Query 032611
Match_columns 137
No_of_seqs 112 out of 235
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:40:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032611.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032611hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2729 ER vesicle integral me 100.0 8E-58 1.7E-62 338.6 15.8 132 3-134 6-137 (137)
2 PF03311 Cornichon: Cornichon 100.0 4.4E-53 9.5E-58 312.6 14.9 126 1-126 1-128 (128)
3 PLN00174 predicted protein; Pr 100.0 6.3E-49 1.4E-53 297.3 14.9 117 15-131 23-140 (160)
4 PF04144 SCAMP: SCAMP family; 66.3 50 0.0011 25.4 7.9 77 5-91 100-177 (177)
5 TIGR00945 tatC Twin arginine t 62.2 46 0.00099 26.2 7.2 24 66-89 63-86 (215)
6 PF00902 TatC: Sec-independent 60.1 68 0.0015 25.0 7.8 25 65-89 66-90 (215)
7 CHL00182 tatC Sec-independent 59.8 48 0.001 27.0 7.0 47 65-122 83-129 (249)
8 TIGR01912 TatC-Arch Twin argin 58.2 55 0.0012 26.4 7.1 45 66-121 71-115 (237)
9 PF07584 BatA: Aerotolerance r 58.1 50 0.0011 21.6 6.1 43 66-108 6-50 (77)
10 PRK10921 twin-arginine protein 55.0 61 0.0013 26.4 6.9 24 66-89 74-97 (258)
11 PF01405 PsbT: Photosystem II 51.3 28 0.00061 19.5 3.0 22 3-24 2-23 (29)
12 cd07153 Fur_like Ferric uptake 49.7 6.3 0.00014 27.3 0.3 37 76-112 15-52 (116)
13 PRK11875 psbT photosystem II r 48.9 32 0.0007 19.6 3.1 22 3-24 2-23 (31)
14 CHL00031 psbT photosystem II p 42.2 32 0.0007 19.8 2.4 22 3-24 2-23 (33)
15 PRK09462 fur ferric uptake reg 34.4 15 0.00033 27.0 0.3 35 77-111 33-68 (148)
16 PF11044 TMEMspv1-c74-12: Plec 33.1 1.1E+02 0.0024 18.9 4.0 26 1-26 1-29 (49)
17 PRK07419 1,4-dihydroxy-2-napht 32.2 3E+02 0.0065 22.9 11.2 88 15-104 183-280 (304)
18 PF04893 Yip1: Yip1 domain; I 31.5 1E+02 0.0022 21.9 4.3 16 92-107 2-17 (172)
19 COG0805 TatC Sec-independent p 28.6 2.2E+02 0.0047 23.5 6.2 26 67-93 78-103 (255)
20 PF09889 DUF2116: Uncharacteri 25.4 1.9E+02 0.0042 18.6 4.6 26 103-128 30-55 (59)
21 PF01475 FUR: Ferric uptake re 25.4 36 0.00079 23.7 1.0 35 77-111 23-58 (120)
22 PRK12592 putative monovalent c 24.4 77 0.0017 23.4 2.6 40 69-108 82-123 (126)
23 TIGR02056 ChlG chlorophyll syn 23.5 4.2E+02 0.0091 21.8 7.5 71 18-88 195-276 (306)
24 PF10840 DUF2645: Protein of u 22.1 1.7E+02 0.0036 21.0 3.9 25 104-128 73-97 (103)
25 PF11119 DUF2633: Protein of u 21.7 1E+02 0.0022 20.0 2.5 27 106-133 5-31 (59)
26 PF00873 ACR_tran: AcrB/AcrD/A 20.9 5E+02 0.011 25.0 7.9 73 53-125 459-543 (1021)
No 1
>KOG2729 consensus ER vesicle integral membrane protein involved in establishing cell polarity, signaling and protein degradation [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=100.00 E-value=8e-58 Score=338.65 Aligned_cols=132 Identities=51% Similarity=0.959 Sum_probs=128.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCHHHhhhhcCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 032611 3 DLFIWLASFFILIALLVLVVYQLMCLADLEFDYINPYDSSSRINKVVLPEFITEGVLCVFFLITGHWFMSLLCVPYLYYN 82 (137)
Q Consensus 3 ~~~~wi~a~~~~~~ll~~~v~~~i~l~DLe~D~iNp~d~~~~lN~lv~pE~~~h~~l~~l~ll~g~W~~~lln~P~l~y~ 82 (137)
+.+.|..+++..++++++++||+|+++|||+||+||+|+|||+|++|+||+++||++|++++++|||+++++|+|+++||
