Query 035015
Match_columns 76
No_of_seqs 102 out of 676
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:30:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035015.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035015hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1773 Stress responsive prot 99.9 5.8E-28 1.3E-32 147.6 5.7 61 1-61 1-61 (63)
2 COG0401 Uncharacterized homolo 99.9 1.1E-25 2.4E-30 134.6 5.0 55 4-58 2-56 (56)
3 PF01679 Pmp3: Proteolipid mem 99.9 1.4E-23 3.1E-28 123.3 3.2 51 6-57 1-51 (51)
4 PF14373 Imm_superinfect: Supe 88.7 0.5 1.1E-05 26.8 2.4 23 30-52 18-42 (43)
5 PF07123 PsbW: Photosystem II 71.1 2.6 5.7E-05 29.3 1.5 26 36-61 104-129 (138)
6 PLN00077 photosystem II reacti 70.7 3 6.5E-05 28.7 1.6 30 36-65 93-122 (128)
7 PLN00082 photosystem II reacti 70.6 3.3 7.1E-05 25.7 1.6 26 37-62 33-58 (67)
8 PLN00092 photosystem I reactio 64.6 4.8 0.0001 27.9 1.7 27 36-62 103-129 (137)
9 PF11298 DUF3099: Protein of u 59.1 6.2 0.00013 24.5 1.3 21 7-27 44-64 (73)
10 PF05478 Prominin: Prominin; 49.0 11 0.00023 31.9 1.6 32 32-63 769-800 (806)
11 cd01784 rasfadin_RA Ubiquitin- 43.6 9 0.0002 24.8 0.3 59 14-73 5-68 (87)
12 PF05393 Hum_adeno_E3A: Human 42.6 13 0.00027 24.5 0.9 10 65-74 59-68 (94)
13 PF09964 DUF2198: Uncharacteri 40.9 23 0.0005 22.3 1.8 45 10-55 2-50 (74)
14 COG4665 FcbT2 TRAP-type mannit 40.5 31 0.00067 25.1 2.7 27 30-56 88-114 (182)
15 KOG3249 Uncharacterized conser 40.2 39 0.00085 24.5 3.2 35 5-45 104-138 (181)
16 PRK10525 cytochrome o ubiquino 40.1 38 0.00082 26.1 3.3 30 33-62 44-73 (315)
17 KOG4040 NADH:ubiquinone oxidor 39.9 29 0.00063 25.2 2.4 27 33-59 127-153 (186)
18 PF15018 InaF-motif: TRP-inter 39.7 40 0.00087 18.6 2.5 27 35-61 8-35 (38)
19 PF04246 RseC_MucC: Positive r 34.1 18 0.0004 23.6 0.7 64 6-70 65-129 (135)
20 CHL00186 psaI photosystem I su 33.7 25 0.00055 19.3 1.1 26 36-61 8-34 (36)
21 TIGR03052 PS_I_psaI photosyste 31.0 21 0.00046 19.0 0.4 23 38-60 7-30 (31)
22 PF06024 DUF912: Nucleopolyhed 30.3 93 0.002 19.8 3.5 9 48-56 77-85 (101)
23 TIGR02230 ATPase_gene1 F0F1-AT 28.9 36 0.00079 22.2 1.4 37 20-57 62-98 (100)
24 PRK13823 conjugal transfer pro 27.6 75 0.0016 20.5 2.7 32 30-62 39-70 (94)
25 COG4897 CsbA Uncharacterized p 25.6 50 0.0011 20.9 1.5 46 10-56 3-52 (78)
26 COG3152 Predicted membrane pro 24.3 1.8E+02 0.0039 19.5 4.1 38 8-46 56-97 (125)
27 PRK09459 pspG phage shock prot 23.1 1E+02 0.0022 19.5 2.6 35 34-69 40-74 (76)
28 COG3086 RseC Positive regulato 21.9 26 0.00057 24.7 -0.3 59 8-67 75-133 (150)
29 PF07225 NDUF_B4: NADH-ubiquin 21.9 55 0.0012 22.2 1.3 22 43-66 90-111 (125)
30 cd01782 AF6_RA_repeat1 Ubiquit 20.8 32 0.00069 23.2 -0.1 25 49-73 70-94 (112)
31 PF04505 Dispanin: Interferon- 20.0 39 0.00085 20.8 0.2 30 30-59 16-45 (82)
No 1
