Query psy3564
Match_columns 102
No_of_seqs 109 out of 207
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 19:52:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2729|consensus 100.0 1.1E-37 2.4E-42 224.3 8.7 82 1-88 56-137 (137)
2 PLN00174 predicted protein; Pr 100.0 2.2E-34 4.7E-39 211.5 8.7 78 1-84 61-139 (160)
3 PF03311 Cornichon: Cornichon 100.0 1.3E-29 2.8E-34 180.0 7.4 74 1-80 55-128 (128)
4 PF00902 TatC: Sec-independent 68.2 37 0.00079 25.4 7.3 25 12-36 65-89 (215)
5 TIGR00945 tatC Twin arginine t 65.6 44 0.00095 25.2 7.3 22 15-36 64-85 (215)
6 CHL00182 tatC Sec-independent 64.0 46 0.001 25.9 7.3 23 14-36 84-106 (249)
7 PRK10921 twin-arginine protein 62.3 49 0.0011 25.8 7.2 22 15-36 75-96 (258)
8 TIGR01912 TatC-Arch Twin argin 62.1 53 0.0012 25.3 7.3 23 14-36 71-93 (237)
9 PF02532 PsbI: Photosystem II 51.8 45 0.00098 19.2 4.3 31 65-97 4-35 (36)
10 PF10840 DUF2645: Protein of u 43.2 44 0.00095 23.3 3.7 27 57-83 72-98 (103)
11 TIGR00870 trp transient-recept 37.3 1.1E+02 0.0025 26.5 6.2 33 55-87 340-372 (743)
12 CHL00024 psbI photosystem II p 37.2 38 0.00082 19.5 2.2 27 69-97 9-35 (36)
13 KOG3801|consensus 31.6 17 0.00036 25.1 0.1 33 28-62 25-62 (94)
14 COG0805 TatC Sec-independent p 30.8 1.4E+02 0.0031 23.6 5.3 22 15-36 78-99 (255)
15 PF02101 Ocular_alb: Ocular al 29.6 1.8E+02 0.0039 24.9 5.9 55 18-81 203-258 (405)
16 PRK02655 psbI photosystem II r 29.4 62 0.0013 18.8 2.2 27 70-98 10-36 (38)
17 KOG1607|consensus 28.5 67 0.0015 26.4 3.1 26 58-83 87-112 (318)
18 PF00873 ACR_tran: AcrB/AcrD/A 28.2 1.2E+02 0.0025 27.8 4.9 74 4-78 462-542 (1021)
19 PRK12592 putative monovalent c 27.1 80 0.0017 22.5 3.0 43 16-63 81-124 (126)
20 KOG2059|consensus 26.6 82 0.0018 29.0 3.6 40 23-68 334-373 (800)
21 PF11119 DUF2633: Protein of u 25.8 68 0.0015 20.3 2.2 27 60-87 5-31 (59)
22 PF07528 DZF: DZF domain; Int 25.3 78 0.0017 24.8 2.9 31 40-72 193-228 (248)
23 PRK02201 putative inner membra 24.3 86 0.0019 26.0 3.1 31 62-92 32-62 (357)
24 COG4781 Membrane domain of mem 21.3 1.8E+02 0.0039 24.3 4.4 45 14-67 166-210 (340)
25 COG1380 Putative effector of m 21.1 80 0.0017 22.6 2.0 25 2-26 8-32 (128)
26 PF08490 DUF1744: Domain of un 20.8 93 0.002 26.0 2.7 52 11-67 269-323 (396)
27 TIGR00054 RIP metalloprotease 20.6 1.7E+02 0.0037 24.2 4.2 66 15-88 349-416 (420)
28 COG0841 AcrB Cation/multidrug 20.4 4.4E+02 0.0096 24.8 7.1 77 4-80 458-538 (1009)
No 1
>KOG2729|consensus
Probab=100.00 E-value=1.1e-37 Score=224.33 Aligned_cols=82 Identities=39% Similarity=0.803 Sum_probs=79.5
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCcccccccccccHHhHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy3564 1 MGAQVGVTVLLLLTGHYYLFLMNVPMSAWNVYEYYSVPSGNMGVFDPTELYNRDSIKNHMRNCLIGMGFYLVIFFVYLYS 80 (102)
Q Consensus 1 ~i~h~~l~~lfLl~g~W~~~llnlPll~y~~~~y~~r~~~~~~l~D~TeIfn~~~L~~~kke~~iKLafYll~FF~yLy~ 80 (102)
