Query 031779
Match_columns 153
No_of_seqs 112 out of 219
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:14:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031779.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031779hhsearch_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 9.1E-59 2E-63 356.2 15.8 134 1-134 3-136 (137)
2 PF03311 Cornichon: Cornichon 100.0 1.6E-53 3.4E-58 324.7 14.6 127 1-127 1-128 (128)
3 PLN00174 predicted protein; Pr 100.0 4.1E-48 9E-53 303.5 14.3 116 22-137 29-145 (160)
4 PF04144 SCAMP: SCAMP family; 72.0 25 0.00055 27.9 7.5 77 6-92 100-177 (177)
5 PF01405 PsbT: Photosystem II 68.1 9 0.0002 22.6 3.1 22 4-25 2-23 (29)
6 PRK11875 psbT photosystem II r 64.8 11 0.00024 22.5 3.1 22 4-25 2-23 (31)
7 CHL00031 psbT photosystem II p 58.4 12 0.00025 22.7 2.4 22 4-25 2-23 (33)
8 TIGR00945 tatC Twin arginine t 53.5 80 0.0017 25.7 7.4 43 45-94 47-89 (215)
9 CHL00182 tatC Sec-independent 50.3 87 0.0019 26.3 7.3 25 66-90 83-107 (249)
10 TIGR01912 TatC-Arch Twin argin 49.2 97 0.0021 25.7 7.4 40 45-90 55-94 (237)
11 PRK10921 twin-arginine protein 47.0 1E+02 0.0022 26.0 7.3 28 66-94 73-100 (258)
12 PF07584 BatA: Aerotolerance r 46.1 80 0.0017 21.4 5.4 41 67-107 6-48 (77)
13 COG0805 TatC Sec-independent p 43.5 1.1E+02 0.0024 26.1 6.9 28 67-95 77-104 (255)
14 cd07153 Fur_like Ferric uptake 39.8 8.8 0.00019 27.3 -0.2 38 76-113 14-52 (116)
15 KOG3801 Uncharacterized conser 39.6 29 0.00063 25.6 2.5 29 80-108 24-61 (94)
16 PF00902 TatC: Sec-independent 37.2 2.2E+02 0.0047 22.9 11.2 40 45-90 51-90 (215)
17 PF11119 DUF2633: Protein of u 36.0 36 0.00078 23.1 2.3 31 107-138 5-35 (59)
18 COG2981 CysZ Uncharacterized p 36.0 2.8E+02 0.0062 23.8 10.2 111 9-120 29-145 (250)
19 COG0382 UbiA 4-hydroxybenzoate 33.4 2.9E+02 0.0062 23.1 9.3 78 18-98 58-145 (289)
20 PF11044 TMEMspv1-c74-12: Plec 30.2 1.3E+02 0.0027 19.6 4.0 24 4-27 3-29 (49)
21 COG0841 AcrB Cation/multidrug 29.2 3.8E+02 0.0083 27.2 9.1 100 49-148 450-559 (1009)
22 PF04893 Yip1: Yip1 domain; I 27.5 1.1E+02 0.0023 22.4 3.9 16 93-108 2-17 (172)
23 PRK09462 fur ferric uptake reg 27.5 19 0.00041 27.3 -0.2 36 77-112 32-68 (148)
24 PRK13553 fumarate reductase cy 24.1 4.7E+02 0.01 22.5 10.9 105 4-128 120-229 (258)
25 COG3647 Predicted membrane pro 24.1 3.1E+02 0.0067 22.7 6.2 31 108-138 126-156 (205)
26 PF09889 DUF2116: Uncharacteri 22.4 2.5E+02 0.0055 18.8 4.7 36 94-129 13-55 (59)
27 KOG3249 Uncharacterized conser 20.4 4.1E+02 0.0089 21.8 6.2 72 43-114 85-178 (181)
28 PF00873 ACR_tran: AcrB/AcrD/A 20.3 4.2E+02 0.0091 26.3 7.5 74 53-126 458-543 (1021)
29 PF01475 FUR: Ferric uptake re 20.2 42 0.00091 24.2 0.4 34 78-111 23-57 (120)
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=9.1e-59 Score=356.25 Aligned_cols=134 Identities=45% Similarity=0.752 Sum_probs=131.2
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccCChHHhhhhcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHH
Q 031779 1 MALIFLFWFLMSAINIALIASTFYQLLCLLDLESDDINPFEASSRINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLV 80 (153)
Q Consensus 1 m~~~~~~~i~a~ll~~~ll~l~vy~lI~l~DLe~D~iNPiD~c~rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll 80 (153)
|.+++++|..+++.++++++.++||+||++|||+||+||+|+|||+|++|+||++.||++|++++++|||+++++|+|++
T Consensus 3 ~~~~~~~~~~~~l~~~~li~~~iy~vI~~~DLe~DyiNPid~c~rlN~lVlPE~ilh~~KOGlfLl~g~W~~fllnlP~l 82 (137)