>KOG1773 consensus Stress responsive protein [General function prediction only]
Probab=99.95 E-value=5.8e-28 Score=147.61 Aligned_cols=61 Identities=49% Similarity=0.949 Sum_probs=59.7
Q ss_pred CCcchHHHHHHHHHHhcchheeehhhcCCChhHHHHHHHHHHHhhhhhhhhhheeeeeCcc
Q 035015 1 MPTRCEIFCEILLAVLLPPVGVCLRHGCCSVEFCICLLLTILGYVPGIIYALYAIVFVDRD 61 (76)
Q Consensus 1 m~~~~~~~~~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~iPg~ihA~y~i~~~~~~ 61 (76)
|++|++|++++++|+|+||+||++++|+|++|++||++||++||+||++||+|++++++|+
T Consensus 1 m~~~~~~~~~iilai~lPP~aV~l~~g~C~~~~~InilL~~L~~iPgiIhA~yii~~~~r~ 61 (63)
T KOG1773|consen 1 MATDCDDILLIILAIFLPPLAVFLRRGGCTVDVLINILLTLLGFIPGIIHAIYIIFFRGRE 61 (63)
T ss_pred CCCcHHHHHHHHHHHHcCchheeeecCCCchhhHHHHHHHHHHHhHHHHhhEEEEEEecCC
Confidence 8899999999999999999999999999999999999999999999999999999999987
No 2
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=99.92 E-value=1.1e-25 Score=134.65 Aligned_cols=55 Identities=51% Similarity=0.849 Sum_probs=52.4
Q ss_pred chHHHHHHHHHHhcchheeehhhcCCChhHHHHHHHHHHHhhhhhhhhhheeeee
Q 035015 4 RCEIFCEILLAVLLPPVGVCLRHGCCSVEFCICLLLTILGYVPGIIYALYAIVFV 58 (76)
Q Consensus 4 ~~~~~~~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~iPg~ihA~y~i~~~ 58 (76)
+..|++++++|+|+||+||++++|.|++|+++|++||++||+||++||+|++.++
T Consensus 2 ~~~d~~~iilaiflPP~~VfL~~G~~~~df~iNiLLtlLg~~PGiiHA~yvi~~~ 56 (56)
T COG0401 2 TLMDFIRIVLAIFLPPLGVFLRRGFGGKDFLINILLTLLGYIPGIIHALYVILRD 56 (56)
T ss_pred cHHHHHHHHHHHHcCchhhhhhccCCcHHHHHHHHHHHHHhhhhhHhheEEEEeC
Confidence 5789999999999999999999998899999999999999999999999999763
No 3
>PF01679 Pmp3: Proteolipid membrane potential modulator; InterPro: IPR000612 Proteolipid membrane potential modulator is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants. Proteins in this entry include the PMP3 as well as several other proteins that have been shown [] to be evolutionary related. These are small proteins of from 52 to 140 amino-acid resiudes that contain two transmembrane domains and belong to the UPF0057 (PMP3) protein family.; GO: 0016021 integral to membrane
Probab=99.88 E-value=1.4e-23 Score=123.33 Aligned_cols=51 Identities=51% Similarity=0.903 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhcchheeehhhcCCChhHHHHHHHHHHHhhhhhhhhhheeee
Q 035015 6 EIFCEILLAVLLPPVGVCLRHGCCSVEFCICLLLTILGYVPGIIYALYAIVF 57 (76)
Q Consensus 6 ~~~~~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~iPg~ihA~y~i~~ 57 (76)
.|++++++|+++||+||++++| |++|+++|++||++||+||++||+|++++
T Consensus 1 ~~~~~~ilai~lPPlaV~~~~g-~~~~~~inl~Ltl~g~iPg~ihA~y~i~~ 51 (51)
T PF01679_consen 1 MDILLIILAIFLPPLAVFLKKG-CSKDFWINLLLTLLGWIPGVIHALYVIYK 51 (51)
T ss_pred CcHHHHHHHHHcccHHHHHHcC-CchhhHHHHHHHHHHHHHHHHHeeEEEeC
Confidence 3689999999999999999999 99999999999999999999999999864
No 4