+++||++|++||++|||+++++|+|+++||+++|++|| |++||||||| +|++||||||+|||||+++||+|+||
T Consensus 56 ~ilh~~KOGlfLl~g~W~~fllnlP~l~y~~~~y~~r~----~l~D~TeI~n--~L~~~~k~~~~KL~fyll~FF~yly~ 129 (137)
T KOG2729|consen 56 FILHGLLCLLFLLTGHWFMFLLNLPLLAYNAWLYMKRP----HLYDPTEIFN--TLSSEKKERWIKLAFYLLSFFYYLYW 129 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcCC----cccCHHHHHH--HhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999997 6999999999 99999999999999999999999999
Q ss_pred HHHHHhcC
Q psy3564 81 MILSLLRD 88 (102)
Q Consensus 81 mI~~lv~~ 88 (102)
||+++|++
T Consensus 130 mI~slv~~ 137 (137)
T KOG2729|consen 130 MIYSLVSS 137 (137)
T ss_pred HHHHHhcC
Confidence 99999975
No 2
>PLN00174 predicted protein; Provisional
Probab=100.00 E-value=2.2e-34 Score=211.52 Aligned_cols=78 Identities=17% Similarity=0.398 Sum_probs=75.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCcccccccccccHHhHhHHHHHHHHHHHHHHHHHHHHHH-
Q psy3564 1 MGAQVGVTVLLLLTGHYYLFLMNVPMSAWNVYEYYSVPSGNMGVFDPTELYNRDSIKNHMRNCLIGMGFYLVIFFVYLY- 79 (102)
Q Consensus 1 ~i~h~~l~~lfLl~g~W~~~llnlPll~y~~~~y~~r~~~~~~l~D~TeIfn~~~L~~~kke~~iKLafYll~FF~yLy- 79 (102)
+++|+++|++||++|||+++++|+|+++||++||.+|| |++||||||| +|++||||||+|||||+++||+|+|
T Consensus 61 yiiH~~l~lLfLltG~W~~fLLNlPll~Yhv~~y~~r~----hL~D~TeIfn--~L~~~kKe~~iKLaFYLl~FF~~ly~ 134 (160)
T PLN00174 61 YLAHLFLSIAFVIRGWWIVGFLNFPFIFYNFAQWYEGK----HQLDSAQIFN--VLSRELRVIKAKSAFFIIIVIYTIWE 134 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC----CCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999875 8999999999 7999999999999999999999999
Q ss_pred HHHHH
Q psy3564 80 SMILS 84 (102)
Q Consensus 80 ~mI~~ 84 (102)
|||++
T Consensus 135 ~mI~~ 139 (160)
T PLN00174 135 WMIWV 139 (160)
T ss_pred HHHcC
Confidence 99987
No 3
>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=99.96 E-value=1.3e-29 Score=179.96 Aligned_cols=74 Identities=41% Similarity=0.917 Sum_probs=71.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCcccccccccccHHhHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy3564 1 MGAQVGVTVLLLLTGHYYLFLMNVPMSAWNVYEYYSVPSGNMGVFDPTELYNRDSIKNHMRNCLIGMGFYLVIFFVYLYS 80 (102)
Q Consensus 1 ~i~h~~l~~lfLl~g~W~~~llnlPll~y~~~~y~~r~~~~~~l~D~TeIfn~~~L~~~kke~~iKLafYll~FF~yLy~ 80 (102)
+++|+++|++++++|||+++++|+|+++||+++|.+| +|++||||||| +|++|||||++|+|||+++||+|+||
T Consensus 55 ~~~h~~l~~l~ll~g~w~~~llnlPl~~y~~~~~~~~----~~l~D~T~If~--~L~~~kk~~~iKl~~yll~ff~yly~ 128 (128)
T PF03311_consen 55 YIIHGFLCLLFLLTGHWFLFLLNLPLLAYHIYRYFRR----QHLYDPTEIFN--QLKREKKESFIKLGFYLLLFFYYLYR 128 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CccccHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4789999999999999999999999999999999998 48999999999 79999999999999999999999997
No 4
>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=68.20 E-value=37 Score=25.36 Aligned_cols=25 Identities=8% Similarity=0.447 Sum_probs=21.1
