Query 026780
Match_columns 233
No_of_seqs 92 out of 105
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 12:35:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026780.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026780hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02729 PSII-Q subunit 100.0 4.3E-70 9.2E-75 475.1 16.4 215 5-233 1-220 (220)
2 PF05757 PsbQ: Oxygen evolving 100.0 4.7E-68 1E-72 461.8 9.5 199 35-233 3-202 (202)
3 PLN02999 photosystem II oxygen 100.0 1.6E-50 3.5E-55 345.9 13.5 160 50-233 30-190 (190)
4 PLN02956 PSII-Q subunit 100.0 5.1E-38 1.1E-42 269.8 17.7 112 121-232 74-185 (185)
5 TIGR03042 PS_II_psbQ_bact phot 100.0 5.5E-29 1.2E-33 207.0 16.4 104 129-232 38-141 (142)
6 PRK11546 zraP zinc resistance 83.4 27 0.00058 29.7 11.3 38 160-198 64-101 (143)
7 PLN00042 photosystem II oxygen 81.0 2.9 6.3E-05 38.7 4.9 30 48-78 38-67 (260)
8 PRK14141 heat shock protein Gr 75.8 50 0.0011 29.5 11.1 110 108-233 12-135 (209)
9 PF14276 DUF4363: Domain of un 71.1 48 0.001 26.1 8.9 83 141-230 30-112 (121)
10 cd07625 BAR_Vps17p The Bin/Amp 67.8 17 0.00036 32.9 6.3 122 93-229 11-132 (230)
11 PRK14151 heat shock protein Gr 64.8 94 0.002 26.9 11.0 51 183-233 64-119 (176)
12 PF13801 Metal_resist: Heavy-m 62.9 20 0.00044 26.6 5.1 45 158-203 60-104 (125)
13 PRK14150 heat shock protein Gr 62.1 1.1E+02 0.0024 26.9 10.1 70 159-233 59-137 (193)
14 PF11221 Med21: Subunit 21 of 56.4 1.1E+02 0.0025 25.2 10.0 56 127-205 62-123 (144)
15 PF10907 DUF2749: Protein of u 55.9 3.5 7.5E-05 30.9 -0.2 50 61-126 1-50 (66)
16 PF06248 Zw10: Centromere/kine 53.5 2.1E+02 0.0047 28.6 11.8 102 127-228 7-141 (593)
17 PRK14154 heat shock protein Gr 51.6 1.8E+02 0.0039 26.1 10.2 50 184-233 97-151 (208)
18 PF01322 Cytochrom_C_2: Cytoch 50.7 54 0.0012 25.7 5.9 42 183-224 72-113 (122)
19 CHL00102 rps20 ribosomal prote 50.7 50 0.0011 26.1 5.5 48 183-230 23-70 (93)
20 KOG0412 Golgi transport comple 50.5 1.2E+02 0.0026 32.2 9.6 87 128-219 109-217 (773)
21 PF05082 Rop-like: Rop-like; 48.5 45 0.00097 25.0 4.7 45 161-206 13-57 (66)
22 PF01025 GrpE: GrpE; InterPro 46.5 1.2E+02 0.0026 24.8 7.5 48 186-233 58-109 (165)
23 PF08281 Sigma70_r4_2: Sigma-7 46.1 86 0.0019 20.8 6.6 52 170-224 1-53 (54)
24 COG5420 Uncharacterized conser 45.3 71 0.0015 24.1 5.3 47 161-208 17-63 (71)
25 PF05957 DUF883: Bacterial pro 44.9 1.3E+02 0.0029 22.6 7.2 66 163-229 4-69 (94)
26 PRK14155 heat shock protein Gr 44.0 1.4E+02 0.0031 26.6 8.1 51 183-233 57-114 (208)
27 PRK14143 heat shock protein Gr 43.5 2.6E+02 0.0056 25.5 11.4 51 183-233 111-166 (238)
28 PRK14156 heat shock protein Gr 43.5 2.2E+02 0.0049 24.8 10.4 53 181-233 69-122 (177)
29 PRK14147 heat shock protein Gr 43.0 2.2E+02 0.0048 24.6 11.2 53 181-233 60-114 (172)
30 PLN03184 chloroplast Hsp70; Pr 42.3 2.6E+02 0.0056 28.8 10.6 74 151-231 560-633 (673)
31 PRK14142 heat shock protein Gr 42.2 1.1E+02 0.0024 27.8 7.1 48 184-233 78-125 (223)
32 PF01627 Hpt: Hpt domain; Int 42.0 1.2E+02 0.0026 21.2 8.3 29 136-164 7-38 (90)
33 PF10399 UCR_Fe-S_N: Ubiquitin 39.2 35 0.00076 23.1 2.7 18 58-75 6-23 (41)
34 PF05960 DUF885: Bacterial pro 39.2 2E+02 0.0044 27.9 9.0 69 155-223 142-233 (549)
35 PRK14145 heat shock protein Gr 39.1 2.8E+02 0.0061 24.6 10.8 51 183-233 89-140 (196)
36 PRK14162 heat shock protein Gr 39.0 2.8E+02 0.006 24.6 10.6 50 184-233 84-137 (194)
37 TIGR01042 V-ATPase_V1_A V-type 38.4 1.6E+02 0.0034 30.5 8.2 79 117-199 497-590 (591)
38 PF13413 HTH_25: Helix-turn-he 37.4 44 0.00094 24.0 3.1 52 125-176 9-62 (62)
39 PRK05685 fliS flagellar protei 37.3 1.4E+02 0.003 24.3 6.4 62 168-232 10-72 (132)
40 PF12732 YtxH: YtxH-like prote 37.2 1.5E+02 0.0032 21.6 6.0 47 183-229 26-72 (74)
41 PRK14164 heat shock protein Gr 37.1 3.1E+02 0.0067 24.8 9.1 49 183-233 114-162 (218)
42 PRK14160 heat shock protein Gr 37.0 3.1E+02 0.0068 24.6 12.1 53 181-233 103-156 (211)
43 PRK14146 heat shock protein Gr 37.0 2.2E+02 0.0048 25.5 8.2 53 181-233 96-152 (215)
44 PF10167 NEP: Uncharacterised 37.0 2.3E+02 0.0051 23.2 9.2 88 131-229 5-95 (118)
45 PF01093 Clusterin: Clusterin; 36.4 72 0.0016 31.7 5.4 74 132-221 14-92 (436)
46 PF06698 DUF1192: Protein of u 36.2 1.1E+02 0.0023 22.4 5.0 29 125-153 19-47 (59)
47 PRK01433 hscA chaperone protei 36.2 3.3E+02 0.0071 27.7 10.1 90 126-229 481-574 (595)
48 TIGR02811 formate_TAT formate 34.2 51 0.0011 24.3 3.1 13 60-72 8-20 (66)
49 PRK14140 heat shock protein Gr 33.5 3.4E+02 0.0074 24.0 11.7 53 181-233 79-135 (191)
50 PF08802 CytB6-F_Fe-S: Cytochr 33.2 52 0.0011 22.3 2.7 20 59-78 4-23 (39)
51 PRK14149 heat shock protein Gr 32.6 3.2E+02 0.0069 24.2 8.3 62 172-233 65-134 (191)
52 PRK14139 heat shock protein Gr 32.0 3.5E+02 0.0077 23.7 11.0 51 183-233 76-128 (185)
53 PRK00239 rpsT 30S ribosomal pr 31.0 2E+02 0.0043 22.3 6.1 26 205-230 38-63 (88)
54 PRK14158 heat shock protein Gr 30.5 3.8E+02 0.0083 23.7 10.6 51 183-233 84-137 (194)
55 TIGR00029 S20 ribosomal protei 30.2 2.1E+02 0.0045 22.2 6.0 26 204-229 37-62 (87)
56 PF12732 YtxH: YtxH-like prote 29.8 1.8E+02 0.0039 21.1 5.4 29 151-179 20-48 (74)
57 KOG4519 Phosphomevalonate kina 29.6 1.4E+02 0.003 29.4 6.0 68 141-208 245-330 (459)
58 PRK14144 heat shock protein Gr 29.2 4.1E+02 0.009 23.7 10.2 51 183-233 89-142 (199)
59 COG5057 LAG1 Phosphotyrosyl ph 29.0 59 0.0013 31.2 3.3 41 192-232 31-71 (353)
60 PRK14161 heat shock protein Gr 28.9 3.9E+02 0.0084 23.2 11.1 53 181-233 61-119 (178)
61 PF03401 TctC: Tripartite tric 28.4 1.5E+02 0.0033 26.5 5.8 33 113-145 199-231 (274)
62 PRK14148 heat shock protein Gr 28.4 4.2E+02 0.0091 23.5 10.4 52 182-233 83-138 (195)
63 PF12729 4HB_MCP_1: Four helix 27.7 2.8E+02 0.0061 21.2 9.3 108 121-228 39-155 (181)
64 KOG1510 RNA polymerase II holo 27.1 2E+02 0.0044 24.5 5.8 58 171-229 70-129 (139)
65 PTZ00400 DnaK-type molecular c 26.7 6.4E+02 0.014 25.9 10.5 49 153-201 564-612 (663)
66 COG3181 Uncharacterized protei 26.2 1.3E+02 0.0028 28.7 5.0 56 95-157 231-289 (319)
67 PRK13411 molecular chaperone D 25.9 7.3E+02 0.016 25.4 11.2 72 154-230 526-597 (653)
68 PRK07502 cyclohexadienyl dehyd 25.8 1.6E+02 0.0035 26.5 5.5 66 163-229 217-289 (307)
69 COG0576 GrpE Molecular chapero 25.7 4.5E+02 0.0098 22.9 10.4 52 182-233 79-135 (193)
70 PF10518 TAT_signal: TAT (twin 25.6 56 0.0012 19.9 1.7 15 61-75 2-16 (26)
71 PRK14163 heat shock protein Gr 25.5 5E+02 0.011 23.4 9.6 47 184-233 85-131 (214)
72 PF12805 FUSC-like: FUSC-like 25.4 3.3E+02 0.0072 24.4 7.4 91 133-227 185-279 (284)
73 PRK06305 DNA polymerase III su 25.3 1.8E+02 0.0039 28.4 6.0 99 114-223 164-275 (451)
74 PRK07417 arogenate dehydrogena 24.7 3.3E+02 0.0072 24.2 7.2 66 163-229 206-278 (279)
75 PRK09706 transcriptional repre 24.4 1.4E+02 0.0031 23.7 4.4 32 171-202 90-121 (135)
76 cd00446 GrpE GrpE is the adeni 23.8 3.9E+02 0.0084 21.5 8.2 51 183-233 29-83 (137)
77 PF08006 DUF1700: Protein of u 23.6 2.9E+02 0.0062 23.2 6.3 26 173-198 10-35 (181)
78 PF02561 FliS: Flagellar prote 23.5 3.1E+02 0.0066 21.6 6.1 47 186-232 20-66 (122)
79 PTZ00208 65 kDa invariant surf 23.0 3.6E+02 0.0078 27.0 7.5 68 153-228 55-138 (436)
80 PRK14157 heat shock protein Gr 23.0 4.2E+02 0.009 24.2 7.5 47 184-233 122-168 (227)
81 PRK06214 sulfite reductase; Pr 22.7 2.1E+02 0.0046 28.9 6.1 71 56-131 8-81 (530)