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=88.66 E-value=0.5 Score=26.79 Aligned_cols=23 Identities=43% Similarity=0.661 Sum_probs=19.3
Q ss_pred ChhHHHHHHH--HHHHhhhhhhhhh
Q 035015 30 SVEFCICLLL--TILGYVPGIIYAL 52 (76)
Q Consensus 30 ~~~~~In~lL--tllg~iPg~ihA~ 52 (76)
..=+++|++| |.+||+-+.++|+
T Consensus 18 ~~I~~~Nl~lGWT~iGWv~aLiwA~ 42 (43)
T PF14373_consen 18 WAIFLLNLLLGWTGIGWVAALIWAL 42 (43)
T ss_pred hhhHhHHHHHHhHHHHHHHHHHHhc
Confidence 3456889998 9999999999885
No 5
>PF07123 PsbW: Photosystem II reaction centre W protein (PsbW); InterPro: IPR009806 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 []. This family represents the low molecular weight transmembrane protein PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.; GO: 0015979 photosynthesis, 0009507 chloroplast, 0009523 photosystem II
Probab=71.08 E-value=2.6 Score=29.33 Aligned_cols=26 Identities=38% Similarity=0.346 Sum_probs=20.6
Q ss_pred HHHHHHHHhhhhhhhhhheeeeeCcc
Q 035015 36 CLLLTILGYVPGIIYALYAIVFVDRD 61 (76)
Q Consensus 36 n~lLtllg~iPg~ihA~y~i~~~~~~ 61 (76)
|++-+++.-++|.||++|.++.++=+
T Consensus 104 ~~LgwIL~gVf~lIWslY~~~~~~l~ 129 (138)
T PF07123_consen 104 NLLGWILLGVFGLIWSLYFVYTSTLD 129 (138)
T ss_pred chhHHHHHHHHHHHHHHHHhhccccC
Confidence 45557788899999999999866654
No 6
>PLN00077 photosystem II reaction centre W protein; Provisional
Probab=70.69 E-value=3 Score=28.69 Aligned_cols=30 Identities=37% Similarity=0.279 Sum_probs=22.1
Q ss_pred HHHHHHHHhhhhhhhhhheeeeeCcchhhh
Q 035015 36 CLLLTILGYVPGIIYALYAIVFVDRDEYFD 65 (76)
Q Consensus 36 n~lLtllg~iPg~ihA~y~i~~~~~~~~~~ 65 (76)
|.+-+++.-+++.||++|.++.++-++..+
T Consensus 93 ~~LgwIL~gVf~liw~ly~~~~~~l~~~ed 122 (128)
T PLN00077 93 NLLGWILLGVFGLIWSLYTTYTSDLPEDEE 122 (128)
T ss_pred chhhHHHHhHHHHHHHHHhheecccCCccc
Confidence 344577778899999999998776654333
No 7
>PLN00082 photosystem II reaction centre W protein (PsbW); Provisional
Probab=70.56 E-value=3.3 Score=25.68 Aligned_cols=26 Identities=35% Similarity=0.240 Sum_probs=19.7
Q ss_pred HHHHHHHhhhhhhhhhheeeeeCcch
Q 035015 37 LLLTILGYVPGIIYALYAIVFVDRDE 62 (76)
Q Consensus 37 ~lLtllg~iPg~ihA~y~i~~~~~~~ 62 (76)
.+-+++.-+++.|+++|.++.+.-++
T Consensus 33 ~LgwIL~gvf~liw~ly~~~~~~l~~ 58 (67)
T PLN00082 33 KLTWILVGVTALIWALYFSYSSTLPE 58 (67)
T ss_pred hhhhHHHHHHHHHHHHHhheecccCC
Confidence 44467777899999999997665554
No 8
>PLN00092 photosystem I reaction center subunit V (PsaG); Provisional
Probab=64.55 E-value=4.8 Score=27.95 Aligned_cols=27 Identities=37% Similarity=0.353 Sum_probs=20.3
Q ss_pred HHHHHHHHhhhhhhhhhheeeeeCcch
Q 035015 36 CLLLTILGYVPGIIYALYAIVFVDRDE 62 (76)
Q Consensus 36 n~lLtllg~iPg~ihA~y~i~~~~~~~ 62 (76)
|.+-+++.-+++.||++|.++.+.-++
T Consensus 103 ~~LgwIL~gVf~lIWslYf~~~~~l~e 129 (137)
T PLN00092 103 NLLGWILLGVFGLIWSLYFVYTSTLEE 129 (137)
T ss_pred cchhhHHHhHHHHHHHHHheeecccCc
Confidence 344477778899999999998765443
