Query 038161
Match_columns 54
No_of_seqs 107 out of 633
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:12:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038161hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0401 Uncharacterized homolo 99.9 4.6E-28 1E-32 136.5 5.0 54 1-54 1-55 (56)
2 PF01679 Pmp3: Proteolipid mem 99.9 5.6E-26 1.2E-30 125.5 4.3 51 4-54 1-51 (51)
3 KOG1773 Stress responsive prot 99.9 4.3E-26 9.3E-31 131.0 3.8 54 1-54 3-57 (63)
4 PF14373 Imm_superinfect: Supe 90.3 0.57 1.2E-05 24.9 3.3 33 17-49 5-42 (43)
5 PF09964 DUF2198: Uncharacteri 67.1 12 0.00026 22.1 3.5 45 8-52 2-50 (74)
6 PF11298 DUF3099: Protein of u 63.9 3.5 7.7E-05 24.0 0.8 22 5-26 44-65 (73)
7 COG4897 CsbA Uncharacterized p 60.3 15 0.00031 22.0 3.0 45 8-52 3-51 (78)
8 COG4665 FcbT2 TRAP-type mannit 53.2 18 0.0004 24.6 2.9 25 27-51 88-112 (182)
9 PF07123 PsbW: Photosystem II 51.6 11 0.00023 24.7 1.6 22 33-54 104-125 (138)
10 PF03376 Adeno_E3B: Adenovirus 41.9 30 0.00064 20.1 2.3 26 15-40 9-34 (67)
11 PF06796 NapE: Periplasmic nit 38.2 40 0.00086 18.8 2.3 31 5-35 19-49 (56)
12 PLN00082 photosystem II reacti 36.6 25 0.00054 20.5 1.4 21 33-53 32-52 (67)
13 TIGR02230 ATPase_gene1 F0F1-AT 35.5 54 0.0012 20.0 2.8 36 19-54 63-98 (100)
14 PLN00077 photosystem II reacti 35.0 26 0.00057 22.6 1.4 43 12-54 66-114 (128)
15 TIGR02973 nitrate_rd_NapE peri 34.2 75 0.0016 16.8 2.9 31 5-35 6-36 (42)
16 TIGR02972 TMAO_torE trimethyla 32.9 79 0.0017 17.1 2.9 31 5-35 11-41 (47)
17 PLN00092 photosystem I reactio 32.8 28 0.00061 22.7 1.3 22 33-54 103-124 (137)
18 COG3093 VapI Plasmid maintenan 31.6 46 0.00099 20.7 2.1 19 16-34 52-72 (104)
19 KOG4040 NADH:ubiquinone oxidor 30.0 60 0.0013 22.1 2.6 23 30-52 127-149 (186)
20 PF05478 Prominin: Prominin; 25.4 70 0.0015 25.2 2.6 22 29-50 769-790 (806)
21 PF05915 DUF872: Eukaryotic pr 24.6 1.7E+02 0.0036 18.1 3.7 24 27-50 73-96 (115)
22 COG5605 Predicted small integr 24.5 64 0.0014 20.3 1.8 16 8-23 77-92 (115)
23 COG3152 Predicted membrane pro 23.7 2E+02 0.0042 18.0 4.5 28 7-34 57-86 (125)
24 PF12555 TPPK_C: Thiamine pyro 22.9 1.4E+02 0.0029 15.9 3.9 35 4-38 14-48 (53)
25 cd00495 Ribosomal_L25_TL5_CTC 22.9 14 0.0003 21.3 -1.3 9 40-48 23-31 (91)
26 PF08139 LPAM_1: Prokaryotic m 22.6 50 0.0011 15.7 0.9 15 13-27 10-24 (25)
27 PRK05943 50S ribosomal protein 21.4 16 0.00034 21.4 -1.3 9 40-48 24-32 (94)
No 1
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=99.95 E-value=4.6e-28 Score=136.51 Aligned_cols=54 Identities=57% Similarity=1.054 Sum_probs=51.9
Q ss_pred CChHHHHHHHHHHhcchhhhhhHhc-cchHHHHHHHHHHHHhhhhhhhhhhheeC
Q 038161 1 MGSETFLEVILAILLPPVGVFLRYG-CGVEFWICLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 1 M~~~~~~~~ilai~lPPlaV~~~~G-~~~~~~in~lLtllg~~Pg~ihA~yii~~ 54 (54)
