Query psy1127
Match_columns 65
No_of_seqs 156 out of 775
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 22:35:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1127hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01151 ELO: GNS1/SUR4 family 99.7 6.3E-18 1.4E-22 111.0 7.5 61 2-62 181-250 (250)
2 PTZ00251 fatty acid elongase; 99.7 1.3E-16 2.8E-21 106.5 8.6 61 2-62 201-270 (272)
3 KOG3071|consensus 99.6 9E-16 1.9E-20 102.7 7.0 59 2-60 203-264 (274)
4 KOG3072|consensus 99.1 6.4E-11 1.4E-15 79.6 2.9 56 2-57 207-268 (282)
5 PRK00753 psbL photosystem II r 58.5 17 0.00037 17.7 2.5 25 27-51 14-38 (39)
6 PF09125 COX2-transmemb: Cytoc 54.1 21 0.00045 17.4 2.4 20 27-46 12-31 (38)
7 CHL00038 psbL photosystem II p 52.0 28 0.00061 16.9 2.9 25 27-51 13-37 (38)
8 CHL00070 petB cytochrome b6 49.1 33 0.00071 22.5 3.5 26 34-59 90-115 (215)
9 PF13631 Cytochrom_B_N_2: Cyto 48.2 22 0.00049 22.1 2.6 22 37-58 3-24 (168)
10 KOG3319|consensus 45.0 36 0.00078 21.4 3.1 33 14-46 33-65 (153)
11 PF11119 DUF2633: Protein of u 44.6 30 0.00064 18.5 2.3 14 36-49 12-25 (59)
12 PHA02692 hypothetical protein; 44.1 56 0.0012 18.0 4.2 30 24-53 40-69 (70)
13 PF02419 PsbL: PsbL protein; 43.9 40 0.00087 16.3 3.4 24 28-51 13-36 (37)
14 PRK03735 cytochrome b6; Provis 43.4 47 0.001 21.9 3.6 26 34-59 98-123 (223)
15 PF12273 RCR: Chitin synthesis 39.4 45 0.00098 19.7 2.9 22 34-56 5-26 (130)
16 cd00284 Cytochrome_b_N Cytochr 37.3 53 0.0011 21.2 3.1 26 34-59 79-104 (200)
17 PHA02650 hypothetical protein; 36.9 81 0.0018 17.8 4.9 32 25-57 45-76 (81)
18 PF10215 Ost4: Oligosaccaryltr 36.4 52 0.0011 15.7 2.3 18 1-18 1-18 (35)
19 PRK13453 F0F1 ATP synthase sub 30.8 1.3E+02 0.0029 18.5 4.1 29 26-54 15-43 (173)
20 COG4277 Predicted DNA-binding 30.8 30 0.00064 24.6 1.2 13 44-56 91-103 (404)
21 PHA02844 putative transmembran 30.1 1.1E+02 0.0023 17.1 3.9 30 26-56 45-74 (75)
22 KOG3894|consensus 29.7 52 0.0011 23.1 2.2 20 33-52 297-316 (316)
23 PHA03291 envelope glycoprotein 28.5 28 0.00061 25.0 0.8 12 2-13 283-294 (401)
24 PF02544 Steroid_dh: 3-oxo-5-a 28.3 1.4E+02 0.0031 18.0 5.7 33 33-65 114-147 (150)
25 TIGR03493 cellullose_BcsF cell 27.0 97 0.0021 16.6 2.6 17 3-19 2-18 (62)
26 PF11120 DUF2636: Protein of u 25.5 1.2E+02 0.0025 16.3 2.7 17 3-19 2-18 (62)
27 PF04061 ORMDL: ORMDL family ; 25.3 1.7E+02 0.0038 18.0 4.0 32 15-46 23-54 (136)
28 PF05545 FixQ: Cbb3-type cytoc 24.8 1E+02 0.0022 15.1 4.2 25 35-59 11-35 (49)
29 PF02009 Rifin_STEVOR: Rifin/s 24.8 1E+02 0.0022 21.3 3.0 27 34-60 261-287 (299)
30 PHA02819 hypothetical protein; 23.3 1.5E+02 0.0032 16.4 4.1 29 25-54 42-70 (71)
31 PRK14473 F0F1 ATP synthase sub 23.0 1.9E+02 0.004 17.5 4.1 28 27-54 6-33 (164)
No 1