No 9
>PF11298 DUF3099: Protein of unknown function (DUF3099); InterPro: IPR021449 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Probab=59.12 E-value=6.2 Score=24.51 Aligned_cols=21 Identities=33% Similarity=0.371 Sum_probs=16.1
Q ss_pred HHHHHHHHHhcchheeehhhc
Q 035015 7 IFCEILLAVLLPPVGVCLRHG 27 (76)
Q Consensus 7 ~~~~~ilai~lPPlaV~l~~g 27 (76)
.+..+..|+++|++||.+-.+
T Consensus 44 a~~~~~~av~LPwvAVviAN~ 64 (73)
T PF11298_consen 44 AWAIIVGAVPLPWVAVVIANA 64 (73)
T ss_pred HHHHHHHhcccchhheeeccC
Confidence 355677888999999988654
No 10
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=48.99 E-value=11 Score=31.90 Aligned_cols=32 Identities=25% Similarity=0.297 Sum_probs=26.0
Q ss_pred hHHHHHHHHHHHhhhhhhhhhheeeeeCcchh
Q 035015 32 EFCICLLLTILGYVPGIIYALYAIVFVDRDEY 63 (76)
Q Consensus 32 ~~~In~lLtllg~iPg~ihA~y~i~~~~~~~~ 63 (76)
-||.++.++.++++|+++.|+-....|++-+.
T Consensus 769 ~fWf~l~~c~~~liP~ii~avkL~k~yrrm~~ 800 (806)
T PF05478_consen 769 GFWFGLGWCTLFLIPSIIFAVKLAKYYRRMDP 800 (806)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHccCCc
Confidence 46999999999999999999998755555433
No 11
>cd01784 rasfadin_RA Ubiquitin-like domain of Rasfadin. rasfadin_RA Rasfadin (RASSF2) belongs to a family of Ras effectors/tumor suppressors that includes RASSF1 and NORE1. RASSF2 binds directly to K-Ras in a GTP-dependent manner via its RA (RAS-associated) domain. RASSF2 promotes apoptosis and cell cycle arrest and is frequently down-regulated in lung tumor cell lines
Probab=43.57 E-value=9 Score=24.78 Aligned_cols=59 Identities=20% Similarity=0.252 Sum_probs=36.9
Q ss_pred HHhcchh----eeehhhcCCChhHHHHHHHHHHHh-hhhhhhhhheeeeeCcchhhhhcCcccCC
Q 035015 14 AVLLPPV----GVCLRHGCCSVEFCICLLLTILGY-VPGIIYALYAIVFVDRDEYFDEYRRPLYA 73 (76)
Q Consensus 14 ai~lPPl----aV~l~~g~~~~~~~In~lLtllg~-iPg~ihA~y~i~~~~~~~~~~~~~Rp~~~ 73 (76)
++|+|+. .|-+... .+.+-.|+.+|-=+-- --.-=+|+|.++....+++-++.++|++.
T Consensus 5 S~f~P~~gs~~~v~VsS~-~tt~eVI~~LL~KFkv~~~p~~FALy~vh~~Ge~rkL~d~E~PL~~ 68 (87)
T cd01784 5 SVFTPAYGSVTNVRINST-MTTPQVLKLLLNKFKIENSAEEFALYIVHTSGEKRKLKATDYPLIA 68 (87)
T ss_pred cEeCCCCCceeEEEEecC-CCHHHHHHHHHHhccccCCHHHeEEEEEeeCCCEEECCCcCCCeeh
Confidence 4667772 3333333 4555566766622211 22245799999888877888999999875
No 12
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=42.61 E-value=13 Score=24.47 Aligned_cols=10 Identities=50% Similarity=1.119 Sum_probs=6.1
Q ss_pred hhcCcccCCC
Q 035015 65 DEYRRPLYAP 74 (76)
Q Consensus 65 ~~~~Rp~~~~ 74 (76)
++.|||||.|
T Consensus 59 krsRrPIYrP 68 (94)
T PF05393_consen 59 KRSRRPIYRP 68 (94)
T ss_pred hhccCCcccc
Confidence 3457777754
No 13
>PF09964 DUF2198: Uncharacterized protein conserved in bacteria (DUF2198); InterPro: IPR019242 This family of various hypothetical archaeal proteins has no known function.
