Query 035185
Match_columns 71
No_of_seqs 101 out of 127
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:54:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035185.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035185hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02755 complex I subunit 100.0 2.7E-35 5.8E-40 179.5 4.6 71 1-71 1-71 (71)
2 PF07225 NDUF_B4: NADH-ubiquin 99.8 1.6E-20 3.5E-25 124.7 5.6 65 6-70 54-121 (125)
3 PF05656 DUF805: Protein of un 51.9 18 0.00039 22.3 2.6 29 25-53 1-29 (120)
4 PF05371 Phage_Coat_Gp8: Phage 50.7 36 0.00078 19.7 3.5 28 32-59 21-48 (52)
5 PF08475 Baculo_VP91_N: Viral 49.4 13 0.00027 26.4 1.8 27 35-61 2-28 (183)
6 PF12823 DUF3817: Domain of un 47.1 17 0.00038 22.6 2.0 30 24-54 59-88 (92)
7 PF06596 PsbX: Photosystem II 46.8 38 0.00083 18.5 3.1 27 31-57 5-34 (39)
8 PF12515 CaATP_NAI: Ca2+-ATPas 44.2 20 0.00044 20.2 1.8 23 11-33 16-41 (47)
9 PF10716 NdhL: NADH dehydrogen 44.1 36 0.00078 21.3 3.0 20 34-53 22-41 (81)
10 PF07172 GRP: Glycine rich pro 41.3 53 0.0012 20.6 3.6 25 32-56 4-28 (95)
11 PF14152 YfhE: YfhE-like prote 36.2 29 0.00062 18.8 1.5 15 54-68 22-36 (37)
12 PF04088 Peroxin-13_N: Peroxin 35.2 42 0.00091 23.0 2.6 44 10-53 103-158 (158)
13 PF12794 MscS_TM: Mechanosensi 34.5 45 0.00097 24.9 2.8 32 23-54 39-70 (340)
14 PF02939 UcrQ: UcrQ family; I 33.7 1.2E+02 0.0025 18.6 4.6 32 33-65 40-75 (80)
15 PF10582 Connexin_CCC: Gap jun 32.3 52 0.0011 19.6 2.4 24 28-51 38-61 (67)
16 PF09446 VMA21: VMA21-like dom 32.3 84 0.0018 18.3 3.2 22 35-56 9-30 (66)
17 PF07109 Mg-por_mtran_C: Magne 28.5 49 0.0011 21.1 1.9 25 19-43 22-46 (97)
18 PF12365 DUF3649: Protein of u 27.8 91 0.002 15.6 2.9 23 29-52 2-24 (28)
19 PLN02177 glycerol-3-phosphate 27.5 68 0.0015 25.5 2.9 16 26-41 238-253 (497)
20 PF06084 Cytomega_TRL10: Cytom 27.4 30 0.00064 23.5 0.8 31 38-70 65-96 (150)
21 PF03804 DUF325: Viral domain 26.4 34 0.00074 20.9 0.8 20 25-44 39-58 (71)
22 PF06024 DUF912: Nucleopolyhed 24.9 24 0.00053 22.1 0.0 6 54-59 88-93 (101)
23 PF09777 OSTMP1: Osteopetrosis 24.8 74 0.0016 22.9 2.5 20 34-53 191-211 (237)
24 PF07331 TctB: Tripartite tric 23.4 1.2E+02 0.0027 18.8 3.1 27 31-57 111-137 (141)
25 PLN02499 glycerol-3-phosphate 23.4 85 0.0018 25.4 2.8 16 26-41 225-240 (498)
26 PF15361 RIC3: Resistance to i 22.9 98 0.0021 20.9 2.7 23 38-60 87-109 (152)
27 PF06390 NESP55: Neuroendocrin 22.8 1.1E+02 0.0025 22.6 3.1 49 14-62 8-56 (257)
28 PTZ00234 variable surface prot 22.1 81 0.0017 24.9 2.4 39 32-70 365-403 (433)
29 PF08260 Kinin: Insect kinin p 21.0 11 0.00024 14.2 -1.3 7 10-16 1-7 (8)
30 TIGR01478 STEVOR variant surfa 20.6 1.3E+02 0.0028 22.9 3.2 25 34-58 264-288 (295)
31 PTZ00370 STEVOR; Provisional 20.0 1.4E+02 0.003 22.8 3.2 25 34-58 260-284 (296)
No 1
>PLN02755 complex I subunit
Probab=100.00 E-value=2.7e-35 Score=179.49 Aligned_cols=71 Identities=86% Similarity=1.483 Sum_probs=70.2
Q ss_pred CCCCCCCccCHHHHHHHHHhhccccceeecchhHHHHHHHHhHHHHHhHHHHhhhhhhhhhhcCCcccCCC
Q 035185 1 MGGGMEANKNRFIEEWGAARENLEHNFRWTRRNLALVGLFGIAVPVFIYKGIVKEFHMQDEDAGRPYRKFL 71 (71)