T Consensus 6 ~~~~~~~~~l~~~~li~~~iy~vI~~~DLe~DyiNPid~c~rlN~lVlPE~ilh~~KOGlfLl~g~W~~fllnlP~l~y~ 85 (137)
T KOG2729|consen 6 AAFLYTLSLLVCAALIFLQIYFVICLADLETDYINPIDLCSRLNRLVLPEFILHGLLCLLFLLTGHWFMFLLNLPLLAYN 85 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHccHHHHHH
Confidence 56677788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccCCcCchhhHhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhcc
Q 032611 83 VRLYTQRQHLVDVTEIFNQLHWEKKQRLFKLAYLIFLLFLSIFWMIWCALED 134 (137)
Q Consensus 83 ~~~~~~~~~l~D~TeIf~~L~~~~k~~~iKl~fyl~~Ff~~ly~mi~~lv~~ 134 (137)
+++|.+|+|++|||||||++++|||||++|+|||+++||+|+||||+|++++
T Consensus 86 ~~~y~~r~~l~D~TeI~n~L~~~~k~~~~KL~fyll~FF~yly~mI~slv~~ 137 (137)
T KOG2729|consen 86 AWLYMKRPHLYDPTEIFNTLSSEKKERWIKLAFYLLSFFYYLYWMIYSLVSS 137 (137)
T ss_pred HHHHHcCCcccCHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999975
No 2
>PF03311 Cornichon: Cornichon protein; InterPro: IPR003377 The drosophila cornichon protein (gene: cni) [] is required in the germline for dorsal-ventral signalling. The dorsal-ventral pattern formation involves a reorganisation of the microtubule network correlated with the movement of the oocyte nucleus, and depending on the initial correct establishment of the anterior-posterior axis via a signal from the oocyte produced by cornichon and gurken and received by torpedo protein in the follicle cells. The biochemical function of the cornichon protein is currently not known. It is a protein of 144 residues that seems to contain three transmembrane regions. ; GO: 0035556 intracellular signal transduction, 0016020 membrane
Probab=100.00 E-value=4.4e-53 Score=312.62 Aligned_cols=126 Identities=50% Similarity=0.980 Sum_probs=122.8
Q ss_pred Ch-hH-HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCHHHhhhhcCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032611 1 MG-DL-FIWLASFFILIALLVLVVYQLMCLADLEFDYINPYDSSSRINKVVLPEFITEGVLCVFFLITGHWFMSLLCVPY 78 (137)
Q Consensus 1 m~-~~-~~wi~a~~~~~~ll~~~v~~~i~l~DLe~D~iNp~d~~~~lN~lv~pE~~~h~~l~~l~ll~g~W~~~lln~P~ 78 (137)
|+ +. +.|++|++++++++++++|+++++||||+||+||+|+|||+||+|+||+++|++++++++++|||+++++|+|+
T Consensus 1 m~~~~~~~~i~alll~~~ll~~~vy~ii~l~DLe~D~iNp~d~c~~lN~lv~pE~~~h~~l~~l~ll~g~w~~~llnlPl 80 (128)
T PF03311_consen 1 MAFDFIVLWILALLLTAALLFIVVYFIICLSDLECDYINPIDLCSRLNPLVLPEYIIHGFLCLLFLLTGHWFLFLLNLPL 80 (128)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55 44 48999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCcCchhhHhhhHHHHHHHhHHHHHHHHHHHHHHHHH
Q 032611 79 LYYNVRLYTQRQHLVDVTEIFNQLHWEKKQRLFKLAYLIFLLFLSIFW 126 (137)
Q Consensus 79 l~y~~~~~~~~~~l~D~TeIf~~L~~~~k~~~iKl~fyl~~Ff~~ly~ 126 (137)
++||+++|.+|+|++|||||||+|+++||||++|+|||+++||+|+||
T Consensus 81 ~~y~~~~~~~~~~l~D~T~If~~L~~~kk~~~iKl~~yll~ff~yly~ 128 (128)
T PF03311_consen 81 LAYHIYRYFRRQHLYDPTEIFNQLKREKKESFIKLGFYLLLFFYYLYR 128 (128)
T ss_pred HHHHHHHHHhcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999999996
No 3
>PLN00174 predicted protein; Provisional
Probab=100.00 E-value=6.3e-49 Score=297.26 Aligned_cols=117 Identities=29% Similarity=0.678 Sum_probs=111.9