Probab=40.91 E-value=23 Score=22.30 Aligned_cols=45 Identities=22% Similarity=0.273 Sum_probs=31.8
Q ss_pred HHHHHHhcchheeehhhcCCChhHHHHHHHHHHHh----hhhhhhhhhee
Q 035015 10 EILLAVLLPPVGVCLRHGCCSVEFCICLLLTILGY----VPGIIYALYAI 55 (76)
Q Consensus 10 ~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~----iPg~ihA~y~i 55 (76)
.+++|.++|=+-|.+-.. .+.+-++-.+||+.-- .-|.-|.+|++
T Consensus 2 ~~~~Al~~P~lLVvlFtr-VT~n~~vg~~lt~~Li~ASvykGyt~~~~ii 50 (74)
T PF09964_consen 2 KYLLALFFPCLLVVLFTR-VTYNHYVGTILTVALIAASVYKGYTHTWWII 50 (74)
T ss_pred HHHHHHHHHHHHHHHhhh-hhHHHHHHHHHHHHHHHHHHHhccccchHHH
Confidence 468999999999988776 6888888888876542 33444444443
No 14
>COG4665 FcbT2 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.53 E-value=31 Score=25.08 Aligned_cols=27 Identities=22% Similarity=0.199 Sum_probs=23.3
Q ss_pred ChhHHHHHHHHHHHhhhhhhhhhheee
Q 035015 30 SVEFCICLLLTILGYVPGIIYALYAIV 56 (76)
Q Consensus 30 ~~~~~In~lLtllg~iPg~ihA~y~i~ 56 (76)
..+.|++++.|+++.+|+.+.-+|+-.
T Consensus 88 R~qa~vDllGtifFLlPfc~l~iy~~~ 114 (182)
T COG4665 88 RTQAWVDLLGTIFFLLPFCLLVIYLSW 114 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 357899999999999999998888753
No 15
>KOG3249 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.19 E-value=39 Score=24.49 Aligned_cols=35 Identities=23% Similarity=0.514 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHhcchheeehhhcCCChhHHHHHHHHHHHhh
Q 035015 5 CEIFCEILLAVLLPPVGVCLRHGCCSVEFCICLLLTILGYV 45 (76)
Q Consensus 5 ~~~~~~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~i 45 (76)
...++.+++-+.+-|+|+-+..| .+=++|+++.|+
T Consensus 104 ~~~~v~vllW~vL~~ia~~l~fG------lvff~lSlf~~i 138 (181)
T KOG3249|consen 104 LKMWVIVLLWFVLAPIAHRLDFG------LVFFLLSLFSII 138 (181)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhh------HHHHHHHHHHHh
Confidence 34467778888899999888777 455556666554
No 16
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional
Probab=40.10 E-value=38 Score=26.14 Aligned_cols=30 Identities=13% Similarity=0.113 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhhhhhhhhheeeeeCcch
Q 035015 33 FCICLLLTILGYVPGIIYALYAIVFVDRDE 62 (76)
Q Consensus 33 ~~In~lLtllg~iPg~ihA~y~i~~~~~~~ 62 (76)
+++.+.+.++.++|-++-++|...+++++.
T Consensus 44 i~~~~~~~liv~i~V~~l~~~f~~ryR~~~ 73 (315)
T PRK10525 44 ILTAFGLMLIVVIPAILMAVGFAWKYRASN 73 (315)
T ss_pred HHHHHHHHHhhHHHHHHHHheeEEEEecCC
Confidence 566777888899999988888887776543
No 17
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=39.88 E-value=29 Score=25.16 Aligned_cols=27 Identities=19% Similarity=0.184 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhhhhhhhhhheeeeeC
Q 035015 33 FCICLLLTILGYVPGIIYALYAIVFVD 59 (76)
Q Consensus 33 ~~In~lLtllg~iPg~ihA~y~i~~~~ 59 (76)
-|-+++.+++|.+|+.+.|+|+.-.+.