Q Consensus 1 MaG~~~l~~dPalerw~~~ren~~~~FR~Tprt~~~~~~~~~~vP~~~yy~~~~~~~~~d~~~G~~~r~f~ 71 (71)
|||++++.+|..||.|++||||+|+||||||||++++++||++||+++||++++||++||.++|||+|||+
T Consensus 1 m~gg~~~~~Nk~iE~~~~~reNrekyFRWT~Rt~~i~~ifgv~VP~liy~giv~eF~~~d~~~grp~~kf~ 71 (71)
T PLN02755 1 MGGGMEVNKNKFIEEWGAARENLEFNFRWTRRNLAVVGIFGIAVPILVYKGIVREFHMQDEDAGRPERKFL 71 (71)
T ss_pred CCCCcccCccHHHHHHHHHHHHHHHheecccchhhhhhhhhhhhhHHhhhhhhhhhcccchhccCCccccC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999996
No 2
>PF07225 NDUF_B4: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4); InterPro: IPR009866 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 contains human NADH-ubiquinone oxidoreductase subunit NDUFB4 and related sequences.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=99.82 E-value=1.6e-20 Score=124.71 Aligned_cols=65 Identities=23% Similarity=0.285 Sum_probs=59.6
Q ss_pred CCccCHHHHHHHHHhh-ccccceeecchhHHHHHHHHhHHHHHhHHHHh--hhhhhhhhhcCCcccCC
Q 035185 6 EANKNRFIEEWGAARE-NLEHNFRWTRRNLALVGLFGIAVPVFIYKGIV--KEFHMQDEDAGRPYRKF 70 (71)
Q Consensus 6 ~l~~dPalerw~~~re-n~~~~FR~Tprt~~~~~~~~~~vP~~~yy~~~--~~~~~~d~~~G~~~r~f 70 (71)
+++.||||+||+++++ |+|+||||||||+++++++++++.+++|++++ ++.++++++.|+.+|.|
T Consensus 54 gli~DPAL~Rw~~a~~~~~y~~FRpTPktsllg~~~~v~P~i~~~~~~KtdRD~~E~~~r~G~~dR~f 121 (125)
T PF07225_consen 54 GLIFDPALQRWAYARAVNIYEYFRPTPKTSLLGLGFGVVPLIFYYYVLKTDRDRKEKLIRTGKLDRPF 121 (125)
T ss_pred CccCChHHHHHHHHHHhCcccccccCchHHHHHHHHHHHHHHHHHhhhccchhHHHHHHhcCccceee
Confidence 5899999999998888 99999999999999999999987788888887 57788899999999998
No 3
>PF05656 DUF805: Protein of unknown function (DUF805); InterPro: IPR008523 This entry is represented by Lactobacillus phage LBR48, DUF805. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0016021 integral to membrane
Probab=51.89 E-value=18 Score=22.29 Aligned_cols=29 Identities=10% Similarity=0.138 Sum_probs=22.5
Q ss_pred cceeecchhHHHHHHHHhHHHHHhHHHHh
Q 035185 25 HNFRWTRRNLALVGLFGIAVPVFIYKGIV 53 (71)
Q Consensus 25 ~~FR~Tprt~~~~~~~~~~vP~~~yy~~~ 53 (71)
|+|.|+.|+++..+++..+...++..+..
T Consensus 1 ~~f~f~GR~~R~~fw~~~l~~~~~~~~~~ 29 (120)
T PF05656_consen 1 NYFNFKGRISRKEFWWFFLINILIFILLL 29 (120)
T ss_pred CcccCcCCcCHHHHHHHHHHHHHHHHHHH
Confidence 57889999999888888877777665543
No 4
>PF05371 Phage_Coat_Gp8: Phage major coat protein, Gp8; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 1IFK_A 2C0W_A 2HI5_A 1FDM_A 1IFJ_A 2C0X_A 1IFI_A 1IFD_A 1MZT_A 1IFL_A ....
Probab=50.69 E-value=36 Score=19.69 Aligned_cols=28 Identities=11% Similarity=-0.186 Sum_probs=23.7
Q ss_pred hhHHHHHHHHhHHHHHhHHHHhhhhhhh
Q 035185 32 RNLALVGLFGIAVPVFIYKGIVKEFHMQ 59 (71)
Q Consensus 32 rt~~~~~~~~~~vP~~~yy~~~~~~~~~ 59 (71)
-|..++..|.+++|+....+..+=|++.
T Consensus 21 At~~i~~aw~vvv~v~gafigirlFKKf 48 (52)
T PF05371_consen 21 ATDLIGYAWPVVVLVTGAFIGIRLFKKF 48 (52)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 4778999999999999998888777764
No 5
>PF08475 Baculo_VP91_N: Viral capsid protein 91 N-terminal; InterPro: IPR013682 This domain is found in Baculoviridae including the nucleopolyhedrovirus at the N terminus of the viral capsid protein 91 (VP91) [].