>PF01151 ELO: GNS1/SUR4 family; InterPro: IPR002076 This group of eukaryotic integral membrane proteins are evolutionary related, but exact function has not yet clearly been established. The proteins have from 290 to 435 amino acid residues. Structurally, they seem to be formed of three sections: a N-terminal region with two transmembrane domains, a central hydrophilic loop and a C-terminal region that contains from one to three transmembrane domains. Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis []. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 (P40319 from SWISSPROT) affects plasma membrane H+-ATPase activity, and may act on a glucose-signalling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1 []. ; GO: 0016021 integral to membrane
Probab=99.74 E-value=6.3e-18 Score=110.95 Aligned_cols=61 Identities=33% Similarity=0.520 Sum_probs=56.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhh------cC---CCcHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCC
Q psy1127 2 RAVYISIQFVLIMVHAFQLLFI------DC---NFPKAFVWWIGSHAVMFFFLFRNFYKEQYVKPVKTAK 62 (65)
Q Consensus 2 iT~~QiiQF~~~~~~~~~~~~~------~C---~~p~~~~~~~~~~~~s~l~LF~~FY~~sY~~~~~~~~ 62 (65)
||.+||+||++++++..+.... || ++|+....++.++++++++||.|||+|+|.+|+++||
T Consensus 181 IT~~Qi~QF~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~s~l~LF~~Fy~~~Y~~~~~~k~ 250 (250)
T PF01151_consen 181 ITSLQIVQFVIGIVHTVYALYYYFFPGGDCDTSGYPKFNAILGLVYYVSYLYLFINFYIKSYIKKKKKKK 250 (250)
T ss_pred HhHHhhhhhHHHHHHHHHHhheeccCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCC
Confidence 8999999999999998887754 89 7789999999999999999999999999999888775
No 2
>PTZ00251 fatty acid elongase; Provisional
Probab=99.69 E-value=1.3e-16 Score=106.47 Aligned_cols=61 Identities=18% Similarity=0.169 Sum_probs=53.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHh--------hcCCCcH-HHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCC
Q psy1127 2 RAVYISIQFVLIMVHAFQLLF--------IDCNFPK-AFVWWIGSHAVMFFFLFRNFYKEQYVKPVKTAK 62 (65)
Q Consensus 2 iT~~QiiQF~~~~~~~~~~~~--------~~C~~p~-~~~~~~~~~~~s~l~LF~~FY~~sY~~~~~~~~ 62 (65)
||.+||+||++++.|..+.+. .+|++|. ...+.+.++++|+++||.|||+|+|.++||+++
T Consensus 201 IT~lQi~Qfv~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~s~l~LF~~Fy~~~Y~~~~~~~~ 270 (272)
T PTZ00251 201 ITLLQITQMVGGLFVSGYVIVQKLTKGDPKGCSGTTMATARGQLMIYIFNFYLFSEMFVKGYVLPRKAKA 270 (272)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCC
Confidence 899999999999999887763 3699887 677778899999999999999999999877664
No 3
>KOG3071|consensus
Probab=99.63 E-value=9e-16 Score=102.66 Aligned_cols=59 Identities=32% Similarity=0.612 Sum_probs=52.8