T KOG2729|consen 3 FTFAAFLYTLSLLVCAALIFLQIYFVICLADLETDYINPIDLCSRLNRLVLPEFILHGLLCLLFLLTGHWFMFLLNLPLL 82 (137)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCccchhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 031779 81 CYHVNLYMKRKHLIDVTEVFRNLKVEKKFRLAKLGFYVIFFALVIANIIAVGKF 134 (153)
Q Consensus 81 ~y~~~~y~~r~~l~D~TeIf~~L~~~kk~~~iKLafyll~Ff~~ly~mI~~lv~ 134 (153)
+||+++|.+|+|++|||||||+|++|||||++|+|||+++||+|+||||+|+++
T Consensus 83 ~y~~~~y~~r~~l~D~TeI~n~L~~~~k~~~~KL~fyll~FF~yly~mI~slv~ 136 (137)
T KOG2729|consen 83 AYNAWLYMKRPHLYDPTEIFNTLSSEKKERWIKLAFYLLSFFYYLYWMIYSLVS 136 (137)
T ss_pred HHHHHHHHcCCcccCHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999985
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=1.6e-53 Score=324.66 Aligned_cols=127 Identities=45% Similarity=0.899 Sum_probs=125.5
Q ss_pred ChhHHH-HHHHHHHHHHHHHHHHHHHHHhhhccccccCChHHhhhhcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHH
Q 031779 1 MALIFL-FWFLMSAINIALIASTFYQLLCLLDLESDDINPFEASSRINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPL 79 (153)
Q Consensus 1 m~~~~~-~~i~a~ll~~~ll~l~vy~lI~l~DLe~D~iNPiD~c~rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPl 79 (153)
|+++.+ .|++|++++++++++++||+++++|||+||+||+|+|||+||+|+||+++|+++|++++++|||+++++|+|+
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 888887 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccCccchhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 031779 80 VCYHVNLYMKRKHLIDVTEVFRNLKVEKKFRLAKLGFYVIFFALVIAN 127 (153)
Q Consensus 80 l~y~~~~y~~r~~l~D~TeIf~~L~~~kk~~~iKLafyll~Ff~~ly~ 127 (153)
++||+++|.+|+|++|||||||+|+++||+|++|+|||+++||+|+||
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=4.1e-48 Score=303.51 Aligned_cols=116 Identities=29% Similarity=0.496 Sum_probs=109.5
Q ss_pred HHHHHHhhhccccccCChHHhhhhcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHHHHHhhccCccchhhhhh
Q 031779 22 TFYQLLCLLDLESDDINPFEASSRINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCYHVNLYMKRKHLIDVTEVFR 101 (153)
Q Consensus 22 ~vy~lI~l~DLe~D~iNPiD~c~rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y~~~~y~~r~~l~D~TeIf~ 101 (153)
..|.-=.+||||+||+||+|+|||+|++|+||+++|+++|++++++|+|+++++|+|+++||++||.+|+|++|||||||
T Consensus 29 ~~~~~~~lsDLE~DYiNPiD~CnrLN~lVlPEyiiH~~l~lLfLltG~W~~fLLNlPll~Yhv~~y~~r~hL~D~TeIfn 108 (160)
T PLN00174 29 LGYTYKLLQDLSTDTVNPVEVCDKVNQLKVPEYLAHLFLSIAFVIRGWWIVGFLNFPFIFYNFAQWYEGKHQLDSAQIFN 108 (160)
T ss_pred hcchHHHHHHhhhccCCHHHHHHHhhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence 34555678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhhhhc
Q 031779 102 NLKVEKKFRLAKLGFYVIFFALVIA-NIIAVGKFWVS 137 (153)
Q Consensus 102 ~L~~~kk~~~iKLafyll~Ff~~ly-~mI~~lv~~~~ 137 (153)
+|++|||+|++|+|||+++||+|+| |||++=-+.+|
T Consensus 109 ~L~~~kKe~~iKLaFYLl~FF~~ly~~mI~~~~~~~~ 145 (160)
T PLN00174 109 VLSRELRVIKAKSAFFIIIVIYTIWEWMIWVPPDYVS 145 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCccc
Confidence 9999999999999999999999999 99987655554
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=71.96 E-value=25 Score=27.92 Aligned_cols=77 Identities=12% Similarity=0.058 Sum_probs=59.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccc-cccCChHHhhhhcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHH
Q 031779 6 LFWFLMSAINIALIASTFYQLLCLLDLE-SDDINPFEASSRINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCYHV 84 (153)
Q Consensus 6 ~~~i~a~ll~~~ll~l~vy~lI~l~DLe-~D~iNPiD~c~rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y~~ 84 (153)