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHhh
Q psy3564 12 LLTGHYYLFLMNVPMSAWNVYEYYS 36 (102)
Q Consensus 12 Ll~g~W~~~llnlPll~y~~~~y~~ 36 (102)
+-..-|+...++.|.+.|++|++.+
T Consensus 65 lk~s~~~~~~~~~P~~~yq~w~Fi~ 89 (215)
T PF00902_consen 65 LKLSFFLGLIISLPYILYQIWAFIA 89 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3345678889999999999999996
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=65.60 E-value=44 Score=25.17 Aligned_cols=22 Identities=5% Similarity=0.294 Sum_probs=19.2
Q ss_pred HHHHHHHhhhhHHHHHHHHHhh
Q psy3564 15 GHYYLFLMNVPMSAWNVYEYYS 36 (102)
Q Consensus 15 g~W~~~llnlPll~y~~~~y~~ 36 (102)
.-++.+.+..|.+.|++|++.+
T Consensus 64 s~~~g~~~~~P~i~yqiw~Fi~ 85 (215)
T TIGR00945 64 SLIVGIILSSPVILYQIWAFIL 85 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 4567788999999999999996
No 6
>CHL00182 tatC Sec-independent translocase component C; Provisional
Probab=64.02 E-value=46 Score=25.92 Aligned_cols=23 Identities=13% Similarity=0.333 Sum_probs=19.6
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhh
Q psy3564 14 TGHYYLFLMNVPMSAWNVYEYYS 36 (102)
Q Consensus 14 ~g~W~~~llnlPll~y~~~~y~~ 36 (102)
..-+..+.+..|.+.|.+|++.+
T Consensus 84 ls~~~g~~~a~P~i~yqiw~Fi~ 106 (249)
T CHL00182 84 ISFYTGLLISSPFIIYQIILFIL 106 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34567788999999999999996
No 7
>PRK10921 twin-arginine protein translocation system subunit TatC; Provisional
Probab=62.33 E-value=49 Score=25.85 Aligned_cols=22 Identities=9% Similarity=0.425 Sum_probs=19.1
Q ss_pred HHHHHHHhhhhHHHHHHHHHhh
Q psy3564 15 GHYYLFLMNVPMSAWNVYEYYS 36 (102)
Q Consensus 15 g~W~~~llnlPll~y~~~~y~~ 36 (102)
.-+....+..|++.|.+|++..
T Consensus 75 sl~~g~~la~P~ilyqiw~Fi~ 96 (258)
T PRK10921 75 TFMVSLILSAPVILYQVWAFIA 96 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 4567788999999999999996
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=62.15 E-value=53 Score=25.30 Aligned_cols=23 Identities=17% Similarity=0.532 Sum_probs=19.7
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhh
Q psy3564 14 TGHYYLFLMNVPMSAWNVYEYYS 36 (102)
Q Consensus 14 ~g~W~~~llnlPll~y~~~~y~~ 36 (102)
..-+..+.+..|.+.|++|++.+
T Consensus 71 ~s~~~g~~~~~P~i~yqiw~Fi~ 93 (237)
T TIGR01912 71 SAFFIGLLLASPVLAYEAYRFIK 93 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34567888999999999999996
No 9
>PF02532 PsbI: Photosystem II reaction centre I protein (PSII 4.8 kDa protein); InterPro: IPR003686 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 PsbI, which is tightly associated with the D1/D2 heterodimer in PSII. The function of PsbI is unknown, but it may be involved in the assembly, dimerisation or stabilisation of PSII dimers [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_i 3ARC_I 3A0B_i 3BZ2_I 3PRQ_I 3KZI_I 3PRR_I 2AXT_i 4FBY_I 1S5L_i ....