Q ss_pred HHHHHHHHHHHhhhhccccccCCHHHhhhhcCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhccCCcCc
Q 032611 15 IALLVLVVYQLMCLADLEFDYINPYDSSSRINKVVLPEFITEGVLCVFFLITGHWFMSLLCVPYLYYNVRLYTQRQHLVD 94 (137)
Q Consensus 15 ~~ll~~~v~~~i~l~DLe~D~iNp~d~~~~lN~lv~pE~~~h~~l~~l~ll~g~W~~~lln~P~l~y~~~~~~~~~~l~D 94 (137)
.....+..+....+||||+||+||+|+|+|+|++|+||+++|+++|++|+++|+|+++++|+|+++||++||.+|+|++|
T Consensus 23 ~~~~~~~~~~~~~lsDLE~DYiNPiD~CnrLN~lVlPEyiiH~~l~lLfLltG~W~~fLLNlPll~Yhv~~y~~r~hL~D 102 (160)
T PLN00174 23 FMVIICLGYTYKLLQDLSTDTVNPVEVCDKVNQLKVPEYLAHLFLSIAFVIRGWWIVGFLNFPFIFYNFAQWYEGKHQLD 102 (160)
T ss_pred HHHHHHhcchHHHHHHhhhccCCHHHHHHHhhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 33455667888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHhhhHHHHHHHhHHHHHHHHHHHHHHHH-HHHHHh
Q 032611 95 VTEIFNQLHWEKKQRLFKLAYLIFLLFLSIF-WMIWCA 131 (137)
Q Consensus 95 ~TeIf~~L~~~~k~~~iKl~fyl~~Ff~~ly-~mi~~l 131 (137)
||||||+|++|||+|++|+|||+++||+|+| |||++.
T Consensus 103 ~TeIfn~L~~~kKe~~iKLaFYLl~FF~~ly~~mI~~~ 140 (160)
T PLN00174 103 SAQIFNVLSRELRVIKAKSAFFIIIVIYTIWEWMIWVP 140 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999999999999 999975
No 4
>PF04144 SCAMP: SCAMP family; InterPro: IPR007273 In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences [].; GO: 0015031 protein transport, 0016021 integral to membrane
Probab=66.32 E-value=50 Score=25.35 Aligned_cols=77 Identities=17% Similarity=0.328 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccc-cccCCHHHhhhhcCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 032611 5 FIWLASFFILIALLVLVVYQLMCLADLE-FDYINPYDSSSRINKVVLPEFITEGVLCVFFLITGHWFMSLLCVPYLYYNV 83 (137)
Q Consensus 5 ~~wi~a~~~~~~ll~~~v~~~i~l~DLe-~D~iNp~d~~~~lN~lv~pE~~~h~~l~~l~ll~g~W~~~lln~P~l~y~~ 83 (137)
.-+...++...+-+..++++.+-..+.- +-.++.+|.-++ |.. +....++.+.-|....+....+...+
T Consensus 100 ~~f~~ff~~~~~~i~f~i~~aIG~p~~G~~G~i~ai~~~~~-~~~---------vgi~~~I~a~~w~~~~~~~~~~l~kv 169 (177)
T PF04144_consen 100 FRFMWFFFFFFVHIIFCIIMAIGIPGWGSCGWITAIDVFSN-NKA---------VGILMLIVAILWTLEAVLSFWLLKKV 169 (177)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHcc-Cch---------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666777777888999999888874 889999999888 755 22233456677777777777888889
Q ss_pred HHHhccCC
Q 032611 84 RLYTQRQH 91 (137)
Q Consensus 84 ~~~~~~~~ 91 (137)
+++.|++|
T Consensus 170 ~~~yR~~G 177 (177)
T PF04144_consen 170 HRYYRGTG 177 (177)
T ss_pred HHHhcCCC
Confidence 99998875
No 5
>TIGR00945 tatC Twin arginine targeting (Tat) protein translocase TatC. This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane. A related model (TIGR01912) represents the archaeal clade of this family. TatC is often found in a gene cluster with the two other components of the system, TatA/E (TIGR01411) and TatB (TIGR01410). A model also exists for the Twin-arginine signal sequence (TIGR01409).
Probab=62.23 E-value=46 Score=26.23 Aligned_cols=24 Identities=13% Similarity=0.227 Sum_probs=20.3
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcc
Q 032611 66 TGHWFMSLLCVPYLYYNVRLYTQR 89 (137)
Q Consensus 66 ~g~W~~~lln~P~l~y~~~~~~~~ 89 (137)
.+-+....+..|...|++|++.+.