+-|...++...+-+..++++.|-..+.- +-.++.+|.-++ |.. ...+.++.+.-|....+....+...+
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 3456666667777888999999888764 889999999888 773 33444566778888888888888999
Q ss_pred HHHhhccC
Q 031779 85 NLYMKRKH 92 (153)
Q Consensus 85 ~~y~~r~~ 92 (153)
++++|++|
T Consensus 170 ~~~yR~~G 177 (177)
T PF04144_consen 170 HRYYRGTG 177 (177)
T ss_pred HHHhcCCC
Confidence 99999875
No 5
>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=68.12 E-value=9 Score=22.57 Aligned_cols=22 Identities=5% Similarity=0.105 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 031779 4 IFLFWFLMSAINIALIASTFYQ 25 (153)
Q Consensus 4 ~~~~~i~a~ll~~~ll~l~vy~ 25 (153)
|++.|.+.++.+.+.+|.++++
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 7899999999998888888764
No 6
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=64.83 E-value=11 Score=22.50 Aligned_cols=22 Identities=5% Similarity=0.046 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 031779 4 IFLFWFLMSAINIALIASTFYQ 25 (153)
Q Consensus 4 ~~~~~i~a~ll~~~ll~l~vy~ 25 (153)
|++.|.+-++.+.+.+|.++++
T Consensus 2 Eal~Ytfll~~tlgiiFFAIfF 23 (31)
T PRK11875 2 ESFAYILILTLALVTLFFAIAF 23 (31)
T ss_pred hhHHHHHHHHHHHHHHHHhhhc
Confidence 7899999999998888888765
No 7
>CHL00031 psbT photosystem II protein T
Probab=58.44 E-value=12 Score=22.71 Aligned_cols=22 Identities=9% Similarity=0.178 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 031779 4 IFLFWFLMSAINIALIASTFYQ 25 (153)
Q Consensus 4 ~~~~~i~a~ll~~~ll~l~vy~ 25 (153)
|++.|.+-++.+.+.+|.++++
T Consensus 2 EalvYtfll~~tlgilFFAI~F 23 (33)
T CHL00031 2 EALVYTFLLVSTLGIIFFAIFF 23 (33)
T ss_pred chhHHHHHHHHHHHHHHHhhee
Confidence 7899999999998888887764
No 8
>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=53.47 E-value=80 Score=25.67 Aligned_cols=43 Identities=12% Similarity=0.170 Sum_probs=29.3
Q ss_pred hcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHHHHHhhccCcc
Q 031779 45 RINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCYHVNLYMKRKHLI 94 (153)
Q Consensus 45 rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y~~~~y~~r~~l~ 94 (153)
+++..-..|... ..+-..-+....++.|...|++|++.+ +|++
T Consensus 47 ~li~t~~~e~f~------~~lk~s~~~g~~~~~P~i~yqiw~Fi~-PgLy 89 (215)
T TIGR00945 47 TFIATSPTEPFF------TYIKLSLIVGIILSSPVILYQIWAFIL-PGLY 89 (215)
T ss_pred CeEecCchHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHhc-cccc
Confidence 455555666542 223345667889999999999999887 4444
No 9
>CHL00182 tatC Sec-independent translocase component C; Provisional
Probab=50.32 E-value=87 Score=26.30 Aligned_cols=25 Identities=16% Similarity=0.477 Sum_probs=21.0
Q ss_pred hhhHHHHHHhhHHHHHHHHHHHhhc
Q 031779 66 VTGHWIMFLLGVPLVCYHVNLYMKR 90 (153)
Q Consensus 66 l~g~W~~~llnlPll~y~~~~y~~r 90 (153)
-..-+....+..|...|.+|++.+.
T Consensus 83 kls~~~g~~~a~P~i~yqiw~Fi~P 107 (249)
T CHL00182 83 KISFYTGLLISSPFIIYQIILFILP 107 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3456788899999999999998874
No 10
>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=49.16 E-value=97 Score=25.75 Aligned_cols=40 Identities=20% Similarity=0.259 Sum_probs=27.7
Q ss_pred hcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHHHHHhhc
Q 031779 45 RINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCYHVNLYMKR 90 (153)
Q Consensus 45 rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y~~~~y~~r 90 (153)
+++..-..|.. ...+-..-+....+..|...|.+|++.+.