Probab=51.83 E-value=45 Score=19.20 Aligned_cols=31 Identities=35% Similarity=0.727 Sum_probs=20.5
Q ss_pred HHHHHH-HHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3564 65 IGMGFY-LVIFFVYLYSMILSLLRDNPLDKPSQH 97 (102)
Q Consensus 65 iKLafY-ll~FF~yLy~mI~~lv~~~~~~~~~~~ 97 (102)
.|+.-| .++||+.| +|.-.+++||.+.++..
T Consensus 4 LK~~Vy~vV~ffv~L--FifGflsnDp~RnP~rk 35 (36)
T PF02532_consen 4 LKIFVYTVVIFFVSL--FIFGFLSNDPGRNPGRK 35 (36)
T ss_dssp HHHHHHHHHHHHHHH--HHHHHHTTCTTSSSSS-
T ss_pred EEEeehhhHHHHHHH--HhccccCCCCCCCCCCC
Confidence 355444 56777777 56777888888776644
No 10
>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=43.15 E-value=44 Score=23.28 Aligned_cols=27 Identities=19% Similarity=0.418 Sum_probs=21.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3564 57 KNHMRNCLIGMGFYLVIFFVYLYSMIL 83 (102)
Q Consensus 57 ~~~kke~~iKLafYll~FF~yLy~mI~ 83 (102)
.++|.+++.+.+.+++.++|.++++-.
T Consensus 72 ~~~k~ks~~~~~~~i~i~~Y~~W~Ff~ 98 (103)
T PF10840_consen 72 FKKKFKSLFRYIVYIAILFYWLWRFFI 98 (103)
T ss_pred HHHHhhcHHHHHHHHHHHHHHHHHHHH
Confidence 455667788888999999999888643
No 11
>TIGR00870 trp transient-receptor-potential calcium channel protein. after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
Probab=37.30 E-value=1.1e+02 Score=26.54 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=29.1
Q ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3564 55 SIKNHMRNCLIGMGFYLVIFFVYLYSMILSLLR 87 (102)
Q Consensus 55 ~L~~~kke~~iKLafYll~FF~yLy~mI~~lv~ 87 (102)
+|.+.|+..++|-.++..++++.+|-++.++..
T Consensus 340 ~l~~~kw~pf~kf~~~~~~~~~fl~l~~~~~~~ 372 (743)
T TIGR00870 340 RLGQFKWKPFIKFIFHSASYLYFLYLIIFTSVA 372 (743)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999999999888887654
No 12
>CHL00024 psbI photosystem II protein I
Probab=37.18 E-value=38 Score=19.53 Aligned_cols=27 Identities=37% Similarity=0.789 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3564 69 FYLVIFFVYLYSMILSLLRDNPLDKPSQH 97 (102)
Q Consensus 69 fYll~FF~yLy~mI~~lv~~~~~~~~~~~ 97 (102)
+-.++||+.| +|.-.+++||.+.++..
T Consensus 9 y~vV~ffvsL--FifGFlsnDp~RnP~rk 35 (36)
T CHL00024 9 YTVVIFFVSL--FIFGFLSNDPGRNPGRK 35 (36)
T ss_pred hhHHHHHHHH--HHccccCCCCCCCCCCC
Confidence 4466777777 46677888888776654
No 13
>KOG3801|consensus
Probab=31.60 E-value=17 Score=25.08 Aligned_cols=33 Identities=27% Similarity=0.471 Sum_probs=24.5
Q ss_pred HHHHHHHhhcCC-----CCcccccccccccHHhHhHHHHH
Q psy3564 28 AWNVYEYYSVPS-----GNMGVFDPTELYNRDSIKNHMRN 62 (102)
Q Consensus 28 ~y~~~~y~~r~~-----~~~~l~D~TeIfn~~~L~~~kke 62 (102)
.||++.|..|.- .|...-||+||-+ ..+..||.