T Consensus 63 ~s~~~g~~~~~P~i~yqiw~Fi~P 86 (215)
T TIGR00945 63 LSLIVGIILSSPVILYQIWAFILP 86 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344578899999999999999985
No 6
>PF00902 TatC: Sec-independent protein translocase protein (TatC); InterPro: IPR002033 Proteins encoded by the mttABC operon (formerly yigTUW), mediate a novel Sec-independent membrane targeting and translocation system in Escherichia coli that interacts with cofactor-containing redox proteins having a S/TRRXFLK "twin arginine" leader motif. This family contains the E. coli mttB gene (TATC) []. A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N and C termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N terminus and the first cytoplasmic loop region of the E. coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon [, ].
Probab=60.11 E-value=68 Score=25.05 Aligned_cols=25 Identities=12% Similarity=0.465 Sum_probs=21.6
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHhcc
Q 032611 65 ITGHWFMSLLCVPYLYYNVRLYTQR 89 (137)
Q Consensus 65 l~g~W~~~lln~P~l~y~~~~~~~~ 89 (137)
-.+-|.....+.|...|++|++.+.
T Consensus 66 k~s~~~~~~~~~P~~~yq~w~Fi~P 90 (215)
T PF00902_consen 66 KLSFFLGLIISLPYILYQIWAFIAP 90 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 4455688999999999999999987
No 7
>CHL00182 tatC Sec-independent translocase component C; Provisional
Probab=59.78 E-value=48 Score=26.97 Aligned_cols=47 Identities=17% Similarity=0.325 Sum_probs=31.5
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHhccCCcCchhhHhhhHHHHHHHhHHHHHHHHHHHHH
Q 032611 65 ITGHWFMSLLCVPYLYYNVRLYTQRQHLVDVTEIFNQLHWEKKQRLFKLAYLIFLLFL 122 (137)
Q Consensus 65 l~g~W~~~lln~P~l~y~~~~~~~~~~l~D~TeIf~~L~~~~k~~~iKl~fyl~~Ff~ 122 (137)
-.+-+....+..|...|.+|++.+. + |.++||+...|.......+|+
T Consensus 83 kls~~~g~~~a~P~i~yqiw~Fi~P-g----------Ly~~Er~~~~~~~~~s~~lF~ 129 (249)
T CHL00182 83 KISFYTGLLISSPFIIYQIILFILP-G----------LTKKERKIILPLLISSLVLFG 129 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc-c----------cCHHHHHHHHHHHHHHHHHHH
Confidence 3445678899999999999999985 2 445555555555544444433
No 8
>TIGR01912 TatC-Arch Twin arginine targeting (Tat) protein translocase TatC, Archaeal clade. This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane. A related model (TIGR00945) represents the bacterial clade of this family. TatC is often found (in bacteria) in a gene cluster with the two other components of the system, TatA/E (TIGR01411) and TatB (TIGR01410). A model also exists for the Twin-arginine signal sequence (TIGR01409).
Probab=58.24 E-value=55 Score=26.36 Aligned_cols=45 Identities=20% Similarity=0.307 Sum_probs=30.0
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhccCCcCchhhHhhhHHHHHHHhHHHHHHHHHHHH
Q 032611 66 TGHWFMSLLCVPYLYYNVRLYTQRQHLVDVTEIFNQLHWEKKQRLFKLAYLIFLLF 121 (137)
Q Consensus 66 ~g~W~~~lln~P~l~y~~~~~~~~~~l~D~TeIf~~L~~~~k~~~iKl~fyl~~Ff 121 (137)
.+-+....+..|...|++|++.+. | |.++||+...|...-....|
T Consensus 71 ~s~~~g~~~~~P~i~yqiw~Fi~P-g----------Ly~~Er~~~~~~~~~~~~lF 115 (237)
T TIGR01912 71 SAFFIGLLLASPVLAYEAYRFIKP-A----------LKPHERRQVRLLGVIAVGLF 115 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc-c----------ccHHHHHHHHHHHHHHHHHH
Confidence 345578899999999999999985 2 33445555555544433333
No 9
>PF07584 BatA: Aerotolerance regulator N-terminal; InterPro: IPR024163 The Batl operon appears to be important in pathogenicity and aerotolerance. BatA ensures bacterial survival in the early stages of the infection process, when the infected sites are aerobic, and is produced under conditions of oxidative stress []. Proteins produced by the Batl operon share a highly-conserved sequence at their N terminus and the full length proteins carry multiple membrane-spanning domains []. This entry represents the conserved N-terminal domain, which is also found in some uncharacterised proteins.