T Consensus 55 ~li~~~~~e~f------~~~lk~s~~~g~~~~~P~i~yqiw~Fi~P 94 (237)
T TIGR01912 55 TLIAPSPFAAL------ELRIKSAFFIGLLLASPVLAYEAYRFIKP 94 (237)
T ss_pred eeEEcCchHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35555555654 22233456778899999999999998874
No 11
>PRK10921 twin-arginine protein translocation system subunit TatC; Provisional
Probab=47.02 E-value=1e+02 Score=25.96 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=22.1
Q ss_pred hhhHHHHHHhhHHHHHHHHHHHhhccCcc
Q 031779 66 VTGHWIMFLLGVPLVCYHVNLYMKRKHLI 94 (153)
Q Consensus 66 l~g~W~~~llnlPll~y~~~~y~~r~~l~ 94 (153)
-..-+....+..|...|.+|++.+ +|++
T Consensus 73 k~sl~~g~~la~P~ilyqiw~Fi~-PgLy 100 (258)
T PRK10921 73 KLTFMVSLILSAPVILYQVWAFIA-PALY 100 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh-ccCC
Confidence 344567789999999999999887 4554
No 12
>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=46.15 E-value=80 Score=21.35 Aligned_cols=41 Identities=20% Similarity=0.354 Sum_probs=22.2
Q ss_pred hhHHHHHHhhHHH-HHHHHHHHhh-ccCccchhhhhhhhHHHH
Q 031779 67 TGHWIMFLLGVPL-VCYHVNLYMK-RKHLIDVTEVFRNLKVEK 107 (153)
Q Consensus 67 ~g~W~~~llnlPl-l~y~~~~y~~-r~~l~D~TeIf~~L~~~k 107 (153)
+.+|+.+++-+|. +.+++....+ ++..+-.++.+++...+.
T Consensus 6 ~P~~L~~Llllp~~i~~~~~~~~~~~~~~fs~~~~l~~~~~~~ 48 (77)
T PF07584_consen 6 NPWYLWLLLLLPLPIIIHYFLRRRRRRVRFSSLRLLKRLPPSR 48 (77)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcccCCCcccCCHHHHHHhCccc
Confidence 3445555666666 4455444444 345566666776544433
No 13
>COG0805 TatC Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]
Probab=43.52 E-value=1.1e+02 Score=26.14 Aligned_cols=28 Identities=18% Similarity=0.413 Sum_probs=23.2
Q ss_pred hhHHHHHHhhHHHHHHHHHHHhhccCccc
Q 031779 67 TGHWIMFLLGVPLVCYHVNLYMKRKHLID 95 (153)
Q Consensus 67 ~g~W~~~llnlPll~y~~~~y~~r~~l~D 95 (153)
..-+...++..|..+|..|++.++ |+|.
T Consensus 77 ~a~~~gl~~a~P~i~yq~w~FiaP-GLy~ 104 (255)
T COG0805 77 LALFAGLLLALPVILYQLWAFIAP-GLYK 104 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCC-ccch
Confidence 455678899999999999998887 7763
No 14
>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=39.78 E-value=8.8 Score=27.35 Aligned_cols=38 Identities=18% Similarity=0.294 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHhhccCc-cchhhhhhhhHHHHHHHHHH
Q 031779 76 GVPLVCYHVNLYMKRKHL-IDVTEVFRNLKVEKKFRLAK 113 (153)
Q Consensus 76 nlPll~y~~~~y~~r~~l-~D~TeIf~~L~~~kk~~~iK 113 (153)
+-|+.+..++...++++. ++.++|+|.|+.-.+.+.++
T Consensus 14 ~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 14 DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence 346778888888877654 89999999998887776543
No 15
>KOG3801 consensus Uncharacterized conserved protein BCN92 [RNA processing and modification]
Probab=39.58 E-value=29 Score=25.62 Aligned_cols=29 Identities=28% Similarity=0.411 Sum_probs=21.4
Q ss_pred HHHHHHHHhhcc---------CccchhhhhhhhHHHHH