|+.+|+.++++|+|+||++|++++| |++|+++|++||++||+||+|||+|+++|
T Consensus 1 ~~~~d~~~iilaiflPP~~VfL~~G~~~~df~iNiLLtlLg~~PGiiHA~yvi~~ 55 (56)
T COG0401 1 MTLMDFIRIVLAIFLPPLGVFLRRGFGGKDFLINILLTLLGYIPGIIHALYVILR 55 (56)
T ss_pred CcHHHHHHHHHHHHcCchhhhhhccCCcHHHHHHHHHHHHHhhhhhHhheEEEEe
Confidence 7889999999999999999999999 57999999999999999999999999986
No 2
>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=99.92 E-value=5.6e-26 Score=125.48 Aligned_cols=51 Identities=57% Similarity=1.111 Sum_probs=48.9
Q ss_pred HHHHHHHHHHhcchhhhhhHhccchHHHHHHHHHHHHhhhhhhhhhhheeC
Q 038161 4 ETFLEVILAILLPPVGVFLRYGCGVEFWICLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 4 ~~~~~~ilai~lPPlaV~~~~G~~~~~~in~lLtllg~~Pg~ihA~yii~~ 54 (54)
+|++++++|+++||+||++++||++|+++|++||++||+||++||+|+++|
T Consensus 1 ~~~~~~ilai~lPPlaV~~~~g~~~~~~inl~Ltl~g~iPg~ihA~y~i~~ 51 (51)
T PF01679_consen 1 MDILLIILAIFLPPLAVFLKKGCSKDFWINLLLTLLGWIPGVIHALYVIYK 51 (51)
T ss_pred CcHHHHHHHHHcccHHHHHHcCCchhhHHHHHHHHHHHHHHHHHeeEEEeC
Confidence 368999999999999999999999999999999999999999999999876
No 3
>KOG1773 consensus Stress responsive protein [General function prediction only]
Probab=99.92 E-value=4.3e-26 Score=131.03 Aligned_cols=54 Identities=54% Similarity=0.970 Sum_probs=50.7
Q ss_pred CChHHHHHHHHHHhcchhhhhhHhc-cchHHHHHHHHHHHHhhhhhhhhhhheeC
Q 038161 1 MGSETFLEVILAILLPPVGVFLRYG-CGVEFWICLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 1 M~~~~~~~~ilai~lPPlaV~~~~G-~~~~~~in~lLtllg~~Pg~ihA~yii~~ 54 (54)
++.+|+.++++|+++||+||++++| |++|++||++||++||+||+|||+|++.+
T Consensus 3 ~~~~~~~~iilai~lPP~aV~l~~g~C~~~~~InilL~~L~~iPgiIhA~yii~~ 57 (63)
T KOG1773|consen 3 TDCDDILLIILAIFLPPLAVFLRRGGCTVDVLINILLTLLGFIPGIIHAIYIIFF 57 (63)
T ss_pred CcHHHHHHHHHHHHcCchheeeecCCCchhhHHHHHHHHHHHhHHHHhhEEEEEE
Confidence 3568999999999999999999998 99999999999999999999999999763
No 4
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=90.32 E-value=0.57 Score=24.93 Aligned_cols=33 Identities=30% Similarity=0.499 Sum_probs=24.6
Q ss_pred hhhhhhHhc---cchHHHHHHHH--HHHHhhhhhhhhh
Q 038161 17 PVGVFLRYG---CGVEFWICLLL--TVLGYIPGIIYAI 49 (54)
Q Consensus 17 PlaV~~~~G---~~~~~~in~lL--tllg~~Pg~ihA~ 49 (54)
|-.+..+++ ...-+.+|+.| |.+||+-+.+.|+
T Consensus 5 P~iiA~~r~~~~~~~I~~~Nl~lGWT~iGWv~aLiwA~ 42 (43)
T PF14373_consen 5 PSIIAFRRKHPNKWAIFLLNLLLGWTGIGWVAALIWAL 42 (43)
T ss_pred hHHHHHHcCCCcchhhHhHHHHHHhHHHHHHHHHHHhc
Confidence 444455554 34568999999 9999999998885
No 5
>PF09964 DUF2198: Uncharacterized protein conserved in bacteria (DUF2198); InterPro: IPR019242 This family of various hypothetical archaeal proteins has no known function.