Probab=49.45 E-value=13 Score=26.41 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=20.4
Q ss_pred HHHHHHHhHHHHHhHHHHhhhhhhhhh
Q 035185 35 ALVGLFGIAVPVFIYKGIVKEFHMQDE 61 (71)
Q Consensus 35 ~~~~~~~~~vP~~~yy~~~~~~~~~d~ 61 (71)
++.++.++++-.++|..++.||++++-
T Consensus 2 Llvai~l~iif~i~y~~I~~dFde~~F 28 (183)
T PF08475_consen 2 LLVAILLIIIFLIYYLIIYNDFDENEF 28 (183)
T ss_pred chhHHHHHHHHHHHHHhhccccchHHH
Confidence 456677777777888888899988754
No 6
>PF12823 DUF3817: Domain of unknown function (DUF3817); InterPro: IPR023845 This domain is associated with, strictly bacterial integral membrane proteins. It occurs in proteins that on rare occasions are fused to transporter domains such as the major facilitator superfamily domain. Of three invariant residues, two occur as a His-Gly dipeptide in the middle of three predicted transmembrane helices.
Probab=47.07 E-value=17 Score=22.56 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=22.3
Q ss_pred ccceeecchhHHHHHHHHhHHHHHhHHHHhh
Q 035185 24 EHNFRWTRRNLALVGLFGIAVPVFIYKGIVK 54 (71)
Q Consensus 24 ~~~FR~Tprt~~~~~~~~~~vP~~~yy~~~~ 54 (71)
-..-||+.+.+..+++.++ +|++.++.=++
T Consensus 59 ~~~~rW~~~~~~~~llas~-iPfg~f~~er~ 88 (92)
T PF12823_consen 59 ASKYRWSLKRTLLALLASV-IPFGTFWFERW 88 (92)
T ss_pred HHHcCCChHHHHHHHHHHc-ccccHHHHHHH
Confidence 3456899999999877776 88887766543
No 7
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=46.82 E-value=38 Score=18.46 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=17.5
Q ss_pred chhHHHHHHHHh---HHHHHhHHHHhhhhh
Q 035185 31 RRNLALVGLFGI---AVPVFIYKGIVKEFH 57 (71)
Q Consensus 31 prt~~~~~~~~~---~vP~~~yy~~~~~~~ 57 (71)
-+|.+.++++|+ ++|+....++.+.++
T Consensus 5 L~nfl~Sl~aG~~iVv~~i~~ali~VSq~D 34 (39)
T PF06596_consen 5 LSNFLLSLVAGAVIVVIPIAGALIFVSQFD 34 (39)
T ss_dssp HHHHHHHHHHHH-HHHHHHHHHHHHHHCCS
T ss_pred HHHHHHHHHhhhhhhhhhhhhheEEEeccC
Confidence 356677777776 567777666666443
No 8
>PF12515 CaATP_NAI: Ca2+-ATPase N terminal autoinhibitory domain; InterPro: IPR024750 This entry represents the N-terminal autoinhibitory calmodulin-binding domain characteristic of certain calcium-transporting ATPases []. This domain binds calmodulin in a calcium-dependent fashion and has a conserved RRFR sequence motif. There are two completely conserved residues (F and W) that may be functionally important.; GO: 0005516 calmodulin binding
Probab=44.24 E-value=20 Score=20.23 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=17.5
Q ss_pred HHHHHHHHHh---hccccceeecchh
Q 035185 11 RFIEEWGAAR---ENLEHNFRWTRRN 33 (71)
Q Consensus 11 Palerw~~~r---en~~~~FR~Tprt 33 (71)
-++.+|-.+= -|.+..||+|.--
T Consensus 16 e~l~rWR~a~~lv~N~~RRFR~~~dL 41 (47)
T PF12515_consen 16 EALRRWRQAVGLVKNARRRFRYTADL 41 (47)
T ss_pred HHHHHHHHHhHHhccccceeeecccH
Confidence 3677787766 4999999999753
No 9
>PF10716 NdhL: NADH dehydrogenase transmembrane subunit; InterPro: IPR019654 NAD(P)H-quinone oxidoreductase subunit L (NdhL) is a component of the NDH-1L complex that is one of the proton-pumping NADH:ubiquinone oxidoreductases that catalyse the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. NDH-1L is essential for photoheterotrophic cell growth. NdhL appears to contain two transmembrane helices and it is necessary for the functioning of though not the correct assembly of the NDH-1 complex in Synechocystis 6803. The conservation between cyanobacteria and green plants suggests that chloroplast NDH-1 complexes contain related subunits []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=44.14 E-value=36 Score=21.33 Aligned_cols=20 Identities=35% Similarity=0.615 Sum_probs=16.2
Q ss_pred HHHHHHHHhHHHHHhHHHHh
Q 035185 34 LALVGLFGIAVPVFIYKGIV 53 (71)
Q Consensus 34 ~~~~~~~~~~vP~~~yy~~~ 53 (71)
+.++++|.+++|.++|+-..