Q 031779 80 VCYHVNLYMKRK---------HLIDVTEVFRNLKVEKK 108 (153)
Q Consensus 80 l~y~~~~y~~r~---------~l~D~TeIf~~L~~~kk 108 (153)
.-||++.|..|+ ..=||+|+-+..+..||
T Consensus 24 p~YNyReY~~RrtRD~Fr~Nkn~~Dp~e~~~l~~eakk 61 (94)
T KOG3801|consen 24 PQYNYREYFQRRTRDTFRANKNVCDPAEIKKLYKEAKK 61 (94)
T ss_pred CcccHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHH
Confidence 359999998763 78899999885444444
No 16
>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=37.20 E-value=2.2e+02 Score=22.87 Aligned_cols=40 Identities=13% Similarity=0.381 Sum_probs=29.1
Q ss_pred hcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHHHHHhhc
Q 031779 45 RINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCYHVNLYMKR 90 (153)
Q Consensus 45 rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y~~~~y~~r 90 (153)
+++..-..|... ..+-..-+.....+.|...|..|++.++
T Consensus 51 ~li~~~~~e~f~------~~lk~s~~~~~~~~~P~~~yq~w~Fi~P 90 (215)
T PF00902_consen 51 KLIFTSPTEAFF------TYLKLSFFLGLIISLPYILYQIWAFIAP 90 (215)
T ss_pred eEEECChHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 555555566542 2334566788999999999999998876
No 17
>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=36.04 E-value=36 Score=23.13 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 031779 107 KKFRLAKLGFYVIFFALVIANIIAVGKFWVSH 138 (153)
Q Consensus 107 kk~~~iKLafyll~Ff~~ly~mI~~lv~~~~~ 138 (153)
++-++.|++ .+++|++..-|++|+.+..-+|
T Consensus 5 ~~~~mtriV-LLISfiIlfgRl~Y~~I~a~~h 35 (59)
T PF11119_consen 5 KNSRMTRIV-LLISFIILFGRLIYSAIGAWVH 35 (59)
T ss_pred ccchHHHHH-HHHHHHHHHHHHHHHHHhHHHH
Confidence 444566655 4678888888999888876665
No 18
>COG2981 CysZ Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism]
Probab=36.00 E-value=2.8e+02 Score=23.83 Aligned_cols=111 Identities=16% Similarity=0.114 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccccccC--ChHHhhhhcCCchhHHHHHHHHHHHHHHhh--hHHHHHHhhHHHHHHHH
Q 031779 9 FLMSAINIALIASTFYQLLCLLDLESDDI--NPFEASSRINFWVEPEFLLQGLFCILLLVT--GHWIMFLLGVPLVCYHV 84 (153)
Q Consensus 9 i~a~ll~~~ll~l~vy~lI~l~DLe~D~i--NPiD~c~rlN~lVlPE~~~h~~l~~l~ll~--g~W~~~llnlPll~y~~ 84 (153)
++-++++.++.+...+..+...|=--|.. ---|=.+=+|.++.|=.++-..+.+-++++ +.|+..-+|- .++--+
T Consensus 29 ilpLl~ni~L~~gl~~~~~~~~~~wid~Lm~~iPdWl~wLs~v~~~la~L~lll~~~~lfs~v~~~IAapFng-~lAEkv 107 (250)
T COG2981 29 ILPLLLNILLWGGLFWLLFSQALPWIDTLMPGIPDWLGWLSYLLWILAVLLLLLVFAFLFSTVANLIAAPFNG-LLAEKV 107 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh-HHHHHH
Confidence 45677888888888888877644222221 123556666666666666555555555444 3444433333 222222
Q ss_pred HHHhhccCccchhhh--hhhhHHHHHHHHHHHHHHHHH
Q 031779 85 NLYMKRKHLIDVTEV--FRNLKVEKKFRLAKLGFYVIF 120 (153)
Q Consensus 85 ~~y~~r~~l~D~TeI--f~~L~~~kk~~~iKLafyll~ 120 (153)
-+-..++..-|+-+. .+.+++...+.+.|+++++.-
T Consensus 108 E~~l~g~~~~d~~~~~l~~dipR~l~re~kkL~~~lp~ 145 (250)
T COG2981 108 EKRLTGETPPDPGGVGLMKDIPRALAREWKKLGYVLPG 145 (250)
T ss_pred HHHHcCCCCCCcchhhhhhhhHHHHHHHHHHHHHHHHh