T Consensus 25 ~YNyReY~~RrtRD~Fr~Nkn~~Dp~e~~~--l~~eakk~ 62 (94)
T KOG3801|consen 25 QYNYREYFQRRTRDTFRANKNVCDPAEIKK--LYKEAKKQ 62 (94)
T ss_pred cccHHHHHHHHHHHHHHHhcccCCHHHHHH--HHHHHHHH
Confidence 599999998762 4788999999996 44444443
No 14
>COG0805 TatC Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]
Probab=30.78 E-value=1.4e+02 Score=23.57 Aligned_cols=22 Identities=9% Similarity=0.452 Sum_probs=18.9
Q ss_pred HHHHHHHhhhhHHHHHHHHHhh
Q psy3564 15 GHYYLFLMNVPMSAWNVYEYYS 36 (102)
Q Consensus 15 g~W~~~llnlPll~y~~~~y~~ 36 (102)
.-+...++..|.++|.+|++.+
T Consensus 78 a~~~gl~~a~P~i~yq~w~Fia 99 (255)
T COG0805 78 ALFAGLLLALPVILYQLWAFIA 99 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC
Confidence 3456778999999999999996
No 15
>PF02101 Ocular_alb: Ocular albinism type 1 protein; InterPro: IPR001414 Ocular albinism type 1 (OA1) is an X-linked disorder characterised by severe impairment of visual acuity, retinal hypopigmentation and the presence of macromelanosomes. A novel transcript from the OA1 critical region is expressed in high levels in RNA samples from retina and from melanoma and encodes a potential integral membrane protein []. This protein is of unknown function but is known to bind heterotrimeric G proteins.; GO: 0016020 membrane
Probab=29.62 E-value=1.8e+02 Score=24.88 Aligned_cols=55 Identities=16% Similarity=0.335 Sum_probs=38.2
Q ss_pred HHHHhhhhHHHHHHHHHhhcCC-CCcccccccccccHHhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3564 18 YLFLMNVPMSAWNVYEYYSVPS-GNMGVFDPTELYNRDSIKNHMRNCLIGMGFYLVIFFVYLYSM 81 (102)
Q Consensus 18 ~~~llnlPll~y~~~~y~~r~~-~~~~l~D~TeIfn~~~L~~~kke~~iKLafYll~FF~yLy~m 81 (102)
++.++..|.++...-+-..+.- +.+| |+ +=+..++...+|+=|+.+++.+|+-|+
T Consensus 203 llVlvaNPiLy~~a~~~V~~~lk~r~g------~y---T~~ER~l~~~IK~kFf~I~lVF~iCWl 258 (405)
T PF02101_consen 203 LLVLVANPILYIKAVRAVASLLKGRQG------IY---TENERRLGAQIKIKFFKIMLVFYICWL 258 (405)
T ss_pred HHHHHhccHHHHHHHHHHHHHHhhccc------cc---cHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4667888999998877776642 3344 44 233445557788888888888887774
No 16
>PRK02655 psbI photosystem II reaction center I protein I; Provisional
Probab=29.40 E-value=62 Score=18.84 Aligned_cols=27 Identities=30% Similarity=0.685 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3564 70 YLVIFFVYLYSMILSLLRDNPLDKPSQHG 98 (102)
Q Consensus 70 Yll~FF~yLy~mI~~lv~~~~~~~~~~~~ 98 (102)
=.+.||+.| +|.-.+++||.+.+...|
T Consensus 10 ~vV~ffvsL--FiFGflsnDP~RnP~rkd 36 (38)
T PRK02655 10 IVVFFFVGL--FVFGFLSSDPTRNPGRKD 36 (38)
T ss_pred hhHHHHHHH--HHcccCCCCCCCCCCccc
Confidence 356677777 466778888887766544
No 17
>KOG1607|consensus
Probab=28.47 E-value=67 Score=26.43 Aligned_cols=26 Identities=23% Similarity=0.342 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3564 58 NHMRNCLIGMGFYLVIFFVYLYSMIL 83 (102)
Q Consensus 58 ~~kke~~iKLafYll~FF~yLy~mI~ 83 (102)
+..+|+.-|..||+.++++.+|.|-.