T Consensus 22 ~~l~~~YLlVvP~~l~~wm~ 41 (81)
T PF10716_consen 22 AALAGLYLLVVPLILYFWMN 41 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45788899999999987664
No 10
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=41.25 E-value=53 Score=20.61 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=11.4
Q ss_pred hhHHHHHHHHhHHHHHhHHHHhhhh
Q 035185 32 RNLALVGLFGIAVPVFIYKGIVKEF 56 (71)
Q Consensus 32 rt~~~~~~~~~~vP~~~yy~~~~~~ 56 (71)
|++++..++.+++.++.--++.++.
T Consensus 4 K~~llL~l~LA~lLlisSevaa~~~ 28 (95)
T PF07172_consen 4 KAFLLLGLLLAALLLISSEVAAREL 28 (95)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhHHh
Confidence 4444444444444444444444444
No 11
>PF14152 YfhE: YfhE-like protein
Probab=36.16 E-value=29 Score=18.81 Aligned_cols=15 Identities=27% Similarity=0.514 Sum_probs=12.2
Q ss_pred hhhhhhhhhcCCccc
Q 035185 54 KEFHMQDEDAGRPYR 68 (71)
Q Consensus 54 ~~~~~~d~~~G~~~r 68 (71)
+||++.|+..|.-+.
T Consensus 22 ~eFK~AdrA~g~t~k 36 (37)
T PF14152_consen 22 REFKKADRAGGYTKK 36 (37)
T ss_pred HHHHHHHHhcccccC
Confidence 799999999886543
No 12
>PF04088 Peroxin-13_N: Peroxin 13, N-terminal region; InterPro: IPR007223 Peroxin-13 is a component of the peroxisomal translocation machinery with Peroxin-14 and Peroxin-17. Both termini of Peroxin-13 are oriented to the cytosol. It is required for peroxisomal association of peroxin-14 []. The proteins also contain an SH3 domain (IPR001452 from INTERPRO).; GO: 0016560 protein import into peroxisome matrix, docking, 0005777 peroxisome, 0016021 integral to membrane
Probab=35.20 E-value=42 Score=23.03 Aligned_cols=44 Identities=16% Similarity=0.113 Sum_probs=28.8
Q ss_pred CHHHHHHHHHhhc------------cccceeecchhHHHHHHHHhHHHHHhHHHHh
Q 035185 10 NRFIEEWGAAREN------------LEHNFRWTRRNLALVGLFGIAVPVFIYKGIV 53 (71)
Q Consensus 10 dPalerw~~~ren------------~~~~FR~Tprt~~~~~~~~~~vP~~~yy~~~ 53 (71)
++..+.|....++ --+.=+.+.+.+++-+...+++|.+++.++|
T Consensus 103 ~~~~~~f~~f~~~~~~~~~~~~~~~~~~~~~~s~~PlllF~~~v~G~PyLi~Klik 158 (158)
T PF04088_consen 103 SLTEDEFSKFESEQNALASNANGQPSGKRPKPSSKPLLLFLAAVFGLPYLIWKLIK 158 (158)
T ss_pred CCCHHHHHHHHhccccccccccccccCCCCCCCcccHHHHHHHHHHHHHHHHHHhC
Confidence 4555666555543 1244566666777777777888999988764
No 13
>PF12794 MscS_TM: Mechanosensitive ion channel inner membrane domain 1
Probab=34.47 E-value=45 Score=24.91 Aligned_cols=32 Identities=22% Similarity=0.295 Sum_probs=28.0
Q ss_pred cccceeecchhHHHHHHHHhHHHHHhHHHHhh
Q 035185 23 LEHNFRWTRRNLALVGLFGIAVPVFIYKGIVK 54 (71)
Q Consensus 23 ~~~~FR~Tprt~~~~~~~~~~vP~~~yy~~~~ 54 (71)
..-.|..||++...+++..+-.|.++..+...
T Consensus 39 ~~D~~~~T~~al~~tll~alp~pl~~~~~g~~ 70 (340)
T PF12794_consen 39 RQDSFSHTPRALLLTLLLALPLPLLLLAIGYL 70 (340)
T ss_pred cCCCchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999999999887763
No 14
>PF02939 UcrQ: UcrQ family; InterPro: IPR004205 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multi-enzyme complex [], which recognises a mitochondrial targeting presequence. The bc1 complex contains 11 subunits: 3 respiratory subunits (cytochrome b, cytochrome c1 and Rieske protein), 2 core proteins and 6 low molecular weight proteins. This family represents the 9.5 kDa subunit of the complex. This subunit together with cytochrome B binds to ubiquinone.; GO: 0008121 ubiquinol-cytochrome-c reductase activity; PDB: 1L0N_G 1SQQ_G 1PP9_G 1PPJ_T 2FYU_G 2BCC_G 1BCC_G 2A06_G 1NTZ_G 2YBB_g ....