Probab=67.08 E-value=12 Score=22.08 Aligned_cols=45 Identities=20% Similarity=0.287 Sum_probs=33.3
Q ss_pred HHHHHHhcchhhhhhHhccchHHHHHHHHHHHH----hhhhhhhhhhhe
Q 038161 8 EVILAILLPPVGVFLRYGCGVEFWICLLLTVLG----YIPGIIYAIYVL 52 (54)
Q Consensus 8 ~~ilai~lPPlaV~~~~G~~~~~~in~lLtllg----~~Pg~ihA~yii 52 (54)
.+++|.++|-+-|.+-+-.+.+-++-.+||... ..-|.-|..|++
T Consensus 2 ~~~~Al~~P~lLVvlFtrVT~n~~vg~~lt~~Li~ASvykGyt~~~~ii 50 (74)
T PF09964_consen 2 KYLLALFFPCLLVVLFTRVTYNHYVGTILTVALIAASVYKGYTHTWWII 50 (74)
T ss_pred HHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhccccchHHH
Confidence 468999999999988778888888888887654 244445555543
No 6
>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=63.86 E-value=3.5 Score=23.96 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=17.4
Q ss_pred HHHHHHHHHhcchhhhhhHhcc
Q 038161 5 TFLEVILAILLPPVGVFLRYGC 26 (54)
Q Consensus 5 ~~~~~ilai~lPPlaV~~~~G~ 26 (54)
.+..+..|+.+|++||.+..+-
T Consensus 44 a~~~~~~av~LPwvAVviAN~~ 65 (73)
T PF11298_consen 44 AWAIIVGAVPLPWVAVVIANAR 65 (73)
T ss_pred HHHHHHHhcccchhheeeccCC
Confidence 4567788999999999887643
No 7
>COG4897 CsbA Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.32 E-value=15 Score=21.95 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=32.2
Q ss_pred HHHHHHhcchhhhhhHhccchHHHHHHHHHHHH----hhhhhhhhhhhe
Q 038161 8 EVILAILLPPVGVFLRYGCGVEFWICLLLTVLG----YIPGIIYAIYVL 52 (54)
Q Consensus 8 ~~ilai~lPPlaV~~~~G~~~~~~in~lLtllg----~~Pg~ihA~yii 52 (54)
..+-|.|+|-+-|.+-.-.+..=++.++||... ..-|.-|..|++
T Consensus 3 ~~~sAlfFPc~LVvLF~riT~n~yVa~vLt~vLi~AS~~kgYt~~~wii 51 (78)
T COG4897 3 QIISALFFPCLLVVLFARITYNRYVALVLTVVLIAASAKKGYTSSFWII 51 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccceeeee
Confidence 357899999999988767766667888887654 344556666654
No 8
>COG4665 FcbT2 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=53.21 E-value=18 Score=24.57 Aligned_cols=25 Identities=28% Similarity=0.522 Sum_probs=21.7
Q ss_pred chHHHHHHHHHHHHhhhhhhhhhhh
Q 038161 27 GVEFWICLLLTVLGYIPGIIYAIYV 51 (54)
Q Consensus 27 ~~~~~in~lLtllg~~Pg~ihA~yi 51 (54)
..+.|++++.|+++.+|+.+.-+|.