Probab=58.12 E-value=50 Score=21.60 Aligned_cols=43 Identities=12% Similarity=0.189 Sum_probs=23.4
Q ss_pred HhHHHHHHHHHHH-HHHHHH-HHhccCCcCchhhHhhhHHHHHHH
Q 032611 66 TGHWFMSLLCVPY-LYYNVR-LYTQRQHLVDVTEIFNQLHWEKKQ 108 (137)
Q Consensus 66 ~g~W~~~lln~P~-l~y~~~-~~~~~~~l~D~TeIf~~L~~~~k~ 108 (137)
+.+|+.+++-+|. +.++.. +-.+++..+-.++.+++...+.+.
T Consensus 6 ~P~~L~~Llllp~~i~~~~~~~~~~~~~~fs~~~~l~~~~~~~~~ 50 (77)
T PF07584_consen 6 NPWYLWLLLLLPLPIIIHYFLRRRRRRVRFSSLRLLKRLPPSRRS 50 (77)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcccCCCcccCCHHHHHHhCcccch
Confidence 3445555556666 444444 444445566677777755554444
No 10
>PRK10921 twin-arginine protein translocation system subunit TatC; Provisional
Probab=55.03 E-value=61 Score=26.44 Aligned_cols=24 Identities=17% Similarity=0.306 Sum_probs=20.2
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcc
Q 032611 66 TGHWFMSLLCVPYLYYNVRLYTQR 89 (137)
Q Consensus 66 ~g~W~~~lln~P~l~y~~~~~~~~ 89 (137)
.+-+....+..|...|.+|++.+.
T Consensus 74 ~sl~~g~~la~P~ilyqiw~Fi~P 97 (258)
T PRK10921 74 LTFMVSLILSAPVILYQVWAFIAP 97 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345577899999999999999985
No 11
>PF01405 PsbT: Photosystem II reaction centre T protein; InterPro: IPR001743 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 PsbT found in PSII, which is thought to be associated with the D1 (PsbA) - D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3BZ1_T 1S5L_t 2AXT_t 3KZI_T 3PRQ_T 3BZ2_T 3PRR_T 4FBY_g 3A0H_t 3A0B_T ....
Probab=51.26 E-value=28 Score=19.54 Aligned_cols=22 Identities=5% Similarity=0.306 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 032611 3 DLFIWLASFFILIALLVLVVYQ 24 (137)
Q Consensus 3 ~~~~wi~a~~~~~~ll~~~v~~ 24 (137)
|.+.+.+.++.+.+.++..+++
T Consensus 2 Ea~vY~~ll~~tlgilffAI~F 23 (29)
T PF01405_consen 2 EALVYTFLLIGTLGILFFAIFF 23 (29)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHS
T ss_pred chhHHHHHHHHHHHHHHhhhhc
Confidence 7788888888877777776653
No 12
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=49.73 E-value=6.3 Score=27.29 Aligned_cols=37 Identities=5% Similarity=0.103 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhccCC-cCchhhHhhhHHHHHHHhHHH
Q 032611 76 VPYLYYNVRLYTQRQH-LVDVTEIFNQLHWEKKQRLFK 112 (137)
Q Consensus 76 ~P~l~y~~~~~~~~~~-l~D~TeIf~~L~~~~k~~~iK 112 (137)
-|+.+..++.-.++++ -++.++++|.|+.....|.++
T Consensus 15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence 4677888887777665 589999999999988887653
No 13
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=48.86 E-value=32 Score=19.58 Aligned_cols=22 Identities=9% Similarity=0.277 Sum_probs=16.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 032611 3 DLFIWLASFFILIALLVLVVYQ 24 (137)
Q Consensus 3 ~~~~wi~a~~~~~~ll~~~v~~ 24 (137)
|.+++.+.+..+.+.+|..+++
T Consensus 2 Eal~Ytfll~~tlgiiFFAIfF 23 (31)
T PRK11875 2 ESFAYILILTLALVTLFFAIAF 23 (31)
T ss_pred hhHHHHHHHHHHHHHHHHhhhc
Confidence 6778888888777777776654
No 14
>CHL00031 psbT photosystem II protein T