Probab=33.68 E-value=1.2e+02 Score=18.62 Aligned_cols=32 Identities=16% Similarity=0.134 Sum_probs=18.0
Q ss_pred hHHHHHHHHhHHHHHhHHHHh----hhhhhhhhhcCC
Q 035185 33 NLALVGLFGIAVPVFIYKGIV----KEFHMQDEDAGR 65 (71)
Q Consensus 33 t~~~~~~~~~~vP~~~yy~~~----~~~~~~d~~~G~ 65 (71)
.+.-.+++ +++|+++.|.++ .+.+...+|+|+
T Consensus 40 R~~~q~~~-v~ppfi~~y~i~~Wa~~~~~~~~rK~p~ 75 (80)
T PF02939_consen 40 RFRSQVLY-VAPPFIVGYLIYDWANEENEYLNRKNPA 75 (80)
T ss_dssp HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHTSCCGC
T ss_pred HHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHcCCCHH
Confidence 34444444 458888888876 233444555554
No 15
>PF10582 Connexin_CCC: Gap junction channel protein cysteine-rich domain; InterPro: IPR019570 The connexins are a family of integral membrane proteins that oligomerise to form intercellular channels that are clustered at gap junctions. These channels are specialised sites of cell-cell contact that allow the passage of ions, intracellular metabolites and messenger molecules (with molecular weight less than 1-2kDa) from the cytoplasm of one cell to its opposing neighbours. They are found in almost all vertebrate cell types, and somewhat similar proteins have been cloned from plant species. Invertebrates utilise a different family of molecules, innexins, that share a similar predicted secondary structure to the vertebrate connexins, but have no sequence identity to them []. Vertebrate gap junction channels are thought to participate in diverse biological functions. For instance, in the heart they permit the rapid cell-cell transfer of action potentials, ensuring coordinated contraction of the cardiomyocytes. They are also responsible for neurotransmission at specialised 'electrical' synapses. In non-excitable tissues, such as the liver, they may allow metabolic cooperation between cells. In the brain, glial cells are extensively-coupled by gap junctions; this allows waves of intracellular Ca2+ to propagate through nervous tissue, and may contribute to their ability to spatially-buffer local changes in extracellular K+ concentration []. The connexin protein family is encoded by at least 13 genes in rodents, with many homologues cloned from other species. They show overlapping tissue expression patterns, most tissues expressing more than one connexin type. Their conductances, permeability to different molecules, phosphorylation and voltage-dependence of their gating, have been found to vary. Possible communication diversity is increased further by the fact that gap junctions may be formed by the association of different connexin isoforms from apposing cells. However, in vitro studies have shown that not all possible combinations of connexins produce active channels [, ]. Hydropathy analysis predicts that all cloned connexins share a common transmembrane (TM) topology. Each connexin is thought to contain 4 TM domains, with two extracellular and three cytoplasmic regions. This model has been validated for several of the family members by in vitro biochemical analysis. Both N- and C-termini are thought to face the cytoplasm, and the third TM domain has an amphipathic character, suggesting that it contributes to the lining of the formed-channel. Amino acid sequence identity between the isoforms is ~50-80%, with the TM domains being well conserved. Both extracellular loops contain characteristically conserved cysteine residues, which likely form intramolecular disulphide bonds. By contrast, the single putative intracellular loop (between TM domains 2 and 3) and the cytoplasmic C terminus are highly variable among the family members. Six connexins are thought to associate to form a hemi-channel, or connexon. Two connexons then interact (likely via the extracellular loops of their connexins) to form the complete gap junction channel. NH2-*** *** *************-COOH ** ** ** ** ** ** ** ** Cytoplasmic ---**----**-----**----**---------------- ** ** ** ** Membrane ** ** ** ** ---**----**-----**----**---------------- ** ** ** ** Extracellular ** ** ** ** ** ** Two sets of nomenclature have been used to identify the connexins. The first, and most commonly used, classifies the connexin molecules according to molecular weight, such as connexin43 (abbreviated to Cx43), indicating a connexin of molecular weight close to 43kDa. However, studies have revealed cases where clear functional homologues exist across species that have quite different molecular masses; therefore, an alternative nomenclature was proposed based on evolutionary considerations, which divides the family into two major subclasses, alpha and beta, each with a number of members []. Due to their ubiquity and overlapping tissue distributions, it has proved difficult to elucidate the functions of individual connexin isoforms. To circumvent this problem, particular connexin-encoding genes have been subjected to targeted-disruption in mice, and the phenotype of the resulting animals investigated. Around half the connexin isoforms have been investigated in this manner []. Further insight into the functional roles of connexins has come from the discovery that a number of human diseases are caused by mutations in connexin genes. For instance, mutations in Cx32 give rise to a form of inherited peripheral neuropathy called X-linked dominant Charcot-Marie-Tooth disease []. Similarly, mutations in Cx26 are responsible for both autosomal recessive and dominant forms of nonsyndromic deafness, a disorder characterised by hearing loss, with no apparent effects on other organ systems. This entry represents the cysteine rich domain of the connexins.; PDB: 2ZW3_F.