82 PF13326 PSII_Pbs27: Photosyst 22.3 1.3E+02 0.0028 25.4 3.9 13 216-228 101-113 (145)
83 TIGR00208 fliS flagellar biosy 21.7 4.3E+02 0.0094 21.3 7.7 55 175-232 14-68 (124)
84 PF14261 DUF4351: Domain of un 21.1 1.5E+02 0.0032 21.2 3.5 44 156-202 10-55 (59)
85 cd02682 MIT_AAA_Arch MIT: doma 21.1 3.3E+02 0.0072 20.6 5.5 36 192-230 6-41 (75)
86 PF11521 TFIIE-A_C-term: C-ter 21.0 1E+02 0.0023 24.0 2.8 32 168-199 50-84 (86)
87 PF12729 4HB_MCP_1: Four helix 20.7 3.9E+02 0.0085 20.4 11.6 13 132-144 80-92 (181)
88 PRK00488 pheS phenylalanyl-tRN 20.5 3.9E+02 0.0085 25.7 7.1 52 151-203 21-72 (339)
No 1
>PLN02729 PSII-Q subunit
Probab=100.00 E-value=4.3e-70 Score=475.10 Aligned_cols=215 Identities=29% Similarity=0.441 Sum_probs=203.1
Q ss_pred hHHhhcccCCCcccchhcccccccCCCcccCCCCCcccccccceEEeec-c-ccCCcchhhHHHHHHHHHHHhhchhhhh
Q 026780 5 MASMAGLRGSSHSQAVLEGSFQLSGPNRLNAPSNSRVAVARPGFTVRAQ-Q-ASNEPETSRRAMLGLVAAGVASGSFVQA 82 (233)
Q Consensus 5 ~~~ma~l~g~s~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~vra~-~-~~~~~~~sRRa~lgl~a~~l~~~~~~~~ 82 (233)
|||+++|+|.+ +++ |.+++|+|.+|. +.++.+.|+.|+.+ + |+++.|++||++|||+++++++++|+++
T Consensus 1 ~~~~~~~~~~~--~~~-~~~~~~~~~~~~------~~~~~~~g~l~~~~~~~~~~~~~~~rr~~lgl~a~~l~~~s~~~~ 71 (220)
T PLN02729 1 MAHLANLNGLT--ETL-PAIPKLRNLQRT------RKRGKIIGFLCKKAENFQEDSFQTTRRLALGLASIALIGNSGNGV 71 (220)
T ss_pred Ccchhcccccc--ccc-ccchhhhcchhh------hhhhhhhhHhhhhhhhcccchhhhhHHHHHHHHHHHHhcchhhhH
Confidence 89999999999 888 999999999887 88899999887776 3 6678999999999999999999999999
Q ss_pred hhhccCCcccCCC-CCCCCCCCCCCCC--CCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHH
Q 026780 83 VLADATPIKVGPP-PPPSGGLPGTLNS--DEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQ 159 (233)
Q Consensus 83 ~~a~~~~i~~~p~-P~ps~~~~Gt~~~--~eardl~l~lk~rf~~q~ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr 159 (233)
++||+.+||++|| ||||. +|+ ||..++|.|+|||||+||++|++|++|||++|++|++||+|||+++|+|||
T Consensus 72 ~~A~~~~i~~~~P~P~pst-----~n~~~~e~~gtRsfLKerfy~~~l~p~~aa~RiK~sA~dLl~vKdLId~~sW~yVq 146 (220)
T PLN02729 72 SLAEDNGFWLDGPLPVPSV-----DNKIVNEKTGTRSFLKKGIYMADIGTKGRMYRVKKYAFDLLALEDLIGPDTLNYVR 146 (220)
T ss_pred HHhcccCceeCCCCCCCcc-----ccccccccchHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHhhCcchHHHHH
Confidence 9999999999888 88884 554 777777779999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 160 NDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 160 ~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
+|||+|++||||||+++|+++|+++||+|++||++||++|++||||+|+||++++++||++|+++|||||++++
T Consensus 147 ~~LRLKAsyL~yDL~tvIsskP~~eKk~L~~LankLFdn~~eLD~AaR~Ks~~eae~yY~~Tv~aLdeVl~k~~ 220 (220)
T PLN02729 147 KYLRLKSTFMYYDFDKLISAAPVDDKQPLTDLANRLFDNFEKLEDASKRKNLSETESSYKDTKTLLQEVMDRMA 220 (220)
T ss_pred HHHHHHHHHHHHHHHHHhccCChhhhHHHHHHHHHHHhhHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999975
No 2
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 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 []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=100.00 E-value=4.7e-68 Score=461.83 Aligned_cols=199 Identities=64% Similarity=0.975 Sum_probs=107.7
Q ss_pred CCCCCcccccccceEEeeccccCCcchhhHHHHH-HHHHHHhhchhhhhhhhccCCcccCCCCCCCCCCCCCCCCCCCCC
Q 026780 35 APSNSRVAVARPGFTVRAQQASNEPETSRRAMLG-LVAAGVASGSFVQAVLADATPIKVGPPPPPSGGLPGTLNSDEPRD 113 (233)
Q Consensus 35 ~~~~~~~~~~~~~~~vra~~~~~~~~~sRRa~lg-l~a~~l~~~~~~~~~~a~~~~i~~~p~P~ps~~~~Gt~~~~eard 113 (233)
++++.++.+.+.+++|||++++++.+++||++|| |+++++++++++++++++++||++++||||++++|||+++||+||
T Consensus 3 ~~~~~~~~~~r~~~~vra~~~~~~~~~~RRa~l~~l~a~~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~g~~~~~~aRd 82 (202)
T PF05757_consen 3 STSSSRVASRRAGVVVRASQSPAQQQTSRRAVLGSLLAAALAGGSFAQAAAAAAWAIKVGLPPPPSGNLPGTNNSDGARD 82 (202)
T ss_dssp ------------------------------------------------------S-EE----------------------
T ss_pred CCcCCccccccccceeccccCcccccccHHHHHHHHHHHHHHhhhcccccccchhhhccCCCCCCCCCCCCccccccccc
Confidence 3455577777888999999988889999999999 999999999999999999999999999999999999999999999
Q ss_pred CCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHH
Q 026780 114 LDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTG 193 (233)
Q Consensus 114 l~l~lk~rf~~q~ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~ 193 (233)
++||||+|||+|++||+|+++|||+++++|+.|++|||+++|+|||+|||+|++||||||++||+++|+++||++++|+|
T Consensus 83 ~~l~lk~rf~~~~l~~~ea~~Rik~sa~~L~~lk~lIdk~sW~~v~~~LRlka~~Lr~DL~~liss~p~~~kk~l~~La~ 162 (202)
T PF05757_consen 83 FDLPLKERFYIQPLSPEEAAARIKESAKRLLSLKELIDKKSWPYVRNYLRLKAGYLRYDLNTLISSKPKDEKKALTDLAN 162 (202)
T ss_dssp -----TT--EE----CCCHHHHHHHHHHHHCCCHHHHHTT-HHHHHHHHHCCCCCHHHHHHHHHCCS-HHHHHHHHHHHH
T ss_pred cccchhhceecCCCCHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHhHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 194 KLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 194 kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
+||++||+||||+|+||++++++||++|+++||+||++||
T Consensus 163 ~lf~~ie~LD~Aar~K~~~~a~~~Y~~t~~~Ldevla~la 202 (202)
T PF05757_consen 163 KLFDNIEELDYAARSKDVPEAEKYYADTVKALDEVLAKLA 202 (202)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHCCH-
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999986
No 3
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=100.00 E-value=1.6e-50 Score=345.88 Aligned_cols=160 Identities=25% Similarity=0.432 Sum_probs=145.4
Q ss_pred EeeccccCCcchhhHHHHH-HHHHHHhhchhhhhhhhccCCcccCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCC
Q 026780 50 VRAQQASNEPETSRRAMLG-LVAAGVASGSFVQAVLADATPIKVGPPPPPSGGLPGTLNSDEPRDLDLPLKERFFIQPLS 128 (233)
Q Consensus 50 vra~~~~~~~~~sRRa~lg-l~a~~l~~~~~~~~~~a~~~~i~~~p~P~ps~~~~Gt~~~~eardl~l~lk~rf~~q~ls 128 (233)
|.++-+..+..++||.++. |++++++|+++. |+....+||| |+|+|||||+||+|
T Consensus 30 ~~~~~~~~~~~~~rr~~~~~~l~~~~~~~~~~---------------~~~~~e~~Gt---------RsfLKerfy~p~ls 85 (190)
T PLN02999 30 VCCTGEPQQDIFTRRRTLTSLITFTVIGGATS---------------SALAQEKWGT---------RSFIKEKYFMPGLS 85 (190)
T ss_pred hhcCCCchhhhHHHHHHHHHHHHHHHHhhccC---------------cHHHHhhhhh---------HHHHHHhccCCCCC
Confidence 4555444566789999888 999999876642 3445555666 45999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhc
Q 026780 129 PAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKI 208 (233)
Q Consensus 129 ~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~ 208 (233)
|+||++|||++|++|+.||+|||+++|+|||+|||++++||||||+++|+++|+++|++|++|+++||+||++||||||+
T Consensus 86 peeAaaRiK~sA~dLl~vK~LId~~aW~YVq~~LRlkasyLryDL~tiIsskP~~eK~~L~~LankLFdnvt~LDyAAR~ 165 (190)
T PLN02999 86 PEDAAARIKQTAEGLRDMREMLDHMSWRYVIFYIRLKQAYLSQDLTNAMNILPESRRNDYVQAANELVENMSELDYYVRT 165 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHhcCCHhhhHHHHHHHHHHhhhHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 209 KSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 209 Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
||++++++||++|+++||||++.||
T Consensus 166 K~~~eae~yY~~Tv~slddVl~~l~ 190 (190)
T PLN02999 166 PKVYESYLYYEKTLKSIDNVVELLA 190 (190)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999886
No 4
>PLN02956 PSII-Q subunit
Probab=100.00 E-value=5.1e-38 Score=269.78 Aligned_cols=112 Identities=33% Similarity=0.553 Sum_probs=110.5
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhh
Q 026780 121 RFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIG 200 (233)
Q Consensus 121 rf~~q~ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le 200 (233)
|||+|++|||||++|||++|++|+.|++||++++|+|||||||+|++||||||++||++||+++|+++++|+++||++|+
T Consensus 74 ~~~~p~~speeA~ar~k~~A~~l~~LK~LI~k~~W~yvrn~LRgp~s~Lr~DL~~Ii~slpp~Drk~a~~La~~LFd~l~ 153 (185)
T PLN02956 74 RLTAPERTVEEAESGVRGHAENLLRVKALIESESWKEAQKALRRSASNLKQDLYAIIQAKPGKDRPQLRRLYSDLFNSVT 153 (185)
T ss_pred eecCCCCCHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHccHHHHHHHHHHHHHhcCHhHhHHHHHHHHHHHHHHH
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHhcCChHHHHHHHHHHHHHHHHHHhhh
Q 026780 201 NLDHAAKIKSTPEAEKYYAETVSTLNDVLSKV 232 (233)
Q Consensus 201 ~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l 232 (233)
+||+|||.||.+++++||++|+++||+||++|
T Consensus 154 ~LD~AAR~kd~~~a~k~Y~~tva~lD~Vl~~i 185 (185)
T PLN02956 154 KLDYAARDKDETRVWEYYENIVASLDDIFSRI 185 (185)
T ss_pred HHHHHHhcCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999986
No 5
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=99.96 E-value=5.5e-29 Score=206.99 Aligned_cols=104 Identities=18% Similarity=0.336 Sum_probs=100.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhc
Q 026780 129 PAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKI 208 (233)
Q Consensus 129 ~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~ 208 (233)
.++++.+|.+++++|.+|+.||++++|++|||+||+++|+||+||++|+++||+++||++++|+++||+++++||+|||.
T Consensus 38 i~~~~~~i~~~~~r~~eLk~lI~kk~W~~vrn~irgp~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA~~ 117 (142)
T TIGR03042 38 IQRQAEGIEAAKDRLPELASLVAKEDWVFTRNLIHGPMGEVRREMTYLNQSLLPKDQKEALALAKELKDDLEKLDEAARL 117 (142)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHhhcchHHHHHHHhccHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHHHHHHhhh
Q 026780 209 KSTPEAEKYYAETVSTLNDVLSKV 232 (233)
Q Consensus 209 Kn~~~a~~~Y~~tv~~LdevLa~l 232 (233)
||.+++++||++++++||++++.|
T Consensus 118 kd~~~a~k~Y~~av~~~dafl~~~ 141 (142)
T TIGR03042 118 QDGPQAQKAYQKAAADFDAYLDLL 141 (142)
T ss_pred cCHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999865
No 6
>PRK11546 zraP zinc resistance protein; Provisional
Probab=83.44 E-value=27 Score=29.68 Aligned_cols=38 Identities=21% Similarity=0.433 Sum_probs=25.9
Q ss_pred HHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHh
Q 026780 160 NDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQT 198 (233)
Q Consensus 160 ~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~ 198 (233)
..||.+.-.-+.+|+.|+++-+.|+ +.+..|++++.+=
T Consensus 64 ~~LRqqL~aKr~ELnALl~~~~pD~-~kI~aL~kEI~~L 101 (143)
T PRK11546 64 SALRQQLVSKRYEYNALLTANPPDS-SKINAVAKEMENL 101 (143)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHHH
Confidence 3577777788999999999885555 3355555555443
No 7
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=81.01 E-value=2.9 Score=38.69 Aligned_cols=30 Identities=43% Similarity=0.607 Sum_probs=19.4
Q ss_pred eEEeeccccCCcchhhHHHHHHHHHHHhhch
Q 026780 48 FTVRAQQASNEPETSRRAMLGLVAAGVASGS 78 (233)
Q Consensus 48 ~~vra~~~~~~~~~sRRa~lgl~a~~l~~~~ 78 (233)
++||||.++. ...|||.+|.+++.+++.++
T Consensus 38 ~~~~~~~~~~-~~~srr~~l~~~~ga~a~~~ 67 (260)
T PLN00042 38 VVCRAQEEDN-SAVSRRAALALLAGAAAAGA 67 (260)
T ss_pred eeeecccccc-ccccHHHHHHHHHHHHHhhc
Confidence 9999986543 44688887766654444333
No 8
>PRK14141 heat shock protein GrpE; Provisional
Probab=75.75 E-value=50 Score=29.54 Aligned_cols=110 Identities=15% Similarity=0.182 Sum_probs=60.5
Q ss_pred CCCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHh----cCChh
Q 026780 108 SDEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIIS----AKPKD 183 (233)
Q Consensus 108 ~~eardl~l~lk~rf~~q~ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlis----skPkd 183 (233)
.|.+||..-|+...-+--..++......|....+++..+++ .|||..+ |+.++-. .+-.-
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~le~e~~elkd-----------~~lR~~A-----e~eN~RKR~~kE~e~~ 75 (209)
T PRK14141 12 ADAARDANNPVDREAKPYEMEDDPEPDPLEALKAENAELKD-----------RMLRLAA-----EMENLRKRTQRDVADA 75 (209)
T ss_pred chhhhhccCccccccccccCCCcchHHHHHHHHHHHHHHHH-----------HHHHHHH-----HHHHHHHHHHHHHHHH
Confidence 56677777676532221122223344455555555554432 3344444 4444422 22344
Q ss_pred hHHHHHHHHHHHHHhhhhhHHHHhcCC----------hHHHHHHHHHHHHHHHHHHhhhC
Q 026780 184 EKQSLKNLTGKLFQTIGNLDHAAKIKS----------TPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 184 ~Kk~l~~La~kLF~~le~LD~AaR~Kn----------~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.+-...+++++|+.-+++|+.|...-. ......=++-|.+.|..+|.+.|
T Consensus 76 ~~~a~~~~~~dLLpViDnLerAl~~~~~~~~~~~~~~~~~l~eGv~mi~k~l~~vLek~G 135 (209)
T PRK14141 76 RAYGIAGFARDMLSVSDNLRRALDAIPAEARAAADAGLKALIEGVEMTERAMLNALERHG 135 (209)
T ss_pred HHHHHHHHHHHHhhhHhHHHHHHhccccccccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 556677889999999999999986321 12233344455667777777654
No 9
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=71.10 E-value=48 Score=26.10 Aligned_cols=83 Identities=13% Similarity=0.127 Sum_probs=56.5
Q ss_pred HHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHH
Q 026780 141 KDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAE 220 (233)
Q Consensus 141 ~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~ 220 (233)
+.|..+++.|+++.|...++.+..=...-. .....++-. -++++ -..+=.++.+|..++..+|.+++-..-..
T Consensus 30 ~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~-k~~~~~~~~--~~h~e----id~i~~sl~rl~~~i~~~dk~~~l~el~~ 102 (121)
T PF14276_consen 30 EQLEQIEEAIENEDWEKAYKETEELEKEWD-KNKKRWSIL--IEHQE----IDNIDISLARLKGYIEAKDKSESLAELAE 102 (121)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHH-hhchheeee--ecHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 456789999999999999887654332222 222222222 11122 45677788999999999999999888888
Q ss_pred HHHHHHHHHh
Q 026780 221 TVSTLNDVLS 230 (233)
Q Consensus 221 tv~~LdevLa 230 (233)
....++.+..
T Consensus 103 lk~~i~~i~~ 112 (121)
T PF14276_consen 103 LKELIEHIPE 112 (121)
T ss_pred HHHHHHHHHH
Confidence 7777766543
No 10
>cd07625 BAR_Vps17p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps17p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=67.85 E-value=17 Score=32.89 Aligned_cols=122 Identities=10% Similarity=0.102 Sum_probs=84.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHH
Q 026780 93 GPPPPPSGGLPGTLNSDEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYD 172 (233)
Q Consensus 93 ~p~P~ps~~~~Gt~~~~eardl~l~lk~rf~~q~ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~D 172 (233)
-|||.|-..+..++ |+=+.||+.-......+.++-.+.++|-.......++-=..-..+-+...+.++..
T Consensus 11 ~~p~d~~~el~~~r----------p~vk~~y~~~~~l~~~~~~lvk~rr~La~~~~dfg~~l~~Ls~~E~~~~L~~a~~k 80 (230)
T cd07625 11 APPYDEYTELAEFR----------PLVKSIYLTAQDLQEKLLRVSKARKQLSLEEADFGQKLIQLSVEETHHGLGNLYEK 80 (230)
T ss_pred CcCCCCCHHHHHhh----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHH
Confidence 56666777665554 89899999999999999999999999986666665555555555566677888888
Q ss_pred HHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 173 LNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 173 L~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
|-.++.+...=+-.+. .++++.--|-|+++++ +...++..+.+=...++++.