T Consensus 127 ~w~~~~mcl~g~~~~~l~~~y~~d~~p 153 (186)
T KOG4040|consen 127 TWNSIVMCLRGLVPMALLAWYFTDEHP 153 (186)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHccccc
Confidence 477888999999999999999875444
No 18
>PF15018 InaF-motif: TRP-interacting helix
Probab=39.70 E-value=40 Score=18.62 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=20.0
Q ss_pred HHHHHHHHHh-hhhhhhhhheeeeeCcc
Q 035015 35 ICLLLTILGY-VPGIIYALYAIVFVDRD 61 (76)
Q Consensus 35 In~lLtllg~-iPg~ihA~y~i~~~~~~ 61 (76)
+.++.++++- ++|+.-|+|+++..+++
T Consensus 8 ~tV~~Yl~~VSl~Ai~LsiYY~f~W~p~ 35 (38)
T PF15018_consen 8 LTVVAYLFSVSLAAIVLSIYYIFFWDPD 35 (38)
T ss_pred HHHHHHHHHHHHHHHHHHHHHheeeCCC
Confidence 4455566554 79999999999877665
No 19
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=34.14 E-value=18 Score=23.60 Aligned_cols=64 Identities=19% Similarity=0.184 Sum_probs=29.8
Q ss_pred HHHHHH-HHHHhcchheeehhhcCCChhHHHHHHHHHHHhhhhhhhhhheeeeeCcchhhhhcCcc
Q 035015 6 EIFCEI-LLAVLLPPVGVCLRHGCCSVEFCICLLLTILGYVPGIIYALYAIVFVDRDEYFDEYRRP 70 (76)
Q Consensus 6 ~~~~~~-ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~iPg~ihA~y~i~~~~~~~~~~~~~Rp 70 (76)
+..++. +++..+|-++.++--. .+..+.-+-...+++-+=|.+-+++++...+++.+.++..+|
T Consensus 65 ~~~~~aa~l~Y~lPll~li~g~~-l~~~~~~~e~~~~l~~l~~l~~~~~~~~~~~~~~~~~~~~~p 129 (135)
T PF04246_consen 65 SSLLKAAFLVYLLPLLALIAGAV-LGSYLGGSELWAILGGLLGLALGFLILRLFDRRLKKKSKFQP 129 (135)
T ss_pred chHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCce
Confidence 344444 4444454444444332 344444444445555555555555555444444333333444
No 20
>CHL00186 psaI photosystem I subunit VIII; Validated
Probab=33.75 E-value=25 Score=19.31 Aligned_cols=26 Identities=23% Similarity=0.442 Sum_probs=18.7
Q ss_pred HHHHHHHHhh-hhhhhhhheeeeeCcc
Q 035015 36 CLLLTILGYV-PGIIYALYAIVFVDRD 61 (76)
Q Consensus 36 n~lLtllg~i-Pg~ihA~y~i~~~~~~ 61 (76)
+++-.+.||+ ||+.-|...++.+++|
T Consensus 8 sI~VPlVGlvfPai~Ma~lf~yIe~~~ 34 (36)
T CHL00186 8 SILVPLVGLVFPAIAMASLFLYIQKDK 34 (36)
T ss_pred hhHHhHHHHHHHHHHHHHHHHHhhhcc
Confidence 5566778885 9999988877655443
No 21
>TIGR03052 PS_I_psaI photosystem I reaction center subunit VIII. Members of this protein family are PsaI, subunit VIII of the photosystem I reaction center. This protein is found in both the Cyanobacteria and the chloroplasts of plants, but is absent from non-oxygenic photosynthetic bacteria such as Rhodobacter sphaeroides. Species that contain photosystem I also contain photosystem II, which splits water and releases molecular oxygen.
Probab=30.96 E-value=21 Score=18.99 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=15.9
Q ss_pred HHHHHHhh-hhhhhhhheeeeeCc
Q 035015 38 LLTILGYV-PGIIYALYAIVFVDR 60 (76)
Q Consensus 38 lLtllg~i-Pg~ihA~y~i~~~~~ 60 (76)
+-.+.||+ ||+.-|...++.+++
T Consensus 7 ~VPlVglvfPai~Ma~lf~yIe~~ 30 (31)
T TIGR03052 7 FVPLVGLVFPAVFMALLFRYIEAD 30 (31)
T ss_pred ehhHHHHHHHHHHHHHHHHheecc
Confidence 34566774 999888887765544
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=30.31 E-value=93 Score=19.82 Aligned_cols=9 Identities=56% Similarity=1.102 Sum_probs=6.1
Q ss_pred hhhhhheee
Q 035015 48 IIYALYAIV 56 (76)
Q Consensus 48 ~ihA~y~i~ 56 (76)
+++|+|+..