Probab=42.21 E-value=32 Score=19.84 Aligned_cols=22 Identities=0% Similarity=0.315 Sum_probs=16.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 032611 3 DLFIWLASFFILIALLVLVVYQ 24 (137)
Q Consensus 3 ~~~~wi~a~~~~~~ll~~~v~~ 24 (137)
|.+++.+.++.+.+.+|..+++
T Consensus 2 EalvYtfll~~tlgilFFAI~F 23 (33)
T CHL00031 2 EALVYTFLLVSTLGIIFFAIFF 23 (33)
T ss_pred chhHHHHHHHHHHHHHHHhhee
Confidence 6778888888777777766653
No 15
>PRK09462 fur ferric uptake regulator; Provisional
Probab=34.39 E-value=15 Score=26.96 Aligned_cols=35 Identities=3% Similarity=-0.053 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhccCC-cCchhhHhhhHHHHHHHhHH
Q 032611 77 PYLYYNVRLYTQRQH-LVDVTEIFNQLHWEKKQRLF 111 (137)
Q Consensus 77 P~l~y~~~~~~~~~~-l~D~TeIf~~L~~~~k~~~i 111 (137)
|+.+..++...++++ -+++++|||+|+.....+.+
T Consensus 33 h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli 68 (148)
T PRK09462 33 HVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIV 68 (148)
T ss_pred CCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCE
Confidence 678888887776654 57999999999988887765
No 16
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=33.15 E-value=1.1e+02 Score=18.94 Aligned_cols=26 Identities=23% Similarity=0.414 Sum_probs=18.7
Q ss_pred ChhHHHHHHHHHHHHHH---HHHHHHHHh
Q 032611 1 MGDLFIWLASFFILIAL---LVLVVYQLM 26 (137)
Q Consensus 1 m~~~~~wi~a~~~~~~l---l~~~v~~~i 26 (137)
|+.-..|+++.++..+. +++++|+=|
T Consensus 1 mp~wlt~iFsvvIil~If~~iGl~IyQki 29 (49)
T PF11044_consen 1 MPTWLTTIFSVVIILGIFAWIGLSIYQKI 29 (49)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677888887766655 778888743
No 17
>PRK07419 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional
Probab=32.19 E-value=3e+02 Score=22.94 Aligned_cols=88 Identities=16% Similarity=0.180 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHhhhhccccccCCH-----HHhhhhcCcchHH-HHHHHHHHHHHHHHHh----HHHHHHHHHHHHHHHHH
Q 032611 15 IALLVLVVYQLMCLADLEFDYINP-----YDSSSRINKVVLP-EFITEGVLCVFFLITG----HWFMSLLCVPYLYYNVR 84 (137)
Q Consensus 15 ~~ll~~~v~~~i~l~DLe~D~iNp-----~d~~~~lN~lv~p-E~~~h~~l~~l~ll~g----~W~~~lln~P~l~y~~~ 84 (137)
.+++...+-++=.+.|.|.|-.|= +-.-+|--+.+.. -...-.+..+.....| ++...++.+|...-+.+
T Consensus 183 ~gll~~~IL~~Nn~rD~e~D~~~Gk~TL~v~lG~~~a~~ly~~l~~~ay~~~i~~v~~g~~p~~~Ll~ll~lPl~~~~~~ 262 (304)
T PRK07419 183 LGLATSLILFCSHFHQVEDDLAAGKRSPIVRLGTKRGAQLLPWIVGLIYALELLPVLLGFWPWTTLLSLLSLPFAIKLIR 262 (304)
T ss_pred HHHHHHHHHHHcCCcchhhHHHcCCcceeeeechHhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 445556666677889999997661 1111111111111 1111111222222232 23567888998888888
Q ss_pred HHhccCCcCchhhHhhhHHH
Q 032611 85 LYTQRQHLVDVTEIFNQLHW 104 (137)
Q Consensus 85 ~~~~~~~l~D~TeIf~~L~~ 104 (137)
+..+.+. |+.+.-+.+++
T Consensus 263 ~~~~~~~--~~~~l~~~l~~ 280 (304)
T PRK07419 263 LVRENHD--QPEKVSNSKFI 280 (304)
T ss_pred HHHHcCC--CHHHHHHHHHH
Confidence 7755422 55555555544
No 18
>PF04893 Yip1: Yip1 domain; InterPro: IPR006977 This entry contains proteins belonging to the Yip1 family and represents the Yip1 domain. The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases [].; GO: 0016020 membrane