Q ss_pred hHHHHHHHHHHHHHHHHHH-Hh-hcCCCcHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q psy1127 2 RAVYISIQFVLIMVHAFQL-LF-IDCNFPKA-FVWWIGSHAVMFFFLFRNFYKEQYVKPVKT 60 (65)
Q Consensus 2 iT~~QiiQF~~~~~~~~~~-~~-~~C~~p~~-~~~~~~~~~~s~l~LF~~FY~~sY~~~~~~ 60 (65)
+|.+|++||++..+|..+. ++ +||++|.+ +++.+.+++++++.||+|||+|+|+|++++
T Consensus 203 ~t~vQlvqf~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~l~LF~nFY~~tY~k~~~~ 264 (274)
T KOG3071|consen 203 ITIVQLVQFLILFVHTLYVHLFKPGCCFGIGAWAFNGSVINVSFLLLFSNFYIKTYKKPKKK 264 (274)
T ss_pred HHHHHHHHHHHHHHHHhheeeecCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 6999999999999999988 55 58999999 877889999999999999999999986544
No 4
>KOG3072|consensus
Probab=99.09 E-value=6.4e-11 Score=79.57 Aligned_cols=56 Identities=18% Similarity=0.227 Sum_probs=47.4
Q ss_pred hHHHHHHHHHHHHHHHHHHH---h-h--cCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy1127 2 RAVYISIQFVLIMVHAFQLL---F-I--DCNFPKAFVWWIGSHAVMFFFLFRNFYKEQYVKP 57 (65)
Q Consensus 2 iT~~QiiQF~~~~~~~~~~~---~-~--~C~~p~~~~~~~~~~~~s~l~LF~~FY~~sY~~~ 57 (65)
||.+||+||+++........ . . +|........++.++.++|++||.|||.++|+++
T Consensus 207 iTtlQi~Qm~i~~~i~~~v~~~~~~~~~~c~~s~~~~~l~~~my~syfvLf~~Ff~~aYi~~ 268 (282)
T KOG3072|consen 207 ITTLQIVQMVIGCYIGTHVYYVKHTHQLLCQQSYKNLSLCFLMYISYFVLFANFFYQAYIKK 268 (282)
T ss_pred HHHHHHHHHHHHHheeeEEEEEEecCCeeeeeeccchhhHHHHHHHHHHHHHHHHHHHHhhh
Confidence 89999999999876544332 1 2 2999888889999999999999999999999986
No 5
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=58.54 E-value=17 Score=17.74 Aligned_cols=25 Identities=8% Similarity=0.163 Sum_probs=20.4
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHH
Q psy1127 27 FPKAFVWWIGSHAVMFFFLFRNFYK 51 (65)
Q Consensus 27 ~p~~~~~~~~~~~~s~l~LF~~FY~ 51 (65)
-.+.-.+++.......-+||++++.
T Consensus 14 LNRTSLy~GlLlifvl~vLFssYff 38 (39)
T PRK00753 14 LNRTSLYLGLLLVFVLGILFSSYFF 38 (39)
T ss_pred echhhHHHHHHHHHHHHHHHHhhcc
Confidence 4566778899999999999998864
No 6
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=54.13 E-value=21 Score=17.37 Aligned_cols=20 Identities=10% Similarity=0.374 Sum_probs=15.1
Q ss_pred CcHHHHHHHHHHHHHHHHHH
Q psy1127 27 FPKAFVWWIGSHAVMFFFLF 46 (65)
Q Consensus 27 ~p~~~~~~~~~~~~s~l~LF 46 (65)
|.++|..+++++.+.|+++-
T Consensus 12 YEr~Wi~F~l~mi~vFi~li 31 (38)
T PF09125_consen 12 YERGWIAFALAMILVFIALI 31 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHH
Confidence 45778888888888887764
No 7
>CHL00038 psbL photosystem II protein L
Probab=51.97 E-value=28 Score=16.89 Aligned_cols=25 Identities=16% Similarity=0.414 Sum_probs=20.1
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHH
Q psy1127 27 FPKAFVWWIGSHAVMFFFLFRNFYK 51 (65)
Q Consensus 27 ~p~~~~~~~~~~~~s~l~LF~~FY~ 51 (65)
-.+.-.+++.......-+||++++.