T Consensus 81 Lg~v~~~v~dl~~~QA---~~d~~tl~d~L~~~~~--~~~~vKealtnR~~~~re~~ 132 (230)
T cd07625 81 FGKVLTAVGDIDSIQA---TVDMATLYDGLEWISR--DAYVVKEALTNRHLLMRELI 132 (230)
T ss_pred HHHHHHHHhhHHHHHH---HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 8888888854332323 4555555566666664 45566666666666665554
No 11
>PRK14151 heat shock protein GrpE; Provisional
Probab=64.80 E-value=94 Score=26.95 Aligned_cols=51 Identities=18% Similarity=0.316 Sum_probs=34.6
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCC--h---HHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKS--T---PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn--~---~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.+-...++.++|+.-+++|+.|....+ . .....=++-+.+.|.++|.+.|
T Consensus 64 ~~~~a~~~~~~~LLpv~DnlerAl~~~~~~~~~~~~~~~Gv~mi~k~l~~~L~k~G 119 (176)
T PRK14151 64 AHKFALEKFAGDLLPVVDSLERGLELSSADDEAIKPMREGVELTLKMFQDTLKRYQ 119 (176)
T ss_pred HHHHHHHHHHHHHhhHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 3445566889999999999999987422 1 2233445566677777777654
No 12
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=62.93 E-value=20 Score=26.60 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=31.4
Q ss_pred HHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhH
Q 026780 158 VQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLD 203 (233)
Q Consensus 158 vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD 203 (233)
-...+|.....++.+|..++.+-|.|. ..+..+.+++.+.-.+++
T Consensus 60 ~~~~~r~~~~~~r~~l~~ll~~~~~D~-~~i~a~~~~~~~~~~~l~ 104 (125)
T PF13801_consen 60 EMRALRQELRAARQELRALLAAPPPDE-AAIEALLEEIREAQAELR 104 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCSSS-H-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHHHHH
Confidence 345677888899999999999887666 456666666655544444
No 13
>PRK14150 heat shock protein GrpE; Provisional
Probab=62.05 E-value=1.1e+02 Score=26.86 Aligned_cols=70 Identities=26% Similarity=0.359 Sum_probs=41.3
Q ss_pred HHHHhhhhhhHHHHHHHHHhcC----ChhhHHHHHHHHHHHHHhhhhhHHHHhcCC--hHHHH---HHHHHHHHHHHHHH
Q 026780 159 QNDLRLRASYLRYDLNTIISAK----PKDEKQSLKNLTGKLFQTIGNLDHAAKIKS--TPEAE---KYYAETVSTLNDVL 229 (233)
Q Consensus 159 r~~LRlka~~Lr~DL~tlissk----Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn--~~~a~---~~Y~~tv~~LdevL 229 (233)
-.|||+.+ |+.++-... ..-.+-....++++|+.-+++|+.|....+ ..... .=++-+.+.|..+|
T Consensus 59 d~~lR~~A-----efeN~rkR~~kE~~~~~~~a~~~~~~~lL~v~DnlerAl~~~~~~~~~~~~~~~Gv~mi~~~l~~~L 133 (193)
T PRK14150 59 DSVLRARA-----EVENIRRRAEQDVEKAHKFALEKFANELLPVIDNLERALQAADKENEALKALIEGVELTLKSLLDTV 133 (193)
T ss_pred HHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHH
Confidence 44555555 555553332 333444666889999999999999986432 22223 33444556666666
Q ss_pred hhhC
Q 026780 230 SKVG 233 (233)
Q Consensus 230 a~l~ 233 (233)
.+.|
T Consensus 134 ~~~G 137 (193)
T PRK14150 134 AKFG 137 (193)
T ss_pred HHCC
Confidence 6544
No 14
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=56.41 E-value=1.1e+02 Score=25.18 Aligned_cols=56 Identities=21% Similarity=0.287 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCCh------hhHHHHHHHHHHHHHhhh
Q 026780 127 LSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPK------DEKQSLKNLTGKLFQTIG 200 (233)
Q Consensus 127 ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPk------d~Kk~l~~La~kLF~~le 200 (233)
.++++....+++.+.+|.. --+++..||+++|. ++-+.+++|-.++=.-=+
T Consensus 62 ~~~~~~~~~~~elA~dIi~-----------------------kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~ 118 (144)
T PF11221_consen 62 DPPEEFEENIKELATDIIR-----------------------KAKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEE 118 (144)
T ss_dssp --HHHHHHHHHHHHHHHHH-----------------------HHHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHH
T ss_pred CChhhHHHHHHHHHHHHHH-----------------------HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4788899999999988874 24688999999987 444445555544443333
Q ss_pred hhHHH
Q 026780 201 NLDHA 205 (233)
Q Consensus 201 ~LD~A 205 (233)
+|-.+
T Consensus 119 el~~~ 123 (144)
T PF11221_consen 119 ELQEA 123 (144)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 33333
No 15
>PF10907 DUF2749: Protein of unknown function (DUF2749); InterPro: IPR024475 This bacterial family of proteins represent the TrbJ and TrbK genes of the Ti plasmid conjugative transfer operon [].
Probab=55.90 E-value=3.5 Score=30.93 Aligned_cols=50 Identities=32% Similarity=0.412 Sum_probs=26.7
Q ss_pred hhhHHHHHHHHHHHhhchhhhhhhhccCCcccCCCCCCCCCCCCCCCCCCCCCCCcccccccccCC
Q 026780 61 TSRRAMLGLVAAGVASGSFVQAVLADATPIKVGPPPPPSGGLPGTLNSDEPRDLDLPLKERFFIQP 126 (233)
Q Consensus 61 ~sRRa~lgl~a~~l~~~~~~~~~~a~~~~i~~~p~P~ps~~~~Gt~~~~eardl~l~lk~rf~~q~ 126 (233)
++||-+|.|+++..+++. -++|+-+.|.|.+.... +|++- ..+|+||=.+
T Consensus 1 ms~~viIaL~~avaa~a~-------~atwviVq~~~a~~p~s------~eeQr---~~re~ff~~~ 50 (66)
T PF10907_consen 1 MSRRVIIALVVAVAAAAG-------AATWVIVQPRPAGNPAS------SEEQR---AHREKFFGGD 50 (66)
T ss_pred CCcchhHHHHHHHHhhhc-------eeEEEEECCCCCCCCCC------hHHHH---HHHHHHcCCC
Confidence 367778887776332211 14777788764444332 22221 4567777554
No 16
>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells. These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking [, ]. Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes []. Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies []. The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores [, , ].; GO: 0007067 mitosis, 0000775 chromosome, centromeric region, 0005634 nucleus
Probab=53.46 E-value=2.1e+02 Score=28.57 Aligned_cols=102 Identities=20% Similarity=0.268 Sum_probs=62.0
Q ss_pred CCHHH---HHHHHHHHHHHHH-HHHHHhhhCC-----hhHHHHHHhhhhhhHHHHHHHHHhc-CChhhHHHHHHHHH---
Q 026780 127 LSPAQ---AAERAKASAKDIL-NVKELIDKKA-----WPYVQNDLRLRASYLRYDLNTIISA-KPKDEKQSLKNLTG--- 193 (233)
Q Consensus 127 ls~~e---a~~RIkesA~~L~-~lk~lIdkks-----W~~vr~~LRlka~~Lr~DL~tliss-kPkd~Kk~l~~La~--- 193 (233)
++.++ ...++....+++. ++.++|++++ |-.--..|-.++.-|..|++.+.+. .+.+-+..+.+..+
T Consensus 7 l~~edl~~~I~~L~~~i~~~k~eV~~~I~~~y~df~~~~~~~~~L~~~~~~l~~eI~d~l~~~~~~~i~~~l~~a~~e~~ 86 (593)
T PF06248_consen 7 LSKEDLRKSISRLSRRIEELKEEVHSMINKKYSDFSPSLQSAKDLIERSKSLAREINDLLQSEIENEIQPQLRDAAEELQ 86 (593)
T ss_pred CCHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHH
Confidence 44444 4444444445554 5666776544 5555667778888888888777666 33333333333322
Q ss_pred --------------------HHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHH
Q 026780 194 --------------------KLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDV 228 (233)
Q Consensus 194 --------------------kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~Ldev 228 (233)
++-+.|++++.|...++...|-...+++...|+++
T Consensus 87 ~L~~eL~~~~~~l~~L~~L~~i~~~l~~~~~al~~~~~~~Aa~~L~~~~~~L~~l 141 (593)
T PF06248_consen 87 ELKRELEENEQLLEVLEQLQEIDELLEEVEEALKEGNYLDAADLLEELKSLLDDL 141 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhc
Confidence 23334555666777778888888888877777764
No 17
>PRK14154 heat shock protein GrpE; Provisional
Probab=51.63 E-value=1.8e+02 Score=26.08 Aligned_cols=50 Identities=24% Similarity=0.307 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHhhhhhHHHHhcC--ChHHHHHH---HHHHHHHHHHHHhhhC
Q 026780 184 EKQSLKNLTGKLFQTIGNLDHAAKIK--STPEAEKY---YAETVSTLNDVLSKVG 233 (233)
Q Consensus 184 ~Kk~l~~La~kLF~~le~LD~AaR~K--n~~~a~~~---Y~~tv~~LdevLa~l~ 233 (233)
.+-...+++++|+.-+|+|+.|...- ..+..... ++-+.+.|..+|.+.|
T Consensus 97 ~~~a~e~~~~~LLpVlDnLeRAL~~~~~~~~~~~~l~eGvemi~k~l~~vL~k~G 151 (208)
T PRK14154 97 IKFGSKQLITDLLPVADSLIHGLESPASEDPQVKSMRDGMSLTLDLLHNTLAKHG 151 (208)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 44556678899999999999998742 22223333 3445556666666543
No 18
>PF01322 Cytochrom_C_2: Cytochrome C'; InterPro: IPR002321 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins []. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein []. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core []. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0005746 mitochondrial respiratory chain; PDB: 1BBH_A 2J9B_B 2J8W_A 1JAF_B 3ZTM_A 2XLD_A 2XL6_A 1E86_A 2YLD_A 2YKZ_A ....