T Consensus 87 ~k~~Es~Wk~~yy~~s~~~glyV~~~ 112 (318)
T KOG1607|consen 87 KKFCESAWKFLYYLVSWIFGLYVMYH 112 (318)
T ss_pred hhhHHHHHHHHHHHHHHHHhhhheec
Confidence 66789999999999999999998754
No 18
>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=28.21 E-value=1.2e+02 Score=27.78 Aligned_cols=74 Identities=19% Similarity=0.194 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCC------ccccc-ccccccHHhHhHHHHHHHHHHHHHHHHHHH
Q psy3564 4 QVGVTVLLLLTGHYYLFLMNVPMSAWNVYEYYSVPSGN------MGVFD-PTELYNRDSIKNHMRNCLIGMGFYLVIFFV 76 (102)
Q Consensus 4 h~~l~~lfLl~g~W~~~llnlPll~y~~~~y~~r~~~~------~~l~D-~TeIfn~~~L~~~kke~~iKLafYll~FF~ 76 (102)
...+++.+.+...|+..+.-+|++++++.+--.++..+ ....+ .+..|. +.|++..|.++.-++..+++|+.
T Consensus 462 ~l~~~v~~al~~Sllval~~~P~l~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~Y~-~lL~~~L~~~~~~l~i~l~l~i~ 540 (1021)
T PF00873_consen 462 PLALTVIIALIASLLVALTLVPALAALFLKPKKKSSKKRFFSKFDRFFDRLQRGYR-RLLRWALRHPKLVLLIALLLLIL 540 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHTTHHHHHHHCS----TT-CCCHHHHHHHHHHHHHHHHH-HHHHHHHHSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccccccccccccccccccccchh-hhhhhhhhcccchhhhhhhhhhh
Confidence 34577888889999999999999988764433332110 00111 122332 46777777888777777777766
Q ss_pred HH
Q psy3564 77 YL 78 (102)
Q Consensus 77 yL 78 (102)
.+
T Consensus 541 s~ 542 (1021)
T PF00873_consen 541 SL 542 (1021)
T ss_dssp HH
T ss_pred hh
Confidence 44
No 19
>PRK12592 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=27.15 E-value=80 Score=22.55 Aligned_cols=43 Identities=12% Similarity=0.156 Sum_probs=31.2
Q ss_pred HHHHHHhhhhHHHHHHHHHhhcCCCCcccc-cccccccHHhHhHHHHHH
Q psy3564 16 HYYLFLMNVPMSAWNVYEYYSVPSGNMGVF-DPTELYNRDSIKNHMRNC 63 (102)
Q Consensus 16 ~W~~~llnlPll~y~~~~y~~r~~~~~~l~-D~TeIfn~~~L~~~kke~ 63 (102)
-|+..++..|..+.-+.|=-.|. |.. |+.++++ ++..+++|+.
T Consensus 81 i~~FlllT~Pvaah~iaRAAyr~----g~~~~~~~~~~-~~~~~~~~~~ 124 (126)
T PRK12592 81 LVLFALLTSPVTAQRVGRVSRRE----GLYGAKDTMSR-NQAPAERKPK 124 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc----CCCCCcccccc-ccccchhhhc
Confidence 35677889999999998876653 455 6666765 6787777763
No 20
>KOG2059|consensus
Probab=26.61 E-value=82 Score=28.98 Aligned_cols=40 Identities=15% Similarity=0.259 Sum_probs=32.3
Q ss_pred hhhHHHHHHHHHhhcCCCCcccccccccccHHhHhHHHHHHHHHHH
Q psy3564 23 NVPMSAWNVYEYYSVPSGNMGVFDPTELYNRDSIKNHMRNCLIGMG 68 (102)
Q Consensus 23 nlPll~y~~~~y~~r~~~~~~l~D~TeIfn~~~L~~~kke~~iKLa 68 (102)