T Consensus 13 LNRTSLy~GLLlifvl~vlfssyff 37 (38)
T CHL00038 13 LNRTSLYWGLLLIFVLAVLFSNYFF 37 (38)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHhc
Confidence 4566778888888899999998864
No 8
>CHL00070 petB cytochrome b6
Probab=49.11 E-value=33 Score=22.52 Aligned_cols=26 Identities=19% Similarity=0.301 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCc
Q psy1127 34 WIGSHAVMFFFLFRNFYKEQYVKPVK 59 (65)
Q Consensus 34 ~~~~~~~s~l~LF~~FY~~sY~~~~~ 59 (65)
..+.....++=++..+|..+|++|++
T Consensus 90 as~~~~~~~lH~~r~~~~gsYk~pre 115 (215)
T CHL00070 90 ASMMVLMMILHVFRVYLTGGFKKPRE 115 (215)
T ss_pred HHHHHHHHHHHHHHHHHHhhhcCCcc
Confidence 34566667778999999999997754
No 9
>PF13631 Cytochrom_B_N_2: Cytochrome b(N-terminal)/b6/petB; PDB: 1KB9_C 2IBZ_C 1P84_C 3CXH_C 1EZV_C 1KYO_C 3CX5_N 1PPJ_P 2A06_P 1SQX_C ....
Probab=48.23 E-value=22 Score=22.07 Aligned_cols=22 Identities=32% Similarity=0.757 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCCC
Q psy1127 37 SHAVMFFFLFRNFYKEQYVKPV 58 (65)
Q Consensus 37 ~~~~s~l~LF~~FY~~sY~~~~ 58 (65)
.....++-++.++|..+|++++
T Consensus 3 ~~~~~~lH~~r~~~~g~y~~~r 24 (168)
T PF13631_consen 3 MFILMYLHMFRGFFYGSYKKPR 24 (168)
T ss_dssp HHHHHHHHHHHHHHTTTTSTTC
T ss_pred ehhHhHHHHHHHhhhccccCCc
Confidence 3566788899999999998775
No 10
>KOG3319|consensus
Probab=44.95 E-value=36 Score=21.42 Aligned_cols=33 Identities=18% Similarity=0.163 Sum_probs=24.7
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHH
Q psy1127 14 MVHAFQLLFIDCNFPKAFVWWIGSHAVMFFFLF 46 (65)
Q Consensus 14 ~~~~~~~~~~~C~~p~~~~~~~~~~~~s~l~LF 46 (65)
.+|..+...+.|+-|+.|....+.+++...+.|
T Consensus 33 ll~l~~ls~p~~s~~~aWTltnl~h~~~tyi~f 65 (153)
T KOG3319|consen 33 LLHLVLLSIPFVSPPWAWTLTNLIHNIGTYIFF 65 (153)
T ss_pred HHHHHHHhCccCCcchhHHHHHHHHHHhHheeE
Confidence 345555555789999999989998888776654
No 11
>PF11119 DUF2633: Protein of unknown function (DUF2633); InterPro: IPR022576 This family is conserved largely in Proteobacteria. Several members are named as YfgG. The function is not known.
Probab=44.58 E-value=30 Score=18.47 Aligned_cols=14 Identities=21% Similarity=0.344 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHH
Q psy1127 36 GSHAVMFFFLFRNF 49 (65)
Q Consensus 36 ~~~~~s~l~LF~~F 49 (65)
.+..+|+++||+++
T Consensus 12 iVLLISfiIlfgRl 25 (59)
T PF11119_consen 12 IVLLISFIILFGRL 25 (59)
T ss_pred HHHHHHHHHHHHHH
Confidence 45567888888854
No 12
>PHA02692 hypothetical protein; Provisional
Probab=44.13 E-value=56 Score=18.01 Aligned_cols=30 Identities=23% Similarity=0.190 Sum_probs=21.5
Q ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1127 24 DCNFPKAFVWWIGSHAVMFFFLFRNFYKEQ 53 (65)
Q Consensus 24 ~C~~p~~~~~~~~~~~~s~l~LF~~FY~~s 53 (65)
.|+.++....+.....+..+++|.=+|.|-
T Consensus 40 ~~~~~~~~~ii~~~~~~~~~vll~flYLK~ 69 (70)
T PHA02692 40 SKGVPWTTVFLIGLIAAAIGVLLCFHYLKL 69 (70)
T ss_pred cCCcchHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 466777776666577777888888887763
No 13
>PF02419 PsbL: PsbL protein; InterPro: IPR003372 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 PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (IPR002682 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex []. In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_L 3A0B_l 3ARC_l 1S5L_l 2AXT_l 3BZ2_L 4FBY_L 3PRQ_L 3PRR_L 3KZI_L ....