Confidence 222233446666554 889999999999999998743
No 19
>COG0382 UbiA 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]
Probab=33.41 E-value=2.9e+02 Score=23.08 Aligned_cols=78 Identities=26% Similarity=0.252 Sum_probs=45.0
Q ss_pred HHHHHHHHHHhhhccccccCChHHhhhhcC--CchhHHHHHHHHHHHHHHhhhHH-------HHHHhh-HHHHHHHHHHH
Q 031779 18 LIASTFYQLLCLLDLESDDINPFEASSRIN--FWVEPEFLLQGLFCILLLVTGHW-------IMFLLG-VPLVCYHVNLY 87 (153)
Q Consensus 18 ll~l~vy~lI~l~DLe~D~iNPiD~c~rlN--~lVlPE~~~h~~l~~l~ll~g~W-------~~~lln-lPll~y~~~~y 87 (153)
..-...|-+==+-|.|-|-+||....+.++ +.-.+|...-+..+....+...| ...+.. +-...| .+
T Consensus 58 ~~~~ag~~iND~~D~eiD~~n~rt~~RPl~sG~vS~~~a~~~~~~~~~~~~~~a~~l~~~~~~l~~~~~~l~~~Y---~~ 134 (289)
T COG0382 58 LARSAGYVINDLADREIDRINPRTKNRPLPSGRVSVKEALLLAILLLLLGLALALLLNPLAFLLSLAALVLALAY---PF 134 (289)
T ss_pred HHHHHhHHHHHHhhhhccCCCCCccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH---HH
Confidence 333445555567899999999997777777 45666666655544443322221 122222 222233 88
Q ss_pred hhccCccchhh
Q 031779 88 MKRKHLIDVTE 98 (153)
Q Consensus 88 ~~r~~l~D~Te 98 (153)
.||...+|..-
T Consensus 135 ~Kr~~~~~~~~ 145 (289)
T COG0382 135 LKRFTFLPQLV 145 (289)
T ss_pred hhcCCchHHHH
Confidence 88876666544
No 20
>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=30.24 E-value=1.3e+02 Score=19.64 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHH
Q 031779 4 IFLFWFLMSAINIAL---IASTFYQLL 27 (153)
Q Consensus 4 ~~~~~i~a~ll~~~l---l~l~vy~lI 27 (153)
..+.|+++.++..+. +++++||=|
T Consensus 3 ~wlt~iFsvvIil~If~~iGl~IyQki 29 (49)
T PF11044_consen 3 TWLTTIFSVVIILGIFAWIGLSIYQKI 29 (49)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788888777666 788888854
No 21
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=29.20 E-value=3.8e+02 Score=27.22 Aligned_cols=100 Identities=16% Similarity=0.180 Sum_probs=76.0
Q ss_pred chhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHHHHHhhccC--------ccchhh--hhhhhHHHHHHHHHHHHHHH
Q 031779 49 WVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCYHVNLYMKRKH--------LIDVTE--VFRNLKVEKKFRLAKLGFYV 118 (153)
Q Consensus 49 lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y~~~~y~~r~~--------l~D~Te--If~~L~~~kk~~~iKLafyl 118 (153)
=..=|+.-|...++...+.-.|+..+.-.|+++-.+-+-.++++ ..|..+ ..+.+++.-+.++.-++.++
T Consensus 450 G~~G~~f~~f~~tia~a~~~S~~vAltltP~L~a~lLk~~~~~~~~~~~~~~~~~~~~~~Y~~~l~~~L~~~~~~~~~~l 529 (1009)
T COG0841 450 GSTGELFRQFAITIAVAMLLSLLVALTLTPALCARLLKPVPPPKGFFGWFNRFFDRLEDRYQRGLRWVLRRRALVLLLYL 529 (1009)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccchhhhhhhhhhHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 34558888888999999999999999999999976665444321 234443 33368888888899999999
Q ss_pred HHHHHHHHHHHHHhhhhhccCCCCCcccee
Q 031779 119 IFFALVIANIIAVGKFWVSHSDFGDLDIRF 148 (153)
Q Consensus 119 l~Ff~~ly~mI~~lv~~~~~~~~~~~~~~~ 148 (153)
.++....+-+...-..|...+|-|.+-+..