Probab=32.32 E-value=52 Score=19.62 Aligned_cols=24 Identities=17% Similarity=0.281 Sum_probs=19.5
Q ss_pred eecchhHHHHHHHHhHHHHHhHHH
Q 035185 28 RWTRRNLALVGLFGIAVPVFIYKG 51 (71)
Q Consensus 28 R~Tprt~~~~~~~~~~vP~~~yy~ 51 (71)
|+|-||..+.+++++....++--+
T Consensus 38 RPtEKtIfl~fM~~~s~vsi~L~l 61 (67)
T PF10582_consen 38 RPTEKTIFLIFMFAVSCVSILLNL 61 (67)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCchhhhHHHHHHHHHHHHHHHHH
Confidence 678899999999999887776544
No 16
>PF09446 VMA21: VMA21-like domain; InterPro: IPR019013 The vacuolar ATPase assembly integral membrane protein VMA21 is required for the assembly of the integral membrane sector (V0 component) of the vacuolar ATPase (V-ATPase) in the endoplasmic reticulum []. This entry represents a putative short domain found in VMA21-like proteins, and which appears to contain two potential transmembrane helices.
Probab=32.30 E-value=84 Score=18.27 Aligned_cols=22 Identities=9% Similarity=0.188 Sum_probs=16.2
Q ss_pred HHHHHHHhHHHHHhHHHHhhhh
Q 035185 35 ALVGLFGIAVPVFIYKGIVKEF 56 (71)
Q Consensus 35 ~~~~~~~~~vP~~~yy~~~~~~ 56 (71)
..--+.++.+|++.|++.+.-.
T Consensus 9 l~fs~~M~~lPl~~ff~~~~~~ 30 (66)
T PF09446_consen 9 LFFSVLMFTLPLGTFFGFKYFL 30 (66)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444567889999999998543
No 17
>PF07109 Mg-por_mtran_C: Magnesium-protoporphyrin IX methyltransferase C-terminus; InterPro: IPR010940 This entry represents the C terminus (approximately 100 residues) of bacterial and eukaryotic Magnesium-protoporphyrin IX methyltransferase (2.1.1.11 from EC). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX metylester using S-adenosyl-L-methionine as a cofactor [].; GO: 0046406 magnesium protoporphyrin IX methyltransferase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process
Probab=28.51 E-value=49 Score=21.15 Aligned_cols=25 Identities=20% Similarity=0.219 Sum_probs=19.8
Q ss_pred HhhccccceeecchhHHHHHHHHhH
Q 035185 19 ARENLEHNFRWTRRNLALVGLFGIA 43 (71)
Q Consensus 19 ~ren~~~~FR~Tprt~~~~~~~~~~ 43 (71)
.|.+----|-|-|||.++.+++.++
T Consensus 22 ~~t~~~~ifTfAP~T~~L~~m~~iG 46 (97)
T PF07109_consen 22 SRTRGSLIFTFAPRTPLLALMHAIG 46 (97)
T ss_pred HhccCcEEEEECCCCHHHHHHHHHh
Confidence 3455556799999999999998764
No 18
>PF12365 DUF3649: Protein of unknown function (DUF3649) ; InterPro: IPR022109 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length.
Probab=27.84 E-value=91 Score=15.61 Aligned_cols=23 Identities=13% Similarity=0.288 Sum_probs=14.0
Q ss_pred ecchhHHHHHHHHhHHHHHhHHHH
Q 035185 29 WTRRNLALVGLFGIAVPVFIYKGI 52 (71)
Q Consensus 29 ~Tprt~~~~~~~~~~vP~~~yy~~ 52 (71)
|..|+++.. +-|+++|.++.+.+
T Consensus 2 Fa~rsa~rA-W~Gll~~a~~l~~~ 24 (28)
T PF12365_consen 2 FAARSAWRA-WLGLLLPAALLALL 24 (28)
T ss_pred cccchHHHH-HHHHHHHHHHHHHH
Confidence 456777766 44566666665544
No 19
>PLN02177 glycerol-3-phosphate acyltransferase
Probab=27.53 E-value=68 Score=25.51 Aligned_cols=16 Identities=25% Similarity=-0.151 Sum_probs=14.6
Q ss_pred ceeecchhHHHHHHHH
Q 035185 26 NFRWTRRNLALVGLFG 41 (71)
Q Consensus 26 ~FR~Tprt~~~~~~~~ 41 (71)
-||+||.+++..++|+
T Consensus 238 ~~~p~~~~~l~~~~~~ 253 (497)
T PLN02177 238 VQRPTPLVALLTFLWM 253 (497)
T ss_pred cCCCCHHHHHHHHHHH
Confidence 4999999999999995
No 20
>PF06084 Cytomega_TRL10: Cytomegalovirus TRL10 protein; InterPro: IPR009284 This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulphide-linked complex [].