Probab=31.50 E-value=1e+02 Score=21.90 Aligned_cols=16 Identities=25% Similarity=0.389 Sum_probs=14.2
Q ss_pred cCchhhHhhhHHHHHH
Q 032611 92 LVDVTEIFNQLHWEKK 107 (137)
Q Consensus 92 l~D~TeIf~~L~~~~k 107 (137)
+.||.|.|++++++++
T Consensus 2 l~~P~~~f~~~~~~~~ 17 (172)
T PF04893_consen 2 LFSPREFFRRLRESPR 17 (172)
T ss_pred ccCHHHHHHHHHhccc
Confidence 4699999999998888
No 19
>COG0805 TatC Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]
Probab=28.59 E-value=2.2e+02 Score=23.48 Aligned_cols=26 Identities=19% Similarity=0.338 Sum_probs=21.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHhccCCcC
Q 032611 67 GHWFMSLLCVPYLYYNVRLYTQRQHLV 93 (137)
Q Consensus 67 g~W~~~lln~P~l~y~~~~~~~~~~l~ 93 (137)
+-+...++..|.++|.+|++.+. |++
T Consensus 78 a~~~gl~~a~P~i~yq~w~FiaP-GLy 103 (255)
T COG0805 78 ALFAGLLLALPVILYQLWAFIAP-GLY 103 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCC-ccc
Confidence 34478899999999999999987 665
No 20
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=25.40 E-value=1.9e+02 Score=18.57 Aligned_cols=26 Identities=12% Similarity=0.437 Sum_probs=13.9
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHH
Q 032611 103 HWEKKQRLFKLAYLIFLLFLSIFWMI 128 (137)
Q Consensus 103 ~~~~k~~~iKl~fyl~~Ff~~ly~mi 128 (137)
++.+|.+..+..++++++.+...++.
T Consensus 30 k~qk~~~~~~~i~~~~~i~~l~v~~~ 55 (59)
T PF09889_consen 30 KRQKRMRKTQYIFFGIFILFLAVWIF 55 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444455566666666654444443
No 21
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=25.38 E-value=36 Score=23.73 Aligned_cols=35 Identities=6% Similarity=0.111 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhccC-CcCchhhHhhhHHHHHHHhHH
Q 032611 77 PYLYYNVRLYTQRQ-HLVDVTEIFNQLHWEKKQRLF 111 (137)
Q Consensus 77 P~l~y~~~~~~~~~-~l~D~TeIf~~L~~~~k~~~i 111 (137)
|+.+..++.-.+++ .-++.++|+|.|+...+.|.+
T Consensus 23 ~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli 58 (120)
T PF01475_consen 23 HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLI 58 (120)
T ss_dssp SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeE
Confidence 55667777655544 578999999999988877643
No 22
>PRK12592 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=24.38 E-value=77 Score=23.43 Aligned_cols=40 Identities=23% Similarity=0.204 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCcC-chhhHhh-hHHHHHHH
Q 032611 69 WFMSLLCVPYLYYNVRLYTQRQHLV-DVTEIFN-QLHWEKKQ 108 (137)
Q Consensus 69 W~~~lln~P~l~y~~~~~~~~~~l~-D~TeIf~-~L~~~~k~ 108 (137)
|+..++..|...+-+.|--.|++.. |+.+++| +..+++|+
T Consensus 82 ~~FlllT~Pvaah~iaRAAyr~g~~~~~~~~~~~~~~~~~~~ 123 (126)
T PRK12592 82 VLFALLTSPVTAQRVGRVSRREGLYGAKDTMSRNQAPAERKP 123 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCccccccccccchhhh
Confidence 4667788999999999988888877 8889988 56666655
No 23
>TIGR02056 ChlG chlorophyll synthase, ChlG. This model represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP).