Probab=43.93 E-value=40 Score=16.30 Aligned_cols=24 Identities=13% Similarity=0.364 Sum_probs=18.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHH
Q psy1127 28 PKAFVWWIGSHAVMFFFLFRNFYK 51 (65)
Q Consensus 28 p~~~~~~~~~~~~s~l~LF~~FY~ 51 (65)
.+.-.+++.......-+||++++.
T Consensus 13 NRTSLY~GLllifvl~vLFssyff 36 (37)
T PF02419_consen 13 NRTSLYWGLLLIFVLAVLFSSYFF 36 (37)
T ss_dssp -CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHhHHHHHHHHHHHHHHhhhhhc
Confidence 344567888888888999998875
No 14
>PRK03735 cytochrome b6; Provisional
Probab=43.38 E-value=47 Score=21.89 Aligned_cols=26 Identities=27% Similarity=0.406 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCc
Q psy1127 34 WIGSHAVMFFFLFRNFYKEQYVKPVK 59 (65)
Q Consensus 34 ~~~~~~~s~l~LF~~FY~~sY~~~~~ 59 (65)
..+.....++=++..||..+|+++++
T Consensus 98 as~~~~~~~lH~~r~~~~gsYk~pre 123 (223)
T PRK03735 98 ASLVIVMMFLHTLRVFFTGGYKKPRE 123 (223)
T ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 35566677788999999999998754
No 15
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=39.41 E-value=45 Score=19.67 Aligned_cols=22 Identities=23% Similarity=0.425 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC
Q psy1127 34 WIGSHAVMFFFLFRNFYKEQYVK 56 (65)
Q Consensus 34 ~~~~~~~s~l~LF~~FY~~sY~~ 56 (65)
+.++..+.++++| -++.++-+|
T Consensus 5 ~~iii~~i~l~~~-~~~~~~rRR 26 (130)
T PF12273_consen 5 FAIIIVAILLFLF-LFYCHNRRR 26 (130)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHH
Confidence 3333333333333 344444433
No 16
>cd00284 Cytochrome_b_N Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms. Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites. The C-terminal portion of cytochrome b is described in a separate CD.
Probab=37.31 E-value=53 Score=21.16 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCc
Q psy1127 34 WIGSHAVMFFFLFRNFYKEQYVKPVK 59 (65)
Q Consensus 34 ~~~~~~~s~l~LF~~FY~~sY~~~~~ 59 (65)
........++-++..+|..+|+++++
T Consensus 79 as~~~~~~~lH~~r~~~~gsY~~pre 104 (200)
T cd00284 79 ASMFFLMLYLHIFRGLYYGSYKKPRE 104 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcchhH
Confidence 35666777888999999999988654
No 17
>PHA02650 hypothetical protein; Provisional
Probab=36.88 E-value=81 Score=17.82 Aligned_cols=32 Identities=16% Similarity=0.163 Sum_probs=22.1
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy1127 25 CNFPKAFVWWIGSHAVMFFFLFRNFYKEQYVKP 57 (65)
Q Consensus 25 C~~p~~~~~~~~~~~~s~l~LF~~FY~~sY~~~ 57 (65)
|+.++.+. +.....+.++++|.=+|.|.+.|.