Probab=27.41 E-value=30 Score=23.53 Aligned_cols=31 Identities=13% Similarity=0.147 Sum_probs=17.9
Q ss_pred HHHHhHHHHHhHHHHh-hhhhhhhhhcCCcccCC
Q 035185 38 GLFGIAVPVFIYKGIV-KEFHMQDEDAGRPYRKF 70 (71)
Q Consensus 38 ~~~~~~vP~~~yy~~~-~~~~~~d~~~G~~~r~f 70 (71)
|+--++|..+++++++ +|..+.| .|+-+-+|
T Consensus 65 fiatliillviffviy~re~~~~~--~gt~~d~~ 96 (150)
T PF06084_consen 65 FIATLIILLVIFFVIYSREEEKNN--NGTEVDQC 96 (150)
T ss_pred HHHHHHHHHHHhheeEeccccccC--CCceechh
Confidence 4455566667777776 4544444 66654444
No 21
>PF03804 DUF325: Viral domain of unknown function; InterPro: IPR003225 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.40 E-value=34 Score=20.86 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=17.3
Q ss_pred cceeecchhHHHHHHHHhHH
Q 035185 25 HNFRWTRRNLALVGLFGIAV 44 (71)
Q Consensus 25 ~~FR~Tprt~~~~~~~~~~v 44 (71)
+.|.|+-|+++++++..+-|
T Consensus 39 ~RFgf~dRnalv~ACM~vnV 58 (71)
T PF03804_consen 39 RRFGFLDRNALVSACMAVNV 58 (71)
T ss_pred HHhCCCcHHHHHHHHHhhee
Confidence 57999999999999987654
No 22
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=24.92 E-value=24 Score=22.11 Aligned_cols=6 Identities=17% Similarity=0.174 Sum_probs=2.9
Q ss_pred hhhhhh
Q 035185 54 KEFHMQ 59 (71)
Q Consensus 54 ~~~~~~ 59 (71)
||+++.
T Consensus 88 Rer~~~ 93 (101)
T PF06024_consen 88 RERQKS 93 (101)
T ss_pred eccccc
Confidence 655443
No 23
>PF09777 OSTMP1: Osteopetrosis-associated transmembrane protein 1 precursor; InterPro: IPR019172 Osteopetrosis-associated transmembrane protein 1 (OSTM1) is required for osteoclast and melanocyte maturation and function. Mutations in OSTM1 give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease [, ].
Probab=24.81 E-value=74 Score=22.89 Aligned_cols=20 Identities=20% Similarity=0.393 Sum_probs=11.7
Q ss_pred HHHHH-HHHhHHHHHhHHHHh
Q 035185 34 LALVG-LFGIAVPVFIYKGIV 53 (71)
Q Consensus 34 ~~~~~-~~~~~vP~~~yy~~~ 53 (71)
+.+++ .+++++|+++|...+
T Consensus 191 ~~i~v~~~vl~lpv~FY~~s~ 211 (237)
T PF09777_consen 191 AVIAVSVFVLFLPVLFYLSSY 211 (237)
T ss_pred HHHHHHHHHHHHHHHHHHhhe
Confidence 44444 444457777776665
No 24
>PF07331 TctB: Tripartite tricarboxylate transporter TctB family; InterPro: IPR009936 This entry contains bacterial proteins of around 150 residues in length, which have 4 transmembrane domains. Some of the sequences in the entry are annotated as the TctB subunit of the tripartite tricarboxylate transport(TTT) family. However there is no direct evidence to support this annotation as characterised members of this family are not associated with the entry.
Probab=23.42 E-value=1.2e+02 Score=18.83 Aligned_cols=27 Identities=19% Similarity=0.189 Sum_probs=18.1
Q ss_pred chhHHHHHHHHhHHHHHhHHHHhhhhh
Q 035185 31 RRNLALVGLFGIAVPVFIYKGIVKEFH 57 (71)
Q Consensus 31 prt~~~~~~~~~~vP~~~yy~~~~~~~ 57 (71)
.|+.+..++..+++++++|+++..-++
T Consensus 111 ~r~~~~~~~~s~~~~~~i~~~F~~~L~ 137 (141)
T PF07331_consen 111 ERRWLRLLLISVVFAAVIYFVFAKLLG 137 (141)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 455566677777788888877765443
No 25
>PLN02499 glycerol-3-phosphate acyltransferase
Probab=23.39 E-value=85 Score=25.42 Aligned_cols=16 Identities=25% Similarity=-0.016 Sum_probs=14.5
Q ss_pred ceeecchhHHHHHHHH
Q 035185 26 NFRWTRRNLALVGLFG 41 (71)
Q Consensus 26 ~FR~Tprt~~~~~~~~ 41 (71)
-||+||.+++..++|+
T Consensus 225 ~~~ptp~~~l~~~~w~ 240 (498)
T PLN02499 225 VKRPTPATALLILLWI 240 (498)
T ss_pred cCCCCHHHHHHHHHHH
Confidence 4999999999999995
No 26
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=22.92 E-value=98 Score=20.90 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=12.7
Q ss_pred HHHHhHHHHHhHHHHhhhhhhhh
Q 035185 38 GLFGIAVPVFIYKGIVKEFHMQD 60 (71)
Q Consensus 38 ~~~~~~vP~~~yy~~~~~~~~~d 60 (71)
=+|+++|-+++.|.+.+-++++|
T Consensus 87 PlYtiGI~~f~lY~l~Ki~~~k~ 109 (152)
T PF15361_consen 87 PLYTIGIVLFILYTLFKIKKKKD 109 (152)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCC
Confidence 35777766666666654333333
No 27
>PF06390 NESP55: Neuroendocrine-specific golgi protein P55 (NESP55); InterPro: IPR009434 This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins [].