T Consensus 530 ~~~~~~~~l~~~vp~~F~P~eD~g~~~v~~ 559 (1009)
T COG0841 530 VLLGGSVLLFLKLPKSFLPEEDQGEFMVQV 559 (1009)
T ss_pred HHHHHHHHHHHhCCCccCCcCCCCEEEEEE
Confidence 998888888887778888888888765554
No 22
>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=27.50 E-value=1.1e+02 Score=22.36 Aligned_cols=16 Identities=31% Similarity=0.549 Sum_probs=13.9
Q ss_pred ccchhhhhhhhHHHHH
Q 031779 93 LIDVTEVFRNLKVEKK 108 (153)
Q Consensus 93 l~D~TeIf~~L~~~kk 108 (153)
+.||.|.|++++++++
T Consensus 2 l~~P~~~f~~~~~~~~ 17 (172)
T PF04893_consen 2 LFSPREFFRRLRESPR 17 (172)
T ss_pred ccCHHHHHHHHHhccc
Confidence 4699999999988887
No 23
>PRK09462 fur ferric uptake regulator; Provisional
Probab=27.47 E-value=19 Score=27.26 Aligned_cols=36 Identities=11% Similarity=0.045 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhhccCc-cchhhhhhhhHHHHHHHHH
Q 031779 77 VPLVCYHVNLYMKRKHL-IDVTEVFRNLKVEKKFRLA 112 (153)
Q Consensus 77 lPll~y~~~~y~~r~~l-~D~TeIf~~L~~~kk~~~i 112 (153)
-|+.++.+++..++++. +++++|||+|+.-...+.+
T Consensus 32 ~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli 68 (148)
T PRK09462 32 HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIV 68 (148)
T ss_pred CCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCE
Confidence 37778888888876654 7889999988877776654
No 24
>PRK13553 fumarate reductase cytochrome b-556 subunit; Provisional
Probab=24.13 E-value=4.7e+02 Score=22.54 Aligned_cols=105 Identities=18% Similarity=0.282 Sum_probs=60.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh-hhccccccCChHHhhhhcCCchhHHHHHHHHHHHHHHhhhHHHHHHhhHHHHHH
Q 031779 4 IFLFWFLMSAINIALIASTFYQLLC-LLDLESDDINPFEASSRINFWVEPEFLLQGLFCILLLVTGHWIMFLLGVPLVCY 82 (153)
Q Consensus 4 ~~~~~i~a~ll~~~ll~l~vy~lI~-l~DLe~D~iNPiD~c~rlN~lVlPE~~~h~~l~~l~ll~g~W~~~llnlPll~y 82 (153)
|.+.|.+=.+--.+++++...|+.. ..|.++ ++|.....|+-. .+.|..=++.+|...+
T Consensus 120 DT~lW~~Q~iTG~ilf~~~~~Hl~~i~~~~~~--Ig~~~Sa~rv~~------------------~~~w~fYlvlL~~v~l 179 (258)
T PRK13553 120 DTSLWFIQAFTGFAMFFLASVHLYVMLTNPDK--IGPYGSSDRVVS------------------QNMWLLYIVLLFAVEL 179 (258)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhhcCccc--cCchhhHHHHhC------------------CcHHHHHHHHHHHHHH
Confidence 5667887777777777777777653 344443 666666665432 2356777778888888
Q ss_pred HHHHHhh----ccCccchhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031779 83 HVNLYMK----RKHLIDVTEVFRNLKVEKKFRLAKLGFYVIFFALVIANI 128 (153)
Q Consensus 83 ~~~~y~~----r~~l~D~TeIf~~L~~~kk~~~iKLafyll~Ff~~ly~m 128 (153)
|..-=.- +=|..+-.+..+.=++-+|-.++-.++++++-...+++.
T Consensus 180 H~~iGLyR~~VKWG~~~~~~~q~~R~~~~~v~~~i~v~f~~lGl~sL~af 229 (258)
T PRK13553 180 HGSIGLYRLAVKWGWFEGKNPKESRKKLKKVKWALSVFFLVLGLLTLAAY 229 (258)
T ss_pred HHHHhhhheeeEEEeecCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8643222 235555444333333444444555555555555555553
No 25
>COG3647 Predicted membrane protein [Function unknown]
Probab=24.12 E-value=3.1e+02 Score=22.66 Aligned_cols=31 Identities=16% Similarity=0.121 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 031779 108 KFRLAKLGFYVIFFALVIANIIAVGKFWVSH 138 (153)
Q Consensus 108 k~~~iKLafyll~Ff~~ly~mI~~lv~~~~~ 138 (153)
+.+.-|++.+..+|+.--..-.|-+++|---
T Consensus 126 ~~~gp~la~ffalf~~msiaA~YElIEWwyA 156 (205)
T COG3647 126 YVRGPKLAAFFALFVAMSIAAMYELIEWWYA 156 (205)
T ss_pred HhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455678888888877666666777776443
No 26
>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=22.36 E-value=2.5e+02 Score=18.80 Aligned_cols=36 Identities=28% Similarity=0.372 Sum_probs=20.4
Q ss_pred cchhhhhh-------hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031779 94 IDVTEVFR-------NLKVEKKFRLAKLGFYVIFFALVIANII 129 (153)
Q Consensus 94 ~D~TeIf~-------~L~~~kk~~~iKLafyll~Ff~~ly~mI 129 (153)
++|.|.|= ..++.+|.+..+..++++++.+-+.++.