T Consensus 88 R~qa~vDllGtifFLlPfc~l~iy~ 112 (182)
T COG4665 88 RTQAWVDLLGTIFFLLPFCLLVIYL 112 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999998877765
No 9
>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=51.61 E-value=11 Score=24.67 Aligned_cols=22 Identities=27% Similarity=0.383 Sum_probs=17.6
Q ss_pred HHHHHHHHhhhhhhhhhhheeC
Q 038161 33 CLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 33 n~lLtllg~~Pg~ihA~yii~~ 54 (54)
|.+-+++.-++|.|+++|.+++
T Consensus 104 ~~LgwIL~gVf~lIWslY~~~~ 125 (138)
T PF07123_consen 104 NLLGWILLGVFGLIWSLYFVYT 125 (138)
T ss_pred chhHHHHHHHHHHHHHHHHhhc
Confidence 4556777889999999998763
No 10
>PF03376 Adeno_E3B: Adenovirus E3B protein; InterPro: IPR005041 Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) []. One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface []. Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID []. This entry represents the E3B region 10.4K protein, also known as the RID alpha subunit.; GO: 0016020 membrane
Probab=41.86 E-value=30 Score=20.15 Aligned_cols=26 Identities=27% Similarity=0.515 Sum_probs=16.6
Q ss_pred cchhhhhhHhccchHHHHHHHHHHHH
Q 038161 15 LPPVGVFLRYGCGVEFWICLLLTVLG 40 (54)
Q Consensus 15 lPPlaV~~~~G~~~~~~in~lLtllg 40 (54)
+||.+|++..+.-.-..++-+.|++.
T Consensus 9 l~pf~vYlif~fv~c~~iCSi~~~~i 34 (67)
T PF03376_consen 9 LPPFAVYLIFAFVTCTCICSIVCFVI 34 (67)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 69999999877533344555554443
No 11
>PF06796 NapE: Periplasmic nitrate reductase protein NapE; InterPro: IPR010649 This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides. NapE is thought to be a transmembrane protein [].
Probab=38.20 E-value=40 Score=18.82 Aligned_cols=31 Identities=19% Similarity=0.430 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcchhhhhhHhccchHHHHHHH
Q 038161 5 TFLEVILAILLPPVGVFLRYGCGVEFWICLL 35 (54)
Q Consensus 5 ~~~~~ilai~lPPlaV~~~~G~~~~~~in~l 35 (54)
+-+..+..+++|=++|..-.|.|.-.|..=+
T Consensus 19 ~~flfl~~~l~PiL~v~~Vg~YGF~VWm~Q~ 49 (56)
T PF06796_consen 19 KAFLFLAVVLFPILAVAFVGGYGFIVWMYQI 49 (56)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788889999999998888887776544
No 12
>PLN00082 photosystem II reaction centre W protein (PsbW); Provisional
Probab=36.55 E-value=25 Score=20.46 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=15.9
Q ss_pred HHHHHHHHhhhhhhhhhhhee
Q 038161 33 CLLLTVLGYIPGIIYAIYVLV 53 (54)
Q Consensus 33 n~lLtllg~~Pg~ihA~yii~ 53 (54)
|.+-+++.-+|+.|+++|.++
T Consensus 32 ~~LgwIL~gvf~liw~ly~~~ 52 (67)
T PLN00082 32 GKLTWILVGVTALIWALYFSY 52 (67)
T ss_pred chhhhHHHHHHHHHHHHHhhe