T Consensus 45 ~~~~~~~~-ii~i~~v~i~~l~~flYLK~~~r~ 76 (81)
T PHA02650 45 SWFNGQNF-IFLIFSLIIVALFSFFVFKGYTRN 76 (81)
T ss_pred CCchHHHH-HHHHHHHHHHHHHHHHHHHHhccc
Confidence 34444443 444677778889999999998764
No 18
>PF10215 Ost4: Oligosaccaryltransferase ; InterPro: IPR018943 Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, 2.4.1.119 from EC, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum. ; PDB: 1RKL_A 2LAT_A.
Probab=36.43 E-value=52 Score=15.66 Aligned_cols=18 Identities=11% Similarity=-0.145 Sum_probs=11.3
Q ss_pred ChHHHHHHHHHHHHHHHH
Q psy1127 1 MRAVYISIQFVLIMVHAF 18 (65)
Q Consensus 1 ~iT~~QiiQF~~~~~~~~ 18 (65)
|||-.|+-.++..+....
T Consensus 1 MIsD~qL~~lan~lG~~~ 18 (35)
T PF10215_consen 1 MISDVQLYTLANFLGVAA 18 (35)
T ss_dssp --SSHHHHHHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHH
Confidence 678888888887665433
No 19
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=30.79 E-value=1.3e+02 Score=18.53 Aligned_cols=29 Identities=10% Similarity=0.019 Sum_probs=20.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1127 26 NFPKAFVWWIGSHAVMFFFLFRNFYKEQY 54 (65)
Q Consensus 26 ~~p~~~~~~~~~~~~s~l~LF~~FY~~sY 54 (65)
+.+++...+.+++-+.++++...|.++-.
T Consensus 15 ~~~~~t~~~~iInFliL~~lL~~~l~~pi 43 (173)
T PRK13453 15 GVEWGTVIVTVLTFIVLLALLKKFAWGPL 43 (173)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566677777887888888888876544
No 20
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=30.76 E-value=30 Score=24.64 Aligned_cols=13 Identities=38% Similarity=0.759 Sum_probs=11.5
Q ss_pred HHHHHHHHHHhcC
Q psy1127 44 FLFRNFYKEQYVK 56 (65)
Q Consensus 44 ~LF~~FY~~sY~~ 56 (65)
-|+.|||.++|+.
T Consensus 91 ~ltlnfYrRnYIe 103 (404)
T COG4277 91 DLTLNFYRRNYIE 103 (404)
T ss_pred HHHHHHHHHhhhh
Confidence 5889999999985
No 21
>PHA02844 putative transmembrane protein; Provisional
Probab=30.13 E-value=1.1e+02 Score=17.12 Aligned_cols=30 Identities=13% Similarity=0.265 Sum_probs=19.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1127 26 NFPKAFVWWIGSHAVMFFFLFRNFYKEQYVK 56 (65)
Q Consensus 26 ~~p~~~~~~~~~~~~s~l~LF~~FY~~sY~~ 56 (65)
+.++.+ ++.....+..+++|.=+|.|...|
T Consensus 45 ~~~~~~-~ii~i~~v~~~~~~~flYLK~~~r 74 (75)
T PHA02844 45 SSSTKI-WILTIIFVVFATFLTFLYLKAVPR 74 (75)
T ss_pred ChhHHH-HHHHHHHHHHHHHHHHHHHheecC
Confidence 344433 344566777788888888877654
No 22
>KOG3894|consensus
Probab=29.72 E-value=52 Score=23.08 Aligned_cols=20 Identities=20% Similarity=0.311 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy1127 33 WWIGSHAVMFFFLFRNFYKE 52 (65)
Q Consensus 33 ~~~~~~~~s~l~LF~~FY~~ 52 (65)
++.+..+.||..||.+.|.+
T Consensus 297 ~lf~llvlsf~lLFldwy~~ 316 (316)
T KOG3894|consen 297 LLFFLLVLSFSLLFLDWYYK 316 (316)
T ss_pred HHHHHHHHHHHHHHHhhcCC
Confidence 46677888999999999863
No 23
>PHA03291 envelope glycoprotein I; Provisional
Probab=28.49 E-value=28 Score=24.95 Aligned_cols=12 Identities=25% Similarity=0.119 Sum_probs=10.2
Q ss_pred hHHHHHHHHHHH
Q psy1127 2 RAVYISIQFVLI 13 (65)