T Consensus 77 ily~IyYFV 85 (101)
T PF06024_consen 77 ILYAIYYFV 85 (101)
T ss_pred HHhhheEEE
Confidence 677887754
No 23
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=28.92 E-value=36 Score=22.23 Aligned_cols=37 Identities=27% Similarity=0.327 Sum_probs=27.1
Q ss_pred heeehhhcCCChhHHHHHHHHHHHhhhhhhhhhheeee
Q 035015 20 VGVCLRHGCCSVEFCICLLLTILGYVPGIIYALYAIVF 57 (76)
Q Consensus 20 laV~l~~g~~~~~~~In~lLtllg~iPg~ihA~y~i~~ 57 (76)
++.++-+. ++.+.+..+.+.++|-.-|...|++.+.+
T Consensus 62 lG~WLD~~-~~t~~~~tl~~lllGv~~G~~n~w~wi~r 98 (100)
T TIGR02230 62 VGIWLDRH-YPSPFSWTLTMLIVGVVIGCLNAWHWVSR 98 (100)
T ss_pred HHHHHHhh-cCCCcHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34555444 45566888889999999999998887754
No 24
>PRK13823 conjugal transfer protein TrbD; Provisional
Probab=27.61 E-value=75 Score=20.46 Aligned_cols=32 Identities=9% Similarity=-0.022 Sum_probs=24.5
Q ss_pred ChhHHHHHHHHHHHhhhhhhhhhheeeeeCcch
Q 035015 30 SVEFCICLLLTILGYVPGIIYALYAIVFVDRDE 62 (76)
Q Consensus 30 ~~~~~In~lLtllg~iPg~ihA~y~i~~~~~~~ 62 (76)
+.+.|++.+..+..|+.++..+.|. .++++.-
T Consensus 39 g~~~~~a~~~gl~lw~v~h~~l~~m-AK~DP~~ 70 (94)
T PRK13823 39 VAQTWRAALFGIALWFGALFALRLM-AKADPKM 70 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HhcChHH
Confidence 4466888888889999998888887 5666643
No 25
>COG4897 CsbA Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.61 E-value=50 Score=20.94 Aligned_cols=46 Identities=22% Similarity=0.299 Sum_probs=31.3
Q ss_pred HHHHHHhcchheeehhhcCCChhHHHHHHHHHHH----hhhhhhhhhheee
Q 035015 10 EILLAVLLPPVGVCLRHGCCSVEFCICLLLTILG----YVPGIIYALYAIV 56 (76)
Q Consensus 10 ~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg----~iPg~ihA~y~i~ 56 (76)
.++.|.|+|=+-|.+-.. .+.+=++.++||... ..-|.-|..|++.
T Consensus 3 ~~~sAlfFPc~LVvLF~r-iT~n~yVa~vLt~vLi~AS~~kgYt~~~wii~ 52 (78)
T COG4897 3 QIISALFFPCLLVVLFAR-ITYNRYVALVLTVVLIAASAKKGYTSSFWIIT 52 (78)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhcccceeeeee
Confidence 457889999988887665 466667777777654 3445556666653
No 26
>COG3152 Predicted membrane protein [Function unknown]
Probab=24.25 E-value=1.8e+02 Score=19.48 Aligned_cols=38 Identities=26% Similarity=0.513 Sum_probs=24.4
Q ss_pred HHHHHHHHhcchheeehhh----cCCChhHHHHHHHHHHHhhh
Q 035015 8 FCEILLAVLLPPVGVCLRH----GCCSVEFCICLLLTILGYVP 46 (76)
Q Consensus 8 ~~~~ilai~lPPlaV~l~~----g~~~~~~~In~lLtllg~iP 46 (76)
...+.+|.++|=+|+..|+ | .+.-..+..+....|++=
T Consensus 56 ~~l~~la~~~p~lal~vrRLHD~g-~sgw~~Ll~lip~vg~iv 97 (125)
T COG3152 56 TALYLLALFLPTLALTVRRLHDRG-RSGWWALLALIPVVGWIV 97 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHHH
Confidence 4678899999999999985 3 244333333345555443
No 27
>PRK09459 pspG phage shock protein G; Reviewed