Probab=50.73 E-value=54 Score=25.69 Aligned_cols=42 Identities=17% Similarity=0.238 Sum_probs=37.5
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHH
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVST 224 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~ 224 (233)
++...+..++..|-...+.|..+++.+|...+...|.++..+
T Consensus 72 ~~~~~F~~~~~~~~~aa~~L~~aa~~~d~~~~~~a~~~v~~~ 113 (122)
T PF01322_consen 72 EDPEDFKQLAQAFQKAAAALAAAAKSGDLAAIKAAFGEVGKS 113 (122)
T ss_dssp HTHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred hCHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 456789999999999999999999999999999999887654
No 19
>CHL00102 rps20 ribosomal protein S20
Probab=50.71 E-value=50 Score=26.06 Aligned_cols=48 Identities=13% Similarity=0.251 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLS 230 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa 230 (233)
..|-.++.+.++|+..++..|.-...+|..+++..|.++.+.||....
T Consensus 23 ~~kS~~rT~iKk~~~ai~~~~~~~~~~d~~~a~~~l~~a~s~iDkaa~ 70 (93)
T CHL00102 23 AYKSSVKTLIKKYLKNLEDYKTSPNSNNKKKVQETLSSVYSKIDKAVK 70 (93)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHHHHH
Confidence 445566666677776666655555557888888888888888887543
No 20
>KOG0412 consensus Golgi transport complex COD1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.52 E-value=1.2e+02 Score=32.19 Aligned_cols=87 Identities=17% Similarity=0.293 Sum_probs=57.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHH----------hhhCChhHHHHHHhhhhhhHHHHHHHHHhc------------CChhhH
Q 026780 128 SPAQAAERAKASAKDILNVKEL----------IDKKAWPYVQNDLRLRASYLRYDLNTIISA------------KPKDEK 185 (233)
Q Consensus 128 s~~ea~~RIkesA~~L~~lk~l----------IdkksW~~vr~~LRlka~~Lr~DL~tliss------------kPkd~K 185 (233)
....+.+||++|-++..+|.++ |+.+.|.-.-..||+=.+. |..-+-+. -|-+.=
T Consensus 109 ~lDla~~Rv~~clq~v~dvrdlk~C~~gv~~Al~seDyE~AA~~IhRflsl---D~~~i~~~~~~~~~~ts~i~~~~~~L 185 (773)
T KOG0412|consen 109 ALDLAQNRVNECLQRVDDVRDLKNCIEGVDTALESEDYEKAATHIHRFLSL---DQALIESRFAKQVVPTSEISDPYETL 185 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhc---CHHHHhhhhhhccCCchhhhhHHHHH
Confidence 3455788898888877665554 5889999998888875544 54433322 132222
Q ss_pred HHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHH
Q 026780 186 QSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYA 219 (233)
Q Consensus 186 k~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~ 219 (233)
+++++=-..||. ++++.|+|+.|.++.+.++.
T Consensus 186 ~~a~e~L~~l~~--~~f~eA~r~~D~~ei~RffK 217 (773)
T KOG0412|consen 186 KEAKERLSKLFK--ERFTEAVRKQDLKEITRFFK 217 (773)
T ss_pred HHHHHHHHHHHH--HHHHHHHhcccHHHHHHHHH
Confidence 333333344444 58899999999999998864
No 21
>PF05082 Rop-like: Rop-like; InterPro: IPR007774 This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons, so are likely to play a role in this process.; PDB: 3CSX_A 2JS5_B.
Probab=48.49 E-value=45 Score=25.01 Aligned_cols=45 Identities=20% Similarity=0.378 Sum_probs=40.1
Q ss_pred HHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHH
Q 026780 161 DLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAA 206 (233)
Q Consensus 161 ~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~Aa 206 (233)
-|..+++.+.-||--|...+|-+- +.+-.+|.+.|+-+.+||.|=
T Consensus 13 KL~~~A~~~kmdLHDLaEdLP~~w-~~i~~vA~~ty~a~~~l~~ak 57 (66)
T PF05082_consen 13 KLNRKATQAKMDLHDLAEDLPTNW-EEIPEVAQKTYDAYAELDEAK 57 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHCTTTTG-GGHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHccchhH-HHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999876 779999999999999998764
No 22
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=46.55 E-value=1.2e+02 Score=24.81 Aligned_cols=48 Identities=21% Similarity=0.313 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHhhhhhHHHHhc----CChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 186 QSLKNLTGKLFQTIGNLDHAAKI----KSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 186 k~l~~La~kLF~~le~LD~AaR~----Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.....+...|+.-++.|+.|... .+......-|.-+...|.++|.+.|
T Consensus 58 ~~~~~~~~~ll~v~D~l~~a~~~~~~~~~~~~~~~g~~~~~~~l~~~L~~~G 109 (165)
T PF01025_consen 58 YALEKFLKDLLPVLDNLERALEAAKSNEEEESLLEGLEMILKQLEDILEKNG 109 (165)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHCC-SHHCTCHHHHHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 35567788899999999999975 4455666778888888888888765
No 23
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=46.09 E-value=86 Score=20.77 Aligned_cols=52 Identities=13% Similarity=0.217 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcC-ChHHHHHHHHHHHHH
Q 026780 170 RYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIK-STPEAEKYYAETVST 224 (233)
Q Consensus 170 r~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~K-n~~~a~~~Y~~tv~~ 224 (233)
|..+...+..+|+.+|+-+ .-.+|+.++--+-|...+ +...++..+..+.+.
T Consensus 1 r~~l~~~l~~L~~~~r~i~---~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 1 REALQQALAQLPERQREIF---LLRYFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHH---HHHHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHH---HHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 5678899999999887644 334555555555555544 666677777666554
No 24
>COG5420 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=45.25 E-value=71 Score=24.14 Aligned_cols=47 Identities=21% Similarity=0.330 Sum_probs=41.2
Q ss_pred HHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhc
Q 026780 161 DLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKI 208 (233)
Q Consensus 161 ~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~ 208 (233)
-|..++|..+-||-.|...+|.+- -++...|.+-|.-+-+||.+-|+
T Consensus 17 kLqsrAg~akm~LhDLAEgLP~~w-tei~~VA~kt~~~yaeLD~~k~E 63 (71)
T COG5420 17 KLQSRAGQAKMELHDLAEGLPVKW-TEIMAVAEKTFEAYAELDAAKRE 63 (71)
T ss_pred HHHHHHHHHHhhHHHHhccCCccH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999866 78999999999999999987653
No 25
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=44.88 E-value=1.3e+02 Score=22.65 Aligned_cols=66 Identities=12% Similarity=0.144 Sum_probs=40.2
Q ss_pred hhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 163 RLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 163 Rlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
......|+.|+..++.+....-.+.+.++..++-+.++..-..+++.- ..+...+.++....++++
T Consensus 4 ~~~l~~l~~d~~~l~~~~~~~~~~~~~~~r~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~~~~~~V 69 (94)
T PF05957_consen 4 KAELEQLRADLEDLARSAADLAGEKADEARDRAEEALDDARDRAEDAA-DQAREQAREAAEQTEDYV 69 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 334456788888888877655556666666666666666555554432 235555566666666554
No 26
>PRK14155 heat shock protein GrpE; Provisional
Probab=44.05 E-value=1.4e+02 Score=26.58 Aligned_cols=51 Identities=16% Similarity=0.294 Sum_probs=32.4
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCC----hHHHHHH---HHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKS----TPEAEKY---YAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn----~~~a~~~---Y~~tv~~LdevLa~l~ 233 (233)
-.+-...+++.+|+.-+++|+.|...-. ......+ ++-+.+.|..+|.+.|
T Consensus 57 ~~~~a~~~~~~~LLpV~DnLerAl~~~~~~~~~~~~~~i~~Gvemi~k~~~~~L~k~G 114 (208)
T PRK14155 57 ARAYAIQKFARDLLGAADNLGRATAASPKDSADPAVKNFIIGVEMTEKELLGAFERNG 114 (208)
T ss_pred HHHHHHHHHHHHHhhHHhhHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHHHCC
Confidence 3445667788999999999999997532 1222333 4445556666665543
No 27
>PRK14143 heat shock protein GrpE; Provisional
Probab=43.47 E-value=2.6e+02 Score=25.51 Aligned_cols=51 Identities=20% Similarity=0.258 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcC--C---hHHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIK--S---TPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~K--n---~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.+....+++++|+.-+++|+.|...- + ...-.+-|+-+.+.|..+|.+.|
T Consensus 111 ~~~~a~~~~~~~lLpV~DnLerAl~~~~~~~~~~~~l~~Gve~i~k~l~~~L~k~G 166 (238)
T PRK14143 111 LRLQLKCNTLSEILPVVDNFERARQQLKPEGEEAQALHRSYQGLYKQLVDVLKRLG 166 (238)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 344566778999999999999997632 1 12334556777777888877765
No 28
>PRK14156 heat shock protein GrpE; Provisional
Probab=43.46 E-value=2.2e+02 Score=24.79 Aligned_cols=53 Identities=15% Similarity=0.269 Sum_probs=35.6
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhcCChH-HHHHHHHHHHHHHHHHHhhhC
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTP-EAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~-~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-...+-...+++++|+.-+|+||.|....+.. .-..-++-+.+.|-.+|.+.|
T Consensus 69 e~~~~~a~~~~~~~LLpVlDnLerAl~~~~~~~~l~~Gv~mi~k~l~~~L~~~G 122 (177)
T PRK14156 69 QQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGLEMVQESLIQALKEEG 122 (177)
T ss_pred HHHHHHHHHHHHHHHhhHHhHHHHHHhCcccchhHHHHHHHHHHHHHHHHHHCC
Confidence 33445567788999999999999998754332 233445666666666666554
No 29
>PRK14147 heat shock protein GrpE; Provisional
Probab=43.03 E-value=2.2e+02 Score=24.57 Aligned_cols=53 Identities=21% Similarity=0.210 Sum_probs=34.8
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhcCCh--HHHHHHHHHHHHHHHHHHhhhC
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKIKST--PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~--~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-...+-...+++.+|+.-+++|+.|...... .....-++-+.+.|..+|.+.|
T Consensus 60 e~~~~~a~~~~~~~lLpv~DnlerAl~~~~~~~~~l~~Gv~mi~k~l~~~L~~~G 114 (172)
T PRK14147 60 EQARKFANEKLLGELLPVFDSLDAGLTAAGTEPSPLRDGLELTYKQLLKVAADNG 114 (172)
T ss_pred HHHHHHHHHHHHHHHhhhhhHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 3344556677899999999999999865322 2222334556666777776654
No 30
>PLN03184 chloroplast Hsp70; Provisional
Probab=42.31 E-value=2.6e+02 Score=28.76 Aligned_cols=74 Identities=15% Similarity=0.093 Sum_probs=47.2
Q ss_pred hhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 026780 151 DKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLS 230 (233)
Q Consensus 151 dkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa 230 (233)
....+.+.++.|..-...+|.-|..+-.-.++++|+++.++-+++.+-|+. -+..+.+..|++....++.+..