Probab=22.78 E-value=1.1e+02 Score=22.64 Aligned_cols=49 Identities=16% Similarity=0.111 Sum_probs=38.7
Q ss_pred HHHHHHhhccccceeecchhHHHHHHHHhHHHHHhHHHHhhhhhhhhhh
Q 035185 14 EEWGAARENLEHNFRWTRRNLALVGLFGIAVPVFIYKGIVKEFHMQDED 62 (71)
Q Consensus 14 erw~~~ren~~~~FR~Tprt~~~~~~~~~~vP~~~yy~~~~~~~~~d~~ 62 (71)
+.|-.+|-|...-.-.-.|.+..+++|.----+++-.++.+.-+.|++.
T Consensus 8 ~~~rrarh~y~dlcppigrraatallwlscsiallrala~s~~raqqra 56 (257)
T PF06390_consen 8 QQWRRARHNYNDLCPPIGRRAATALLWLSCSIALLRALATSNARAQQRA 56 (257)
T ss_pred HHHHHhhhcccccCCchhhHHHHHHHHHHhHHHHHHHHHhcchHHHHHH
Confidence 5688888888887888889999999999887777777777655555553
No 28
>PTZ00234 variable surface protein Vir12; Provisional
Probab=22.09 E-value=81 Score=24.92 Aligned_cols=39 Identities=10% Similarity=-0.029 Sum_probs=21.8
Q ss_pred hhHHHHHHHHhHHHHHhHHHHhhhhhhhhhhcCCcccCC
Q 035185 32 RNLALVGLFGIAVPVFIYKGIVKEFHMQDEDAGRPYRKF 70 (71)
Q Consensus 32 rt~~~~~~~~~~vP~~~yy~~~~~~~~~d~~~G~~~r~f 70 (71)
|++..++.-.+.+-+++||......+-+-.+.-|+.++|
T Consensus 365 rniim~~ailGtifFlfyyn~ss~lks~~~krkrkk~~~ 403 (433)
T PTZ00234 365 RHSIVGASIIGVLVFLFFFFKSTPIRSQTNKGEKKKRKP 403 (433)
T ss_pred HHHHHHHHHHHHHHHhhhhhcccchhccccchhhcccch
Confidence 456666655566667777766655544444444444443
No 29
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=21.03 E-value=11 Score=14.18 Aligned_cols=7 Identities=14% Similarity=0.729 Sum_probs=4.2
Q ss_pred CHHHHHH
Q 035185 10 NRFIEEW 16 (71)
Q Consensus 10 dPalerw 16 (71)
||++..|
T Consensus 1 ~pafnsw 7 (8)
T PF08260_consen 1 DPAFNSW 7 (8)
T ss_pred Ccccccc
Confidence 5666655
No 30
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=20.63 E-value=1.3e+02 Score=22.92 Aligned_cols=25 Identities=20% Similarity=0.183 Sum_probs=18.0
Q ss_pred HHHHHHHHhHHHHHhHHHHhhhhhh
Q 035185 34 LALVGLFGIAVPVFIYKGIVKEFHM 58 (71)
Q Consensus 34 ~~~~~~~~~~vP~~~yy~~~~~~~~ 58 (71)
+.++++-.++|.+++|...++.++.
T Consensus 264 aalvllil~vvliiLYiWlyrrRK~ 288 (295)
T TIGR01478 264 AALVLIILTVVLIILYIWLYRRRKK 288 (295)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4566677777888888888876543
No 31
>PTZ00370 STEVOR; Provisional
Probab=20.02 E-value=1.4e+02 Score=22.80 Aligned_cols=25 Identities=24% Similarity=0.186 Sum_probs=17.8
Q ss_pred HHHHHHHHhHHHHHhHHHHhhhhhh
Q 035185 34 LALVGLFGIAVPVFIYKGIVKEFHM 58 (71)
Q Consensus 34 ~~~~~~~~~~vP~~~yy~~~~~~~~ 58 (71)
+.++++-.++|.+++|...++.++.
T Consensus 260 aalvllil~vvliilYiwlyrrRK~ 284 (296)
T PTZ00370 260 AALVLLILAVVLIILYIWLYRRRKN 284 (296)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4566667777888888888876543
Done!