscle. It is presumed to play a role in binding and stabilising F-actin [], essentially by providing a template for actin polymerisation (i.e., acting as an "actin zipper"). The amino acid sequence shows a uniform repeating pattern along its length, a repeated 35-residue motif constituting up to 97% of the polypeptide. Analysis of individual repeats reveals a progressive N- to C-terminal divergence, coupled with an increasing alpha-helix propensity. This correlates with a higher binding affinity for F-actin at the C terminus. Thus, it is postulated that once the repeats have formed an initiation complex, the whole length of the nebulin molecule may then associate in a highly co-operative process with the thin filament, in a manner similar to the closing of a zipper [].
Probab=34.01 E-value=12 Score=19.79 Aligned_cols=14 Identities=43% Similarity=0.598 Sum_probs=11.4
Q ss_pred CCccchhhhhhccc
Q 034437 43 DEPYYLHAKHMYNL 56 (95)
Q Consensus 43 deP~YiHAkhMYnl 56 (95)
|.|.++||+.+..+
T Consensus 1 Dtp~~~~ak~~~~~ 14 (29)
T PF00880_consen 1 DTPEMVHAKKAAQL 14 (29)
T ss_pred CCHHHHHHHHHHHH
Confidence 67999999988654
No 8
>PF13786 DUF4179: Domain of unknown function (DUF4179); PDB: 3FBQ_A.
Probab=33.28 E-value=14 Score=23.10 Aligned_cols=20 Identities=15% Similarity=0.154 Sum_probs=0.0
Q ss_pred hhhhhhhhcccccceEEEEE
Q 034437 68 LAVFSAFSIGVGVPIYAVIF 87 (95)
Q Consensus 68 lav~~a~~iGv~vPv~Av~F 87 (95)
+++.+++.++++.|++|-..
T Consensus 14 aaaa~~~v~~~~~~~~A~~~ 33 (94)
T PF13786_consen 14 AAAAALAVLLISSPAFAANI 33 (94)
T ss_dssp --------------------
T ss_pred HHHHHHHHHHhhhHHHHhhC
Confidence 44455556677789988654
No 9
>PF14143 YrhC: YrhC-like protein
Probab=27.96 E-value=24 Score=23.61 Aligned_cols=19 Identities=42% Similarity=0.460 Sum_probs=15.7
Q ss_pred hhhhhhhhhhcccccceEE
Q 034437 66 MSLAVFSAFSIGVGVPIYA 84 (95)
Q Consensus 66 ~~lav~~a~~iGv~vPv~A 84 (95)
+-||+.+|+-||.-||.-+
T Consensus 16 vLLAvs~FlYiG~viP~~~ 34 (72)
T PF14143_consen 16 VLLAVSTFLYIGTVIPIGA 34 (72)
T ss_pred HHHHHHHHHHHHhhCCccc
Confidence 3478999999999999644
No 10
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=25.73 E-value=37 Score=24.05 Aligned_cols=14 Identities=21% Similarity=0.788 Sum_probs=11.2
Q ss_pred hhcccccceEEEEE
Q 034437 74 FSIGVGVPIYAVIF 87 (95)
Q Consensus 74 ~~iGv~vPv~Av~F 87 (95)
++.|++||||-+..
T Consensus 18 ~~~~~~~~~~~~~q 31 (111)
T PLN03165 18 IAVGIGIPVFYETQ 31 (111)
T ss_pred hhhccCCcEEEEEe
Confidence 56799999998754
No 11
>TIGR02184 Myco_arth_vir_N Mycoplasma virulence family signal region. This model represents the N-terminal region, including a probable signal sequence or signal anchor which in most instances has four consecutive Lys residues before the hydrophobic stretch, of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum.
Probab=24.08 E-value=45 Score=19.78 Aligned_cols=31 Identities=19% Similarity=0.211 Sum_probs=22.4
Q ss_pred hcccccccccchhhhhhhhhhhhcccccceE
Q 034437 53 MYNLDRMKHQGLKMSLAVFSAFSIGVGVPIY 83 (95)
Q Consensus 53 MYnl~~mK~qklk~~lav~~a~~iGv~vPv~ 83 (95)
||.+-.=|+.=+.++++...+.+.-++.-||
T Consensus 1 M~~~KKKKnkIl~~al~a~l~~S~s~g~ViY 31 (33)
T TIGR02184 1 MYFSKKKKNKIATLVIVTSLLTSLTISGVIY 31 (33)
T ss_pred CchhhhhhhheehHHHHHHHHHhheeeeEEE
Confidence 6777777888888888877777666655444
No 12
>KOG4631 consensus NADH:ubiquinone oxidoreductase, NDUFB3/B12 subunit [Energy production and conversion]
Probab=23.42 E-value=42 Score=24.16 Aligned_cols=7 Identities=57% Similarity=1.047 Sum_probs=4.8
Q ss_pred CCCCCCc
Q 034437 39 GHGHDEP 45 (95)
Q Consensus 39 gHgHdeP 45 (95)
|++|+||
T Consensus 2 Gg~Hhep 8 (100)
T KOG4631|consen 2 GGEHHEP 8 (100)
T ss_pred CCCCCCc
Confidence 4456899
No 13
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=23.40 E-value=27 Score=31.19 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=21.3
Q ss_pred ccceecccccccc--C-----CCCCCccchhhhhhcccc
Q 034437 26 NRAFHSTGVKRMG--G-----HGHDEPYYLHAKHMYNLD 57 (95)
Q Consensus 26 sR~fhsTg~krmg--g-----HgHdeP~YiHAkhMYnl~ 57 (95)
+|=|-.+=.|++- | =-|||||++||+-...+.
T Consensus 484 RR~FY~~lLp~LK~qGKTI~aIsHDd~YF~~ADrll~~~ 522 (546)
T COG4615 484 RREFYQVLLPLLKEQGKTIFAISHDDHYFIHADRLLEMR 522 (546)
T ss_pred HHHHHHHHhHHHHHhCCeEEEEecCchhhhhHHHHHHHh
Confidence 4556666665552 2 128999999999776543
Done!