Q Consensus 2 iT~~QiiQF~~~ 13 (65)
+|..||+|..+=
T Consensus 283 Lt~~qiiQiAIP 294 (401)
T PHA03291 283 LTVTQIIQIAIP 294 (401)
T ss_pred hhhhhhheeccc
Confidence 689999999863
No 24
>PF02544 Steroid_dh: 3-oxo-5-alpha-steroid 4-dehydrogenase ; InterPro: IPR001104 Synonym(s): Steroid 5-alpha-reductase 3-oxo-5-alpha-steroid 4-dehydrogenases, 1.3.99.5 from EC catalyse the conversion of 3-oxo-5-alpha-steroid + acceptor to 3-oxo-delta(4)-steroid + reduced acceptor. The steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during foetal development []. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related steroid reductase enzyme, DET2, is found in plants such as Arabidopsis. Mutations in this enzyme cause defects in light-regulated development []. This domain is present in both type 1 and type 2 forms.; GO: 0016627 oxidoreductase activity, acting on the CH-CH group of donors, 0006629 lipid metabolic process, 0005737 cytoplasm, 0016021 integral to membrane
Probab=28.28 E-value=1.4e+02 Score=17.96 Aligned_cols=33 Identities=12% Similarity=0.286 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcC-CCccCCCCC
Q psy1127 33 WWIGSHAVMFFFLFRNFYKEQYVK-PVKTAKFFP 65 (65)
Q Consensus 33 ~~~~~~~~s~l~LF~~FY~~sY~~-~~~~~~~~~ 65 (65)
.+...+...=...=.+.|.++..+ +|+++.+.|
T Consensus 114 ~~~~~~l~~~A~~~h~wY~~~F~~yp~~R~~lIP 147 (150)
T PF02544_consen 114 LFVVVNLSPRAVQTHRWYKKKFKEYPKNRKALIP 147 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCccccCCCeEecC
Confidence 344444444455556778877744 344555554
No 25
>TIGR03493 cellullose_BcsF celllulose biosynthesis operon protein BcsF/YhjT. Members of this protein family are found invariably together with genes of bacterial cellulose biosynthesis, and are presumed to be involved in the process. Members average about 63 amino acids in length and are not uncharacterized. The gene has been designated both YhjT and BcsF (bacterial cellulose synthesis F).
Probab=27.01 E-value=97 Score=16.65 Aligned_cols=17 Identities=24% Similarity=0.274 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy1127 3 AVYISIQFVLIMVHAFQ 19 (65)
Q Consensus 3 T~~QiiQF~~~~~~~~~ 19 (65)
|..+|+|-++..+-.+.
T Consensus 2 ~i~DilQli~lcALIf~ 18 (62)
T TIGR03493 2 NISDILQLVLLCALIFF 18 (62)
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 67889999887654443
No 26
>PF11120 DUF2636: Protein of unknown function (DUF2636); InterPro: IPR019995 Members of this protein family are found invariably together with genes of bacterial cellulose biosynthesis, and are presumed to be involved in the process []. Members average about 63 amino acids in length and are not uncharacterised. The gene has been designated both YhjT and BcsF (bacterial cellulose synthesis F).
Probab=25.47 E-value=1.2e+02 Score=16.31 Aligned_cols=17 Identities=18% Similarity=0.249 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy1127 3 AVYISIQFVLIMVHAFQ 19 (65)
Q Consensus 3 T~~QiiQF~~~~~~~~~ 19 (65)
+..||+|-++..+-.+.