Confidence 344466777899999999875
No 13
>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=35.48 E-value=54 Score=20.04 Aligned_cols=36 Identities=19% Similarity=0.272 Sum_probs=26.2
Q ss_pred hhhhHhccchHHHHHHHHHHHHhhhhhhhhhhheeC
Q 038161 19 GVFLRYGCGVEFWICLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 19 aV~~~~G~~~~~~in~lLtllg~~Pg~ihA~yii~~ 54 (54)
+.++.+-.+.+.+..+.+.++|-.-|...|.+.+.|
T Consensus 63 G~WLD~~~~t~~~~tl~~lllGv~~G~~n~w~wi~r 98 (100)
T TIGR02230 63 GIWLDRHYPSPFSWTLTMLIVGVVIGCLNAWHWVSR 98 (100)
T ss_pred HHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445544456666888889999999998888776654
No 14
>PLN00077 photosystem II reaction centre W protein; Provisional
Probab=35.00 E-value=26 Score=22.62 Aligned_cols=43 Identities=23% Similarity=0.320 Sum_probs=25.6
Q ss_pred HHhcchhhhhhHh----ccchHHHH--HHHHHHHHhhhhhhhhhhheeC
Q 038161 12 AILLPPVGVFLRY----GCGVEFWI--CLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 12 ai~lPPlaV~~~~----G~~~~~~i--n~lLtllg~~Pg~ihA~yii~~ 54 (54)
+.-.|-+|..-.+ |-|-.+=+ |.+-+++.-+++.|+++|.+++
T Consensus 66 a~a~PA~AlVDeRlsteGtGl~lGlsn~~LgwIL~gVf~liw~ly~~~~ 114 (128)
T PLN00077 66 AYAHPAFALVDERMSTEGTGLSLGLSNNLLGWILLGVFGLIWSLYTTYT 114 (128)
T ss_pred hccccHHHHHhHhhcCCCccccccccCchhhHHHHhHHHHHHHHHhhee
Confidence 3445666654443 22222222 4555777778999999998763
No 15
>TIGR02973 nitrate_rd_NapE periplasmic nitrate reductase, NapE protein. NapE, homologous to TorE (TIGR02972), is a membrane protein of unknown function that is part of the periplasmic nitrate reductase system; it may be part of the enzyme complex. The periplasmic nitrate reductase allows for nitrate respiration in anaerobic conditions.
Probab=34.18 E-value=75 Score=16.82 Aligned_cols=31 Identities=19% Similarity=0.455 Sum_probs=24.7
Q ss_pred HHHHHHHHHhcchhhhhhHhccchHHHHHHH
Q 038161 5 TFLEVILAILLPPVGVFLRYGCGVEFWICLL 35 (54)
Q Consensus 5 ~~~~~ilai~lPPlaV~~~~G~~~~~~in~l 35 (54)
+-+..+..+++|=++|..-.|.|.-.|..=+
T Consensus 6 ~~flfl~~~l~PiLsV~~V~~YGF~vWm~Q~ 36 (42)
T TIGR02973 6 NTFLFLAAVIWPVLSVITVGGYGFAVWMYQI 36 (42)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788889999999998888887776544
No 16
>TIGR02972 TMAO_torE trimethylamine N-oxide reductase system, TorE protein. Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA.
Probab=32.93 E-value=79 Score=17.11 Aligned_cols=31 Identities=26% Similarity=0.415 Sum_probs=24.9
Q ss_pred HHHHHHHHHhcchhhhhhHhccchHHHHHHH
Q 038161 5 TFLEVILAILLPPVGVFLRYGCGVEFWICLL 35 (54)
Q Consensus 5 ~~~~~ilai~lPPlaV~~~~G~~~~~~in~l 35 (54)
+-+..+..+++|=++|..-.|.|.-.|..=+