-.|++-+.+..=.+| .-||++|||...|...+-+.+.|++
T Consensus 334 ~~pfl~~L~~~ei~r------tqD~NTlFRgNSLasK~mde~mkl~ 373 (800)
T KOG2059|consen 334 IVPFLSALAVNEIKR------TQDPNTIFRGNSLASKMMDEFMKLA 373 (800)
T ss_pred hHHHHHHHHHHHHHh------cCCCceeeeccchHHHHHHHHHHHh
Confidence 456666666555554 7899999999999999999999986
No 21
>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=25.76 E-value=68 Score=20.31 Aligned_cols=27 Identities=15% Similarity=0.271 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3564 60 MRNCLIGMGFYLVIFFVYLYSMILSLLR 87 (102)
Q Consensus 60 kke~~iKLafYll~FF~yLy~mI~~lv~ 87 (102)
+.-++.|+. .+++|.+..-|++++.++
T Consensus 5 ~~~~mtriV-LLISfiIlfgRl~Y~~I~ 31 (59)
T PF11119_consen 5 KNSRMTRIV-LLISFIILFGRLIYSAIG 31 (59)
T ss_pred ccchHHHHH-HHHHHHHHHHHHHHHHHh
Confidence 334555554 466777777778887765
No 22
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=25.35 E-value=78 Score=24.78 Aligned_cols=31 Identities=19% Similarity=0.340 Sum_probs=24.6
Q ss_pred CCcccccccc-----cccHHhHhHHHHHHHHHHHHHHH
Q psy3564 40 GNMGVFDPTE-----LYNRDSIKNHMRNCLIGMGFYLV 72 (102)
Q Consensus 40 ~~~~l~D~Te-----Ifn~~~L~~~kke~~iKLafYll 72 (102)
++.|+.||.| +.. .+..++||-..--|=.++
T Consensus 193 ~~~gl~DPcE~~~~~~~~--~lt~qq~e~it~sAQ~~L 228 (248)
T PF07528_consen 193 GSPGLRDPCEKDPVDVLD--TLTLQQREDITSSAQTAL 228 (248)
T ss_pred CCCCCcCCCCCCCceeec--cCCHHHHHHHHHHHHHHH
Confidence 5789999998 665 788999998877776554
No 23
>PRK02201 putative inner membrane protein translocase component YidC; Provisional
Probab=24.30 E-value=86 Score=26.00 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy3564 62 NCLIGMGFYLVIFFVYLYSMILSLLRDNPLD 92 (102)
Q Consensus 62 e~~iKLafYll~FF~yLy~mI~~lv~~~~~~ 92 (102)
--|+|+.+|+++|.+-|+.-+.+.+...+..
T Consensus 32 ~k~~ki~~~~~~~~~~l~gc~q~~~~~~~~~ 62 (357)
T PRK02201 32 WKWLKIFFYIFLFGIGLTGCVQSFVVKSSTN 62 (357)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhheeeecccc
Confidence 3689999999999999999999976544433
No 24
>COG4781 Membrane domain of membrane-anchored glycerophosphoryl diester phosphodiesterase [Energy production and conversion]
Probab=21.34 E-value=1.8e+02 Score=24.29 Aligned_cols=45 Identities=13% Similarity=0.237 Sum_probs=28.4
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhhcCCCCcccccccccccHHhHhHHHHHHHHHH
Q psy3564 14 TGHYYLFLMNVPMSAWNVYEYYSVPSGNMGVFDPTELYNRDSIKNHMRNCLIGM 67 (102)
Q Consensus 14 ~g~W~~~llnlPll~y~~~~y~~r~~~~~~l~D~TeIfn~~~L~~~kke~~iKL 67 (102)
+|.|+..+.-+-.-+-+++..+.-| --|.|+.++++..||||-|.