T Consensus 560 ~~~~~~eakN~lE~~iy~~r~~l~e~~~~~~~eer~~l~~~l~~~e~wL~~-------~d~~~ik~~~~~l~~~l~~l~~ 632 (673)
T PLN03184 560 EKRDAVDTKNQADSVVYQTEKQLKELGDKVPADVKEKVEAKLKELKDAIAS-------GSTQKMKDAMAALNQEVMQIGQ 632 (673)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHHHHhc-------CCHHHHHHHHHHHHHHHHHHHH
Confidence 344455566655554444444443333345888889998888888887764 3556777777777777777665
Q ss_pred h
Q 026780 231 K 231 (233)
Q Consensus 231 ~ 231 (233)
+
T Consensus 633 ~ 633 (673)
T PLN03184 633 S 633 (673)
T ss_pred H
Confidence 4
No 31
>PRK14142 heat shock protein GrpE; Provisional
Probab=42.16 E-value=1.1e+02 Score=27.79 Aligned_cols=48 Identities=15% Similarity=0.273 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 184 EKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 184 ~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.+-...+++++|+.-+++|+.|....+... .-+..+.+.|..+|.++|
T Consensus 78 ~~~A~e~~~kdLLpVlDnLERAL~~~~~~~--~~v~~I~kqL~~iLek~G 125 (223)
T PRK14142 78 ADRAKASVVSQLLGVLDDLERARKHGDLES--GPLKSVADKLDSALTGLG 125 (223)
T ss_pred HHHHHHHHHHHHhchHhHHHHHHhcccccc--HHHHHHHHHHHHHHHHCC
Confidence 445567889999999999999997543321 124556777777777664
No 32
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=42.01 E-value=1.2e+02 Score=21.18 Aligned_cols=29 Identities=7% Similarity=0.314 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHh---hhCChhHHHHHHhh
Q 026780 136 AKASAKDILNVKELI---DKKAWPYVQNDLRL 164 (233)
Q Consensus 136 IkesA~~L~~lk~lI---dkksW~~vr~~LRl 164 (233)
+.+..+.+..++..+ +...|+.++..+|.
T Consensus 7 ~~~~~~~~~~l~~~~~~~~~~d~~~l~~~~H~ 38 (90)
T PF01627_consen 7 LEEAPEDLEQLEQALQALEQEDWEELRRLAHR 38 (90)
T ss_dssp HHHHHHHHHHHHHHHCSSHHCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHH
Confidence 356677788899988 88899999988875
No 33
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=39.21 E-value=35 Score=23.13 Aligned_cols=18 Identities=22% Similarity=0.457 Sum_probs=10.2
Q ss_pred CcchhhHHHHHHHHHHHh
Q 026780 58 EPETSRRAMLGLVAAGVA 75 (233)
Q Consensus 58 ~~~~sRRa~lgl~a~~l~ 75 (233)
+.+.+||-+|.+++.++.
T Consensus 6 ~~~~~RRdFL~~at~~~g 23 (41)
T PF10399_consen 6 PVDPTRRDFLTIATSAVG 23 (41)
T ss_dssp ----HHHHHHHHHHHHHH
T ss_pred CCCchHHHHHHHHHHHHH
Confidence 356799999987664443
No 34
>PF05960 DUF885: Bacterial protein of unknown function (DUF885); InterPro: IPR010281 This family consists of hypothetical bacterial proteins.; PDB: 3O0Y_B 3U24_A 3IUK_A.
Probab=39.19 E-value=2e+02 Score=27.91 Aligned_cols=69 Identities=14% Similarity=0.225 Sum_probs=48.9
Q ss_pred hhHHHHHHhhhhh------hHHHHHHHHHh-cCChhhHHHHHHHHHHHHH-----hhhhhHHHHhc-----------CCh
Q 026780 155 WPYVQNDLRLRAS------YLRYDLNTIIS-AKPKDEKQSLKNLTGKLFQ-----TIGNLDHAAKI-----------KST 211 (233)
Q Consensus 155 W~~vr~~LRlka~------~Lr~DL~tlis-skPkd~Kk~l~~La~kLF~-----~le~LD~AaR~-----------Kn~ 211 (233)
..-+...++.-.. +|..++...+. .+++++++.+..-+.+.+. .++++-...++ -+.
T Consensus 142 ~e~~i~q~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~~l~~~~~~ai~~~v~pA~~~~~~~L~~~~~~~~~~~G~~~~ 221 (549)
T PF05960_consen 142 VERAIAQLRGFIDADPEESFLYEDFPERLAASLSEEQKEALIAQAREAIEEYVIPAYERLRDFLESEYLPAANSSGLSDL 221 (549)
T ss_dssp HHHHHHHHHHHCSS-GGCTCHHHHHHHHHCCCS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTCCCCSHHSGCGS
T ss_pred HHHHHHHHHHHHccCcccchHHHHHHHhccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCcccC
Confidence 3445666776666 89999999998 6799999999888888777 78887666652 133
Q ss_pred HHHHHHHHHHHH
Q 026780 212 PEAEKYYAETVS 223 (233)
Q Consensus 212 ~~a~~~Y~~tv~ 223 (233)
+.-+.+|+..+.
T Consensus 222 ~~G~~~Y~~~l~ 233 (549)
T PF05960_consen 222 PNGKEYYERLLR 233 (549)
T ss_dssp TTHHHHHHHHHH
T ss_pred CCcHHHHHHHHH
Confidence 456667765543
No 35
>PRK14145 heat shock protein GrpE; Provisional
Probab=39.06 E-value=2.8e+02 Score=24.64 Aligned_cols=51 Identities=12% Similarity=0.132 Sum_probs=35.3
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcC-ChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIK-STPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~K-n~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.+-...+++++|+.-+++|+.|.... +......-.+-|.+.|..+|.+.|
T Consensus 89 ~~~~a~e~~~~~LLpV~DnLerAl~~~~~~~~l~~Gv~mi~k~l~~vL~k~G 140 (196)
T PRK14145 89 MVEYGKEQVILELLPVMDNFERALASSGDYNSLKEGIELIYRQFKKILDKFG 140 (196)
T ss_pred HHHHHHHHHHHHHHhHHhHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHCC
Confidence 344566788999999999999998762 222233455666677777776654
No 36
>PRK14162 heat shock protein GrpE; Provisional
Probab=39.00 E-value=2.8e+02 Score=24.57 Aligned_cols=50 Identities=22% Similarity=0.284 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHHHhhhhhHHHHhcCChH----HHHHHHHHHHHHHHHHHhhhC
Q 026780 184 EKQSLKNLTGKLFQTIGNLDHAAKIKSTP----EAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 184 ~Kk~l~~La~kLF~~le~LD~AaR~Kn~~----~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.+-...+++.+|+.-+++||.|....... .-..=++-+.+.|..+|.+.|
T Consensus 84 ~~~a~~~~~~~LLpV~DnLerAl~~~~~~~~~~~l~~Gvemi~k~l~~vL~~~G 137 (194)
T PRK14162 84 IKYESQSLAKDVLPAMDNLERALAVKADDEAAKQLKKGVQMTLDHLVKALKDHG 137 (194)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 44556678999999999999998754322 223344556666666666654
No 37
>TIGR01042 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=38.37 E-value=1.6e+02 Score=30.51 Aligned_cols=79 Identities=18% Similarity=0.268 Sum_probs=41.6
Q ss_pred ccccccccCC--------CCHHHHHHHHHHHHHHHHHHHHHhhhC-------ChhHHHHHHhhhhhhHHHHHHHHHhcCC
Q 026780 117 PLKERFFIQP--------LSPAQAAERAKASAKDILNVKELIDKK-------AWPYVQNDLRLRASYLRYDLNTIISAKP 181 (233)
Q Consensus 117 ~lk~rf~~q~--------ls~~ea~~RIkesA~~L~~lk~lIdkk-------sW~~vr~~LRlka~~Lr~DL~tlisskP 181 (233)
++++.|..|+ -++++....++.--.=-..-+..|++. +|..+++.+ +-++.++..+=-..|
T Consensus 497 ~i~e~FLqQ~a~~~~d~~~~~~kt~~~L~~i~~~~~~~~~~~~~~~~~~~ki~~~~i~~~~----~~~~~~~~~~k~~~~ 572 (591)
T TIGR01042 497 LIKEDFLQQNGYTPYDRFCPFYKTVGMMRNMIAFYDLARQAVERTAQDDNKITWSIIKESL----GDLLYRLSSMKFEDP 572 (591)
T ss_pred HHHHHhCCCCCCCCccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCccccccHHHHHHHH----HHHHHHHHHhcCCCc
Confidence 4557787777 244444444433321112333344332 277777543 122333333322337
Q ss_pred hhhHHHHHHHHHHHHHhh
Q 026780 182 KDEKQSLKNLTGKLFQTI 199 (233)
Q Consensus 182 kd~Kk~l~~La~kLF~~l 199 (233)
++..+.+.++.++|++.|
T Consensus 573 ~~~~~~~~~~~~kl~~ei 590 (591)
T TIGR01042 573 SDGEAKIKADYEKLNEDM 590 (591)
T ss_pred cchHHHHHHHHHHHHHhh
Confidence 777788888888888875
No 38
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=37.44 E-value=44 Score=23.97 Aligned_cols=52 Identities=25% Similarity=0.279 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH-hhh-CChhHHHHHHhhhhhhHHHHHHHH
Q 026780 125 QPLSPAQAAERAKASAKDILNVKEL-IDK-KAWPYVQNDLRLRASYLRYDLNTI 176 (233)
Q Consensus 125 q~ls~~ea~~RIkesA~~L~~lk~l-Idk-ksW~~vr~~LRlka~~Lr~DL~tl 176 (233)
+++|.++.....+=...-|..++.- .+. ..+.|++.|||.=+.+|.-|-+.|
T Consensus 9 ~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 9 KGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp TT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HHHH
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCcccC
Confidence 4688999998888888888887763 333 578999999999999998876543
No 39
>PRK05685 fliS flagellar protein FliS; Validated
Probab=37.29 E-value=1.4e+02 Score=24.30 Aligned_cols=62 Identities=11% Similarity=0.259 Sum_probs=49.6
Q ss_pred hHHHHHHHHHhcC-ChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhh
Q 026780 168 YLRYDLNTIISAK-PKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKV 232 (233)
Q Consensus 168 ~Lr~DL~tlissk-Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l 232 (233)
|...++.+=+.+. |. +-+.-|+..++.+++.-..|...+|.++....-.++...|.++.+-|