T Consensus 11 ~~flfl~v~l~PiLsV~~Vg~YGF~vWm~Q~ 41 (47)
T TIGR02972 11 KALGFIIVVLFPILSVAGIGGYGFIIWMIQA 41 (47)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788889999999998888887776544
No 17
>PLN00092 photosystem I reaction center subunit V (PsaG); Provisional
Probab=32.80 E-value=28 Score=22.70 Aligned_cols=22 Identities=27% Similarity=0.383 Sum_probs=17.0
Q ss_pred HHHHHHHHhhhhhhhhhhheeC
Q 038161 33 CLLLTVLGYIPGIIYAIYVLVG 54 (54)
Q Consensus 33 n~lLtllg~~Pg~ihA~yii~~ 54 (54)
|.+-+++.-+++.|+++|.+++
T Consensus 103 ~~LgwIL~gVf~lIWslYf~~~ 124 (137)
T PLN00092 103 NLLGWILLGVFGLIWSLYFVYT 124 (137)
T ss_pred cchhhHHHhHHHHHHHHHheee
Confidence 3455777778999999998763
No 18
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=31.59 E-value=46 Score=20.68 Aligned_cols=19 Identities=32% Similarity=0.634 Sum_probs=13.0
Q ss_pred chhhhhhHh--ccchHHHHHH
Q 038161 16 PPVGVFLRY--GCGVEFWICL 34 (54)
Q Consensus 16 PPlaV~~~~--G~~~~~~in~ 34 (54)
|..|+=+.+ |-+.|||+|+
T Consensus 52 ~dmAlrL~k~fGtspefWlNl 72 (104)
T COG3093 52 ADMALRLAKVFGTSPEFWLNL 72 (104)
T ss_pred HHHHHHHHHHhCCCHHHHHHH
Confidence 344444444 7899999997
No 19
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=29.99 E-value=60 Score=22.10 Aligned_cols=23 Identities=22% Similarity=0.563 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHhhhhhhhhhhhe
Q 038161 30 FWICLLLTVLGYIPGIIYAIYVL 52 (54)
Q Consensus 30 ~~in~lLtllg~~Pg~ihA~yii 52 (54)
-|-.++.|++|.+|+.+.+.|+.
T Consensus 127 ~w~~~~mcl~g~~~~~l~~~y~~ 149 (186)
T KOG4040|consen 127 TWNSIVMCLRGLVPMALLAWYFT 149 (186)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHc
Confidence 46778889999999999999874
No 20
>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=25.36 E-value=70 Score=25.23 Aligned_cols=22 Identities=41% Similarity=0.684 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhhhhhhhhhh
Q 038161 29 EFWICLLLTVLGYIPGIIYAIY 50 (54)
Q Consensus 29 ~~~in~lLtllg~~Pg~ihA~y 50 (54)
-||..+.++.++++|++|.|.-
T Consensus 769 ~fWf~l~~c~~~liP~ii~avk 790 (806)
T PF05478_consen 769 GFWFGLGWCTLFLIPSIIFAVK 790 (806)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999998864
No 21
>PF05915 DUF872: Eukaryotic protein of unknown function (DUF872); InterPro: IPR008590 This entry represents several uncharacterised eukaryotic transmembrane proteins. The function of this currently unknown.
Probab=24.59 E-value=1.7e+02 Score=18.08 Aligned_cols=24 Identities=29% Similarity=0.513 Sum_probs=19.2
Q ss_pred chHHHHHHHHHHHHhhhhhhhhhh
Q 038161 27 GVEFWICLLLTVLGYIPGIIYAIY 50 (54)
Q Consensus 27 ~~~~~in~lLtllg~~Pg~ihA~y 50 (54)
+.+.+.=+++.++-++||.-|-..