T Consensus 13 Ip~~~~fCS~~C~~~~~k~qk~~~~~~~i~~~~~i~~l~v~~~ 55 (59)
T PF09889_consen 13 IPPDESFCSPKCREEYRKRQKRMRKTQYIFFGIFILFLAVWIF 55 (59)
T ss_pred CCcchhhhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55556554 2344455555677777776665544444
No 27
>KOG3249 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.38 E-value=4.1e+02 Score=21.76 Aligned_cols=72 Identities=19% Similarity=0.251 Sum_probs=41.9
Q ss_pred hhhcCCchhHHHHHHHHHHHHHHh----------hhHHHHHHhhHHHHHHHHHHHhh----ccCccchhhhhh-------
Q 031779 43 SSRINFWVEPEFLLQGLFCILLLV----------TGHWIMFLLGVPLVCYHVNLYMK----RKHLIDVTEVFR------- 101 (153)
Q Consensus 43 c~rlN~lVlPE~~~h~~l~~l~ll----------~g~W~~~llnlPll~y~~~~y~~----r~~l~D~TeIf~------- 101 (153)
.++.|+..+|.+..+.+++....+ -.+|+-+.+-.-++--..+-|.+ ++|=.-+-.|||
T Consensus 85 t~k~n~~~lp~~w~~~~ls~~~~v~vllW~vL~~ia~~l~fGlvff~lSlf~~iy~n~~~rk~gEmSAYSVFN~nce~l~ 164 (181)
T KOG3249|consen 85 TRKLNKLKLPDIWLMFSLSLKMWVIVLLWFVLAPIAHRLDFGLVFFLLSLFSIIYLNTGKRKRGEMSAYSVFNENCEELP 164 (181)
T ss_pred ccccccCCCchHHHHhhhhhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHheecCCCCCCCccchhhhhccchhhcC
Confidence 578999999999988766543211 12333222222222222333443 457788888888
Q ss_pred -hhHHHHHHHHHHH
Q 031779 102 -NLKVEKKFRLAKL 114 (153)
Q Consensus 102 -~L~~~kk~~~iKL 114 (153)
+++.++-||=++.
T Consensus 165 GTltAEqfERdir~ 178 (181)
T KOG3249|consen 165 GTLTAEQFERDIRA 178 (181)
T ss_pred CcccHHHHHHHHHc
Confidence 5777777765553
No 28
>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=20.30 E-value=4.2e+02 Score=26.27 Aligned_cols=74 Identities=14% Similarity=0.159 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHhhHHHHHHHHHHHhhccCc------cc-----hhhhhh-hhHHHHHHHHHHHHHHHHH
Q 031779 53 EFLLQGLFCILLLVTGHWIMFLLGVPLVCYHVNLYMKRKHL------ID-----VTEVFR-NLKVEKKFRLAKLGFYVIF 120 (153)
Q Consensus 53 E~~~h~~l~~l~ll~g~W~~~llnlPll~y~~~~y~~r~~l------~D-----~TeIf~-~L~~~kk~~~iKLafyll~ 120 (153)
++.-....++.+.+...|+..+.-+|.+++++.+-.+++.. .| .++.|+ .|++..|.++.-++..+++
T Consensus 458 ~~~~~l~~~v~~al~~Sllval~~~P~l~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~Y~~lL~~~L~~~~~~l~i~l~l 537 (1021)
T PF00873_consen 458 QFFRPLALTVIIALIASLLVALTLVPALAALFLKPKKKSSKKRFFSKFDRFFDRLQRGYRRLLRWALRHPKLVLLIALLL 537 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHCS----TT-CCCHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccccccccccccccccccccchhhhhhhhhhcccchhhhhhhh
Confidence 44445556677788899999999999999887554443221 01 111222 4556666666666666666
Q ss_pred HHHHHH
Q 031779 121 FALVIA 126 (153)
Q Consensus 121 Ff~~ly 126 (153)
++..++
T Consensus 538 ~i~s~~ 543 (1021)
T PF00873_consen 538 LILSLF 543 (1021)
T ss_dssp HHHHHH
T ss_pred hhhhhc
Confidence 655444
No 29
>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=20.15 E-value=42 Score=24.16 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhhcc-CccchhhhhhhhHHHHHHHH
Q 031779 78 PLVCYHVNLYMKRK-HLIDVTEVFRNLKVEKKFRL 111 (153)
Q Consensus 78 Pll~y~~~~y~~r~-~l~D~TeIf~~L~~~kk~~~ 111 (153)
|+.+..+++-.+.+ .-++.++|+|.|+.-.+.+.
T Consensus 23 ~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gl 57 (120)
T PF01475_consen 23 HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGL 57 (120)
T ss_dssp SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTS
T ss_pred CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCe
Confidence 55566666666654 35788888888887766553
Done!