T Consensus 10 Y~~~~~~~~v~tasp~---~Li~mLydgai~~l~~A~~ai~~~~~~~~~~~l~ka~~Ii~eL~~sL 72 (132)
T PRK05685 10 YQQVSVESQVSSASPH---KLIQMLYEGALSFLAQAKLAIEQGDIEAKGEYLSKAINIINGLRNSL 72 (132)
T ss_pred HHhccchhhhhcCCHH---HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 4444443444444 44 56888999999999999999999999999999999999999987654
No 40
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=37.21 E-value=1.5e+02 Score=21.56 Aligned_cols=47 Identities=21% Similarity=0.227 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
+-|+.+.+-++++-++++++=.-++++=...++...+++....++++
T Consensus 26 e~R~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~e~~~e~~ 72 (74)
T PF12732_consen 26 ETREKLKDKAEDLKDKAKDLYEEAKEKVKEKAEETADEAKEKAKELK 72 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44444444444444444444443333322233333344444444444
No 41
>PRK14164 heat shock protein GrpE; Provisional
Probab=37.12 E-value=3.1e+02 Score=24.75 Aligned_cols=49 Identities=16% Similarity=0.167 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.+-...+++++|+.-+++|+.|....+..+- -+..+.+.|..+|.+.|
T Consensus 114 ~~~~a~~~~~~~LLpVlDnLerAl~~~~~~~g--~l~~i~~~l~~vL~k~G 162 (218)
T PRK14164 114 IIETAKAGVATDLLPILDDLDLAEQHGDLNEG--PLKAFSDKLTNVLAGLK 162 (218)
T ss_pred HHHHHHHHHHHHHhhHHhHHHHHHhccccccc--HHHHHHHHHHHHHHHCC
Confidence 34455677899999999999999876544211 13446666777776654
No 42
>PRK14160 heat shock protein GrpE; Provisional
Probab=37.05 E-value=3.1e+02 Score=24.62 Aligned_cols=53 Identities=23% Similarity=0.298 Sum_probs=37.5
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhc-CChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKI-KSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~-Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
..-.+-...++.++|+.-+++|+.|... ++......-++-|.+.|..+|.+.|
T Consensus 103 e~~~~~a~e~~~~~LLpVlDnLerAl~~~~~~~~l~~Gv~mi~kql~~vL~k~G 156 (211)
T PRK14160 103 EGIYSDACEDVLKELLPVLDNLERAAAVEGSVEDLKKGIEMTVKQFKTSLEKLG 156 (211)
T ss_pred HHHHHHHHHHHHHHHhhHHhHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHCC
Confidence 3445566778899999999999999875 3333344556666777777777665
No 43
>PRK14146 heat shock protein GrpE; Provisional
Probab=37.04 E-value=2.2e+02 Score=25.49 Aligned_cols=53 Identities=17% Similarity=0.209 Sum_probs=35.5
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhcCCh----HHHHHHHHHHHHHHHHHHhhhC
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKIKST----PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~----~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.-.+-...+++++|+.-+++|+.|....+. ..-..=++-+.+.|..+|.+.|
T Consensus 96 e~~~~~a~e~~~~~lLpv~DnlerAl~~~~~~~~~~~l~~Gv~mi~k~l~~~L~k~G 152 (215)
T PRK14146 96 VSIRKEAVKSLVSGFLNPIDNLERVGATQNQSEELKPFVEGVKMILKEFYSVLEKSN 152 (215)
T ss_pred HHHHHHHHHHHHHHHhhHHhHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHCc
Confidence 3344556778899999999999999865322 2223345566677777777654
No 44
>PF10167 NEP: Uncharacterised conserved protein; InterPro: IPR019320 This entry represents the uncharacterised protein family UPF0402. It contains a characteristic NEP sequence motif. Their function is not known.
Probab=37.04 E-value=2.3e+02 Score=23.18 Aligned_cols=88 Identities=17% Similarity=0.230 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcCCh--hhHHHHHHHHHHHHHhhhhhHHHHh-
Q 026780 131 QAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPK--DEKQSLKNLTGKLFQTIGNLDHAAK- 207 (233)
Q Consensus 131 ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlisskPk--d~Kk~l~~La~kLF~~le~LD~AaR- 207 (233)
+...++++..+++.++=-++..+ |+=-||+=---+-.++|+ +.|..+.++..++-....++|||..
T Consensus 5 ~~~~~~~~~~~~~se~i~~~ANE-----------PSlgLYrlQeHvrkslP~lv~~k~~v~~~~~~~~g~~~D~eya~~a 73 (118)
T PF10167_consen 5 ELEDKVKKVTERISENIHIVANE-----------PSLGLYRLQEHVRKSLPKLVELKKEVQELSQELQGACYDLEYAISA 73 (118)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcC-----------chHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccceecHHHHHHH
Confidence 45667777777776543333222 333445544555566775 7888999999999999999999985
Q ss_pred cCChHHHHHHHHHHHHHHHHHH
Q 026780 208 IKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 208 ~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
-|+-.++...+.++...|+.-+
T Consensus 74 VksM~~a~~~F~nI~~lL~~si 95 (118)
T PF10167_consen 74 VKSMKKAESSFSNIQELLKNSI 95 (118)
T ss_pred HHHHHhhHHHHHHHHHHHHHHH
Confidence 4677888888888888888554
No 45
>PF01093 Clusterin: Clusterin; InterPro: IPR000753 Clusterin is a vertebrate glycoprotein [], the exact function of which is not yet clear. Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is further glycosylated and proteolytically cleaved into alpha- and beta-subunits, held together by disulphide bonds. External sCLU is an 80kDa protein and may act as a molecular chaperone, scavenging denatured proteins outside cells following specific stress-induced injury such as heat shock. sCLU possesses nonspecific binding activity to hydrophobic domains of various proteins in vitro []. A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death. Clusterin is synthesized as a precursor polypeptide of about 400 amino acids which is post-translationally cleaved to form two subunits of about 200 amino acids each. The two subunits are linked by five disulphide bonds to form an antiparallel ladder-like structure []. In each of the mature subunits the five cysteines that are involved in disulphide bonds are clustered in domains of about 30 amino acids located in the central part of the subunits. This entry represents the clusterin precursor and related proteins.; GO: 0008219 cell death
Probab=36.36 E-value=72 Score=31.68 Aligned_cols=74 Identities=14% Similarity=0.212 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhcC--ChhhHHHHHHHHHHHHHhhhhhHHHHhc-
Q 026780 132 AAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAK--PKDEKQSLKNLTGKLFQTIGNLDHAAKI- 208 (233)
Q Consensus 132 a~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlissk--Pkd~Kk~l~~La~kLF~~le~LD~AaR~- 208 (233)
--.-|+.+-.++..||.++++.. .+-..|+.++ .+++|+++.+++++....|++-..-+..
T Consensus 14 vdeEik~Al~GvKqMK~~Mek~e----------------eeh~~Lm~tL~k~kk~KeeAl~l~~e~e~kLee~e~~Cn~s 77 (436)
T PF01093_consen 14 VDEEIKNALNGVKQMKTMMEKTE----------------EEHKELMKTLEKSKKEKEEALKLANEVEEKLEEEEEVCNES 77 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44568888888999999998764 3445566665 6799999999999999999887665431
Q ss_pred --CChHHHHHHHHHH
Q 026780 209 --KSTPEAEKYYAET 221 (233)
Q Consensus 209 --Kn~~~a~~~Y~~t 221 (233)
-.-.+++-|.++|
T Consensus 78 m~~lWeECkpCL~~t 92 (436)
T PF01093_consen 78 MMALWEECKPCLKQT 92 (436)
T ss_pred HHHHHHHHHHHHHHH
Confidence 2344555555444
No 46
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=36.18 E-value=1.1e+02 Score=22.43 Aligned_cols=29 Identities=28% Similarity=0.276 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhhhC
Q 026780 125 QPLSPAQAAERAKASAKDILNVKELIDKK 153 (233)
Q Consensus 125 q~ls~~ea~~RIkesA~~L~~lk~lIdkk 153 (233)
..+|++|-..||-.-..+|..++.-|.+|
T Consensus 19 s~lSv~EL~~RIa~L~aEI~R~~~~~~~K 47 (59)
T PF06698_consen 19 SLLSVEELEERIALLEAEIARLEAAIAKK 47 (59)
T ss_pred hhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35899999999999999999998888654
No 47
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=36.16 E-value=3.3e+02 Score=27.69 Aligned_cols=90 Identities=9% Similarity=0.104 Sum_probs=50.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHhc----CChhhHHHHHHHHHHHHHhhhh
Q 026780 126 PLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISA----KPKDEKQSLKNLTGKLFQTIGN 201 (233)
Q Consensus 126 ~ls~~ea~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tliss----kPkd~Kk~l~~La~kLF~~le~ 201 (233)
.++.+|-...++++.+.. .++....-+.+.+.++..|-+...+++.. ++.++|+.+..+-+++-+-|+.