T Consensus 73 ~~~~~~llilG~L~fIPG~Y~~~i 96 (115)
T PF05915_consen 73 RDRGWALLILGILCFIPGFYHTRI 96 (115)
T ss_pred CcccchHHHHHHHHHhccHHHHHH
Confidence 556788889999999999866543
No 22
>COG5605 Predicted small integral membrane protein [Function unknown]
Probab=24.52 E-value=64 Score=20.28 Aligned_cols=16 Identities=38% Similarity=0.723 Sum_probs=12.1
Q ss_pred HHHHHHhcchhhhhhH
Q 038161 8 EVILAILLPPVGVFLR 23 (54)
Q Consensus 8 ~~ilai~lPPlaV~~~ 23 (54)
-.+-|+++||+-|..-
T Consensus 77 al~yaiilppllvlvf 92 (115)
T COG5605 77 ALVYAIILPPLLVLVF 92 (115)
T ss_pred HHHHHHHhhHHHHHHH
Confidence 3467899999987653
No 23
>COG3152 Predicted membrane protein [Function unknown]
Probab=23.69 E-value=2e+02 Score=18.01 Aligned_cols=28 Identities=29% Similarity=0.496 Sum_probs=20.7
Q ss_pred HHHHHHHhcchhhhhhHh--ccchHHHHHH
Q 038161 7 LEVILAILLPPVGVFLRY--GCGVEFWICL 34 (54)
Q Consensus 7 ~~~ilai~lPPlaV~~~~--G~~~~~~in~ 34 (54)
..+.+|.++|=+|+..|+ +.|+.-|..+
T Consensus 57 ~l~~la~~~p~lal~vrRLHD~g~sgw~~L 86 (125)
T COG3152 57 ALYLLALFLPTLALTVRRLHDRGRSGWWAL 86 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCchHHHH
Confidence 567889999999999997 4555444433
No 24
>PF12555 TPPK_C: Thiamine pyrophosphokinase C terminal; InterPro: IPR022215 This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyses the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme.
Probab=22.93 E-value=1.4e+02 Score=15.92 Aligned_cols=35 Identities=23% Similarity=0.113 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhcchhhhhhHhccchHHHHHHHHHH
Q 038161 4 ETFLEVILAILLPPVGVFLRYGCGVEFWICLLLTV 38 (54)
Q Consensus 4 ~~~~~~ilai~lPPlaV~~~~G~~~~~~in~lLtl 38 (54)
..+...++|-++|=.++...++.+.+++=++..+.
T Consensus 14 ~~~~~lvlaaLvav~v~l~~s~~g~~~~~~l~~~w 48 (53)
T PF12555_consen 14 WALALLVLAALVAVAVALLISPAGQSFLDLLADTW 48 (53)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence 45788889999998888888888888877776653
No 25
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=22.90 E-value=14 Score=21.27 Aligned_cols=9 Identities=44% Similarity=1.150 Sum_probs=7.1
Q ss_pred Hhhhhhhhh
Q 038161 40 GYIPGIIYA 48 (54)
Q Consensus 40 g~~Pg~ihA 48 (54)
|++||++|.
T Consensus 23 G~iPavvYG 31 (91)
T cd00495 23 GKVPAVIYG 31 (91)
T ss_pred CCCCEEEEC
Confidence 678888875
No 26
>PF08139 LPAM_1: Prokaryotic membrane lipoprotein lipid attachment site; InterPro: IPR012640 In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [,]. This lipid attachment site is found in homologues of the VirB proteins of type IV secretion systems (T4SS). Conjugal transfer across the cell envelope of Gram-negative bacteria is mediated by a supramolecular structure termed mating pair formation (Mpf) complex. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now known as T4SS. T4SS are involved in the delivery of effector molecules to eukaryotic target cells; each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection [].
Probab=22.65 E-value=50 Score=15.66 Aligned_cols=15 Identities=40% Similarity=0.961 Sum_probs=9.8
Q ss_pred HhcchhhhhhHhccc
Q 038161 13 ILLPPVGVFLRYGCG 27 (54)
Q Consensus 13 i~lPPlaV~~~~G~~ 27 (54)
+++|=+|++.-.||+
T Consensus 10 il~~l~a~~~LagCs 24 (25)
T PF08139_consen 10 ILFPLLALFMLAGCS 24 (25)
T ss_pred HHHHHHHHHHHhhcc
Confidence 345566777667885
No 27
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=21.36 E-value=16 Score=21.41 Aligned_cols=9 Identities=56% Similarity=1.106 Sum_probs=7.0
Q ss_pred Hhhhhhhhh
Q 038161 40 GYIPGIIYA 48 (54)
Q Consensus 40 g~~Pg~ihA 48 (54)
|++||++|.
T Consensus 24 G~vPaViYG 32 (94)
T PRK05943 24 GKFPAIIYG 32 (94)
T ss_pred CCCCEEEEC
Confidence 688888874
Done!