T Consensus 2 ~i~DiiQii~l~AlI~~ 18 (62)
T PF11120_consen 2 NISDIIQIIILCALIFF 18 (62)
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 56789998876654443
No 27
>PF04061 ORMDL: ORMDL family ; InterPro: IPR007203 ORMDL1 belongs to a novel gene family comprising three genes in humans (ORMDL1, ORMDL2 and ORMDL3), and homologs in yeast, microsporidia, plants, Drosophila, urochordates and vertebrates. ORMDLs are involved in protein folding in the endoplasmic reticulum. ; GO: 0016021 integral to membrane
Probab=25.25 E-value=1.7e+02 Score=17.99 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=23.7
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHH
Q psy1127 15 VHAFQLLFIDCNFPKAFVWWIGSHAVMFFFLF 46 (65)
Q Consensus 15 ~~~~~~~~~~C~~p~~~~~~~~~~~~s~l~LF 46 (65)
++......+.|+.+..|......+++.-+++|
T Consensus 23 ~~l~~~~ip~~s~~~~WTltn~~h~~~ty~~f 54 (136)
T PF04061_consen 23 LKLILLSIPGFSQEWAWTLTNLIHNIITYIFF 54 (136)
T ss_pred HHHHHHhccCCCccchhHHHHHHHHHHHHhhe
Confidence 34444445789999988888888888777665
No 28
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=24.83 E-value=1e+02 Score=15.10 Aligned_cols=25 Identities=24% Similarity=0.285 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCc
Q psy1127 35 IGSHAVMFFFLFRNFYKEQYVKPVK 59 (65)
Q Consensus 35 ~~~~~~s~l~LF~~FY~~sY~~~~~ 59 (65)
.....+.+++.|.--..-.|.+++|
T Consensus 11 ~~~~~v~~~~~F~gi~~w~~~~~~k 35 (49)
T PF05545_consen 11 RSIGTVLFFVFFIGIVIWAYRPRNK 35 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHcccch
Confidence 3444444555555556677765543
No 29
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=24.82 E-value=1e+02 Score=21.25 Aligned_cols=27 Identities=11% Similarity=0.135 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcc
Q psy1127 34 WIGSHAVMFFFLFRNFYKEQYVKPVKT 60 (65)
Q Consensus 34 ~~~~~~~s~l~LF~~FY~~sY~~~~~~ 60 (65)
...+..+.-++|-.=+++=.|+|+||-
T Consensus 261 SiiaIliIVLIMvIIYLILRYRRKKKm 287 (299)
T PF02009_consen 261 SIIAILIIVLIMVIIYLILRYRRKKKM 287 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 344445555566666677778875543
No 30
>PHA02819 hypothetical protein; Provisional
Probab=23.29 E-value=1.5e+02 Score=16.40 Aligned_cols=29 Identities=24% Similarity=0.513 Sum_probs=17.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1127 25 CNFPKAFVWWIGSHAVMFFFLFRNFYKEQY 54 (65)
Q Consensus 25 C~~p~~~~~~~~~~~~s~l~LF~~FY~~sY 54 (65)
|+.++.+. +.....+.++++|.=+|.|..
T Consensus 42 ~~~~~~~~-ii~l~~~~~~~~~~flYLK~~ 70 (71)
T PHA02819 42 KSFLRYYL-IIGLVTIVFVIIFIIFYLKVI 70 (71)
T ss_pred CChhHHHH-HHHHHHHHHHHHHHHHHHHhc
Confidence 34444443 344666777778887887754
No 31
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=22.96 E-value=1.9e+02 Score=17.53 Aligned_cols=28 Identities=14% Similarity=0.210 Sum_probs=18.7
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1127 27 FPKAFVWWIGSHAVMFFFLFRNFYKEQY 54 (65)
Q Consensus 27 ~p~~~~~~~~~~~~s~l~LF~~FY~~sY 54 (65)
.+++...+.+++-+.++++...|.++--
T Consensus 6 ~~~~~~~~~~inflil~~lL~~fl~kpi 33 (164)
T PRK14473 6 INLGLLIAQLINFLLLIFLLRTFLYRPV 33 (164)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566777777777777777776544
Done!