Probab=23.53 E-value=4.2e+02 Score=21.80 Aligned_cols=71 Identities=13% Similarity=0.154 Sum_probs=35.6
Q ss_pred HHHHHHHHhhhhccccccCC-----HHHhhhhcCcchHH-HHH-HHHHHHHHHHHHh---HH-HHHHHHHHHHHHHHHHH
Q 032611 18 LVLVVYQLMCLADLEFDYIN-----PYDSSSRINKVVLP-EFI-TEGVLCVFFLITG---HW-FMSLLCVPYLYYNVRLY 86 (137)
Q Consensus 18 l~~~v~~~i~l~DLe~D~iN-----p~d~~~~lN~lv~p-E~~-~h~~l~~l~ll~g---~W-~~~lln~P~l~y~~~~~ 86 (137)
....+...=.+.|.|.|-.+ |+..-+|--..+-- ... ............+ +| ...++.+|...++.+++
T Consensus 195 ~~~~i~~~n~~~D~e~D~~~G~~Tlpv~lG~~~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ll~ll~~p~~~~~~~~~ 274 (306)
T TIGR02056 195 AGLGIAIVNDFKSVEGDRALGLQSLPVAFGIETAAWICVGAIDIFQGLIAAYLLAIGENLYAAALVALIIPQITFQDKYF 274 (306)
T ss_pred HHHHHHHHHHccChHHHHHcCCcCcchhcChHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHH
Confidence 44444555667888888644 44443331111100 011 1222222222222 22 45888899999998877
Q ss_pred hc
Q 032611 87 TQ 88 (137)
Q Consensus 87 ~~ 88 (137)
.+
T Consensus 275 ~~ 276 (306)
T TIGR02056 275 LK 276 (306)
T ss_pred Hh
Confidence 76
No 24
>PF10840 DUF2645: Protein of unknown function (DUF2645); InterPro: IPR022553 This family of proteins appears to be restricted to Enterobacteriaceae. Some members in the family are annotated as inner membrane protein YjeO. However no function is currently known.
Probab=22.09 E-value=1.7e+02 Score=21.05 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=18.8
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHH
Q 032611 104 WEKKQRLFKLAYLIFLLFLSIFWMI 128 (137)
Q Consensus 104 ~~~k~~~iKl~fyl~~Ff~~ly~mi 128 (137)
++|.++..+...++++++|.++++-
T Consensus 73 ~~k~ks~~~~~~~i~i~~Y~~W~Ff 97 (103)
T PF10840_consen 73 KKKFKSLFRYIVYIAILFYWLWRFF 97 (103)
T ss_pred HHHhhcHHHHHHHHHHHHHHHHHHH
Confidence 4466777888888888888888763
No 25
>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=21.70 E-value=1e+02 Score=20.02 Aligned_cols=27 Identities=19% Similarity=0.422 Sum_probs=18.3
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHhhc
Q 032611 106 KKQRLFKLAYLIFLLFLSIFWMIWCALE 133 (137)
Q Consensus 106 ~k~~~iKl~fyl~~Ff~~ly~mi~~lv~ 133 (137)
++.++.|+. .+++|++..-|++|+.+.
T Consensus 5 ~~~~mtriV-LLISfiIlfgRl~Y~~I~ 31 (59)
T PF11119_consen 5 KNSRMTRIV-LLISFIILFGRLIYSAIG 31 (59)
T ss_pred ccchHHHHH-HHHHHHHHHHHHHHHHHh
Confidence 344555554 567788888888888774
No 26
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=20.91 E-value=5e+02 Score=24.99 Aligned_cols=73 Identities=22% Similarity=0.329 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhccCCcC------c-----hhhHhh-hHHHHHHHhHHHHHHHHHHH
Q 032611 53 FITEGVLCVFFLITGHWFMSLLCVPYLYYNVRLYTQRQHLV------D-----VTEIFN-QLHWEKKQRLFKLAYLIFLL 120 (137)
Q Consensus 53 ~~~h~~l~~l~ll~g~W~~~lln~P~l~y~~~~~~~~~~l~------D-----~TeIf~-~L~~~~k~~~iKl~fyl~~F 120 (137)
+.-....++.+.+...|+..+.-+|.+++++.+-.+++..- | .++.|+ -|++.-|.++.-++..++++
T Consensus 459 ~~~~l~~~v~~al~~Sllval~~~P~l~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~Y~~lL~~~L~~~~~~l~i~l~l~ 538 (1021)
T PF00873_consen 459 FFRPLALTVIIALIASLLVALTLVPALAALFLKPKKKSSKKRFFSKFDRFFDRLQRGYRRLLRWALRHPKLVLLIALLLL 538 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTHHHHHHHCS----TT-CCCHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccccccccccccccccccccchhhhhhhhhhcccchhhhhhhhh
Confidence 33334466677888889999999999998876544443210 1 122222 45666666666666666666
Q ss_pred HHHHH
Q 032611 121 FLSIF 125 (137)
Q Consensus 121 f~~ly 125 (137)
+..+.
T Consensus 539 i~s~~ 543 (1021)
T PF00873_consen 539 ILSLF 543 (1021)
T ss_dssp HHHHH
T ss_pred hhhhc
Confidence 55443
Done!