T Consensus 166 ~~~~l~~~~l~liFyis~RLif~LP---------l~i~~~~tv~~Air~Swk~T 210 (340)
T COG4781 166 WGWWLLILFLALIFYISVRLIFALP---------LIILDQLTVREAIRESWKKT 210 (340)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhH---------HHHHhhhhHHHHHHHHHHHH
Confidence 4566665555444445666666554 34677778888888888653
No 25
>COG1380 Putative effector of murein hydrolase LrgA [General function prediction only]
Probab=21.11 E-value=80 Score=22.60 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhhH
Q psy3564 2 GAQVGVTVLLLLTGHYYLFLMNVPM 26 (102)
Q Consensus 2 i~h~~l~~lfLl~g~W~~~llnlPl 26 (102)
..|..+-..|++.|+|+..++.+|+
T Consensus 8 ~~q~~ii~~~~~~G~~i~~~l~lpl 32 (128)
T COG1380 8 LRQLAIILGFLFLGEWIASLLHLPL 32 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 3566777788889999999999885
No 26
>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus
Probab=20.84 E-value=93 Score=25.95 Aligned_cols=52 Identities=19% Similarity=0.289 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHh---hhhHHHHHHHHHhhcCCCCcccccccccccHHhHhHHHHHHHHHH
Q psy3564 11 LLLTGHYYLFLM---NVPMSAWNVYEYYSVPSGNMGVFDPTELYNRDSIKNHMRNCLIGM 67 (102)
Q Consensus 11 fLl~g~W~~~ll---nlPll~y~~~~y~~r~~~~~~l~D~TeIfn~~~L~~~kke~~iKL 67 (102)
-++.++|--..- .+-.+.=|++||.+.|. ..+|||. +.+ .+..-+|..+..|
T Consensus 269 ~mv~~w~~d~~~~n~~AD~ll~~f~rWl~sp~--S~LyDPa-L~~--~v~~LmkK~flqL 323 (396)
T PF08490_consen 269 SMVKSWLRDALKGNSFADSLLQHFYRWLSSPS--SLLYDPA-LHR--MVHNLMKKVFLQL 323 (396)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHHHcCCc--ccccCHH-HHH--HHHHHHHHHHHHH
Confidence 345555554221 14456779999999984 6789998 444 6666666654433
No 27
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=20.59 E-value=1.7e+02 Score=24.15 Aligned_cols=66 Identities=17% Similarity=0.330 Sum_probs=45.3
Q ss_pred HHHHHHHhhhhHHHHHHHHHhhcCC--CCcccccccccccHHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3564 15 GHYYLFLMNVPMSAWNVYEYYSVPS--GNMGVFDPTELYNRDSIKNHMRNCLIGMGFYLVIFFVYLYSMILSLLRD 88 (102)
Q Consensus 15 g~W~~~llnlPll~y~~~~y~~r~~--~~~~l~D~TeIfn~~~L~~~kke~~iKLafYll~FF~yLy~mI~~lv~~ 88 (102)
.-|++.++|+=+-..|. +=-|. |+.=++..-|.-+|+.++...++..-+.++-+++.+ |+++..+|
T Consensus 349 ~l~~~a~iSi~Lgi~NL---LPiP~LDGG~llf~~iE~i~gkpv~~~~~~~~~~iG~~lll~L-----m~~~~~nD 416 (420)
T TIGR00054 349 LLQFGAFLSINLGIMNL---LPIPALDGGQLLFLFIEAIRGKPLPEKVQAFVYRIGVAFLLFL-----MGLGLFND 416 (420)
T ss_pred HHHHHHHHHHHHHHHHh---cCCCCCCcHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH-----HHHHHHHH
Confidence 34566667776666665 23343 566667778888888999999988888888777666 55555543
No 28
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=20.35 E-value=4.4e+02 Score=24.84 Aligned_cols=77 Identities=16% Similarity=0.115 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCC----CCcccccccccccHHhHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3564 4 QVGVTVLLLLTGHYYLFLMNVPMSAWNVYEYYSVPS----GNMGVFDPTELYNRDSIKNHMRNCLIGMGFYLVIFFVYLY 79 (102)
Q Consensus 4 h~~l~~lfLl~g~W~~~llnlPll~y~~~~y~~r~~----~~~~l~D~TeIfn~~~L~~~kke~~iKLafYll~FF~yLy 79 (102)
+..+|+.+-+.-.|+..+.-.|+++-.+-+-.++|. ......|..+=.-++.+.+..+.++.-++.+++++...++
T Consensus 458 ~f~~tia~a~~~S~~vAltltP~L~a~lLk~~~~~~~~~~~~~~~~~~~~~~Y~~~l~~~L~~~~~~~~~~l~~~~~~~~ 537 (1009)
T COG0841 458 QFAITIAVAMLLSLLVALTLTPALCARLLKPVPPPKGFFGWFNRFFDRLEDRYQRGLRWVLRRRALVLLLYLVLLGGSVL 537 (1009)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccchhhhhhhhhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 567788888888999999999999877644443321 0122456666555678888888888888888888775444
Q ss_pred H
Q psy3564 80 S 80 (102)
Q Consensus 80 ~ 80 (102)
-
T Consensus 538 l 538 (1009)
T COG0841 538 L 538 (1009)
T ss_pred H
Confidence 3
Done!