Probab=23.13 E-value=1e+02 Score=19.52 Aligned_cols=35 Identities=14% Similarity=0.324 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhhhhhhhhhheeeeeCcchhhhhcCc
Q 035015 34 CICLLLTILGYVPGIIYALYAIVFVDRDEYFDEYRR 69 (76)
Q Consensus 34 ~In~lLtllg~iPg~ihA~y~i~~~~~~~~~~~~~R 69 (76)
...+++=++=|+--++-++|+.- ...+++.++++|
T Consensus 40 m~~lviKLLPWLil~~v~vW~~r-~~~~~~~~~y~~ 74 (76)
T PRK09459 40 MFALMIKLLPWLLLAVVVVWVIR-AIKAPKVPRYQR 74 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-Hhhccccccccc
Confidence 44555566668877778888763 323334455554
No 28
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=21.95 E-value=26 Score=24.71 Aligned_cols=59 Identities=19% Similarity=0.179 Sum_probs=36.8
Q ss_pred HHHHHHHHhcchheeehhhcCCChhHHHHHHHHHHHhhhhhhhhhheeeeeCcchhhhhc
Q 035015 8 FCEILLAVLLPPVGVCLRHGCCSVEFCICLLLTILGYVPGIIYALYAIVFVDRDEYFDEY 67 (76)
Q Consensus 8 ~~~~ilai~lPPlaV~l~~g~~~~~~~In~lLtllg~iPg~ihA~y~i~~~~~~~~~~~~ 67 (76)
+.--++..++|.+..++..= .......|=.+.+++-+=|...++|+.-.|.|+.+.+.-
T Consensus 75 L~sA~LvYi~PL~~l~v~~~-La~~L~~~e~~~~~~~~lg~~l~fl~~r~ysRkl~~~~~ 133 (150)
T COG3086 75 LKSALLVYIFPLVGLFLGAI-LAQYLFFSELIVIFGAFLGLALGFLLARRYSRKLAKRTE 133 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence 34456677888887776432 223344455566777777888888888766665554433
No 29
>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=21.85 E-value=55 Score=22.20 Aligned_cols=22 Identities=41% Similarity=0.581 Sum_probs=12.0
Q ss_pred HhhhhhhhhhheeeeeCcchhhhh
Q 035015 43 GYVPGIIYALYAIVFVDRDEYFDE 66 (76)
Q Consensus 43 g~iPg~ihA~y~i~~~~~~~~~~~ 66 (76)
|..|.+++ |++.+.++|++.+.
T Consensus 90 ~v~P~i~~--~~~~KtdRD~~E~~ 111 (125)
T PF07225_consen 90 GVVPLIFY--YYVLKTDRDRKEKL 111 (125)
T ss_pred HHHHHHHH--HhhhccchhHHHHH
Confidence 44565544 45556666665443
No 30
>cd01782 AF6_RA_repeat1 Ubiquitin domain of AT-6, first repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=20.81 E-value=32 Score=23.24 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=20.7
Q ss_pred hhhhheeeeeCcchhhhhcCcccCC
Q 035015 49 IYALYAIVFVDRDEYFDEYRRPLYA 73 (76)
Q Consensus 49 ihA~y~i~~~~~~~~~~~~~Rp~~~ 73 (76)
=+|+|.++....+++-.+.++|++.
T Consensus 70 ~FALYevh~nGe~RKL~d~E~PL~~ 94 (112)
T cd01782 70 TYSLYEVHENGEERRLLDDEKPLVV 94 (112)
T ss_pred ceEEEEEecCCceEEcCCcCCCeEE
Confidence 6899999887777788888999864
No 31
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=20.02 E-value=39 Score=20.84 Aligned_cols=30 Identities=17% Similarity=0.020 Sum_probs=18.9
Q ss_pred ChhHHHHHHHHHHHhhhhhhhhhheeeeeC
Q 035015 30 SVEFCICLLLTILGYVPGIIYALYAIVFVD 59 (76)
Q Consensus 30 ~~~~~In~lLtllg~iPg~ihA~y~i~~~~ 59 (76)
...+..+++.|+|.+.|=-+-|++.-.+-+
T Consensus 16 ~~yl~~sI~s~l~Cc~PlGi~Ai~~s~kv~ 45 (82)
T PF04505_consen 16 PDYLVLSIFSTLCCCWPLGIVAIVYSSKVR 45 (82)
T ss_pred CCceeHHHHHHHHHHhhHHHHHheechhhH
Confidence 446678888888876675555665544333
Done!