T Consensus 481 ~ls~~ei~~~~~~~~~~~-------~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~~~~~~~~~l~~ 553 (595)
T PRK01433 481 GIDKTEIDIMLENAYKNA-------KIDYTTRLLQEAVIEAEALIFNIERAIAELTTLLSESEISIINSLLDNIKEAVHA 553 (595)
T ss_pred CCCHHHHHHHHHHHHhhh-------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHhc
Confidence 367777766666654221 12222223333444555566666666653 5888888888887777776653
Q ss_pred hHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 202 LDHAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 202 LD~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
.|....++..++....++++|
T Consensus 554 -------~~~~~~~~~~~~~~~~~~~~~ 574 (595)
T PRK01433 554 -------RDIILINNSIKEFKSKIKKSM 574 (595)
T ss_pred -------CCHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555533
No 48
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=34.17 E-value=51 Score=24.31 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=9.0
Q ss_pred chhhHHHHHHHHH
Q 026780 60 ETSRRAMLGLVAA 72 (233)
Q Consensus 60 ~~sRRa~lgl~a~ 72 (233)
..|||-+|-++.+
T Consensus 8 ~~sRR~Flk~lg~ 20 (66)
T TIGR02811 8 DPSRRDLLKGLGV 20 (66)
T ss_pred CccHHHHHHHHHH
Confidence 4599998775543
No 49
>PRK14140 heat shock protein GrpE; Provisional
Probab=33.46 E-value=3.4e+02 Score=23.96 Aligned_cols=53 Identities=25% Similarity=0.330 Sum_probs=35.1
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHH-HH---HHHHHHHHHHHHHHhhhC
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPE-AE---KYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~-a~---~~Y~~tv~~LdevLa~l~ 233 (233)
....+-...++.++|+.-+++|+.|....+... .. .-++-+.+.|..+|.+.|
T Consensus 79 ~~~~~~a~~~~~~~LLpvlDnLerAl~~~~~~~~~~~i~~Gv~mi~k~l~~~L~k~G 135 (191)
T PRK14140 79 EAAEKYRAQSLASDLLPALDNFERALQIEADDEQTKSLLKGVEMVHRQLLEALKKEG 135 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 334455677889999999999999997643322 22 234455666666666654
No 50
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=33.16 E-value=52 Score=22.32 Aligned_cols=20 Identities=30% Similarity=0.620 Sum_probs=13.0
Q ss_pred cchhhHHHHHHHHHHHhhch
Q 026780 59 PETSRRAMLGLVAAGVASGS 78 (233)
Q Consensus 59 ~~~sRRa~lgl~a~~l~~~~ 78 (233)
+.++||.+|.++..+.+++.
T Consensus 4 Pdm~RR~lmN~ll~Gava~~ 23 (39)
T PF08802_consen 4 PDMSRRQLMNLLLGGAVAVP 23 (39)
T ss_dssp --HHHHHHHHHHHHHHHHHH
T ss_pred CChhHHHHHHHHHHhhHHHH
Confidence 45899999887775555333
No 51
>PRK14149 heat shock protein GrpE; Provisional
Probab=32.61 E-value=3.2e+02 Score=24.19 Aligned_cols=62 Identities=19% Similarity=0.214 Sum_probs=38.6
Q ss_pred HHHHHHhcC----ChhhHHHHHHHHHHHHHhhhhhHHHHhcCCh----HHHHHHHHHHHHHHHHHHhhhC
Q 026780 172 DLNTIISAK----PKDEKQSLKNLTGKLFQTIGNLDHAAKIKST----PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 172 DL~tlissk----Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~----~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
|+.+.-... ....+-...+++++|+.-+++|+.|....+. .....=++-|.+.|..+|.+.|
T Consensus 65 efEN~rKR~~kE~e~~~~~a~~~~~~~LLpVlDnLerAl~~~~~~~~~~~l~~Gv~mi~k~l~~vL~k~G 134 (191)
T PRK14149 65 DFENVKKRLERDKSMALEYAYEKIALDLLPVIDALLGALKSAAEVDKESALTKGLELTMEKLHEVLARHG 134 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHCC
Confidence 555553332 3344556677899999999999999875432 2223344456666666666654
No 52
>PRK14139 heat shock protein GrpE; Provisional
Probab=31.99 E-value=3.5e+02 Score=23.73 Aligned_cols=51 Identities=16% Similarity=0.148 Sum_probs=35.5
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCCh--HHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKST--PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~--~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.+-...++.++|+.-+|+|+.|....+. .....=++-+.+.|..+|.+.|
T Consensus 76 ~~~~a~~~~~~~LLpv~DnLerAl~~~~~~~~~l~~Gv~mi~k~l~~vL~k~G 128 (185)
T PRK14139 76 AHKFAIESFAESLLPVKDSLEAALADESGDLEKLREGVELTLKQLTSAFEKGR 128 (185)
T ss_pred HHHHHHHHHHHHHhhHHhHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 34445667889999999999999976543 2233445567777777777654
No 53
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=31.02 E-value=2e+02 Score=22.32 Aligned_cols=26 Identities=19% Similarity=0.156 Sum_probs=18.1
Q ss_pred HHhcCChHHHHHHHHHHHHHHHHHHh
Q 026780 205 AAKIKSTPEAEKYYAETVSTLNDVLS 230 (233)
Q Consensus 205 AaR~Kn~~~a~~~Y~~tv~~LdevLa 230 (233)
|+..+|..++...|..+.+.||....
T Consensus 38 ai~~~~~~~a~~~~~~a~s~iDka~~ 63 (88)
T PRK00239 38 AIAAGDKEAAEEALKAAQSKIDKAAS 63 (88)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 44457777788888888777776543
No 54
>PRK14158 heat shock protein GrpE; Provisional
Probab=30.54 E-value=3.8e+02 Score=23.69 Aligned_cols=51 Identities=20% Similarity=0.161 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCCh---HHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKST---PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~---~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
-.+-...+++++|+.-+|+|+.|....+. .....=++-+.+.|..+|.+.|
T Consensus 84 ~~~~a~~~~~~~lLpV~DnLerAl~~~~~~~~~~i~~Gv~mi~k~l~~vLek~G 137 (194)
T PRK14158 84 LLKYGNESLILEILPAVDNMERALDHADEESMSAIIEGIRMTLSMLLSTLKKFG 137 (194)
T ss_pred HHHHHHHHHHHHHHhHHhHHHHHHhccCcchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 34456677899999999999999875432 2233444555666666666544
No 55
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=30.24 E-value=2.1e+02 Score=22.24 Aligned_cols=26 Identities=15% Similarity=0.216 Sum_probs=17.4
Q ss_pred HHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 204 HAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 204 ~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
.|+..+|..+++..|.++.+.||...
T Consensus 37 ~ai~~~d~~~a~~~l~~a~s~iDkaa 62 (87)
T TIGR00029 37 AAIAAGDKDKAQEAFKEAAKKLDRAA 62 (87)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34444666777777777777777654
No 56
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=29.77 E-value=1.8e+02 Score=21.09 Aligned_cols=29 Identities=14% Similarity=0.123 Sum_probs=13.6
Q ss_pred hhCChhHHHHHHhhhhhhHHHHHHHHHhc
Q 026780 151 DKKAWPYVQNDLRLRASYLRYDLNTIISA 179 (233)
Q Consensus 151 dkksW~~vr~~LRlka~~Lr~DL~tliss 179 (233)
..++=.++|..|+.....++..+..+...
T Consensus 20 aP~sG~e~R~~l~~~~~~~~~~~~~~~~~ 48 (74)
T PF12732_consen 20 APKSGKETREKLKDKAEDLKDKAKDLYEE 48 (74)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444445555555444444444444433
No 57
>KOG4519 consensus Phosphomevalonate kinase [Lipid transport and metabolism]
Probab=29.63 E-value=1.4e+02 Score=29.42 Aligned_cols=68 Identities=18% Similarity=0.230 Sum_probs=50.0
Q ss_pred HHHHHHHHHhhhCChhHHHHHHhhhhhh---------------HHHHHHHHH-hcCChhhH--HHHHHHHHHHHHhhhhh
Q 026780 141 KDILNVKELIDKKAWPYVQNDLRLRASY---------------LRYDLNTII-SAKPKDEK--QSLKNLTGKLFQTIGNL 202 (233)
Q Consensus 141 ~~L~~lk~lIdkksW~~vr~~LRlka~~---------------Lr~DL~tli-sskPkd~K--k~l~~La~kLF~~le~L 202 (233)
-=+.+|...|.++.|+.+++.-+++.++ |-.-.++-- +..|++.| +.+-+++.+|-+.+.+|
T Consensus 245 ~~~~el~~~V~k~~W~~~~~~f~LP~~~~L~mGd~~gGSsTp~mV~kVk~Wq~s~~pe~~k~~~~lddansr~~~~l~kl 324 (459)
T KOG4519|consen 245 LPLNELIGTVLKGKWDNKRTEFSLPPLMNLFMGDGSGGSSTPSMVGKVKKWQMSDPPEARKNWQNLDDANSRLETKLNKL 324 (459)
T ss_pred ChhHHHHHHhhhhhcccccccccCCceeeeeeecCCCCCCcHHHHHHHHHHhhcCChhHhhhhcchhhHHHHHHhhhhhh
Confidence 3345788999999999999999999875 233333333 33466665 67778888898888888
Q ss_pred HHHHhc
Q 026780 203 DHAAKI 208 (233)
Q Consensus 203 D~AaR~ 208 (233)
|.-+++
T Consensus 325 ~~l~~~ 330 (459)
T KOG4519|consen 325 SKLAKD 330 (459)
T ss_pred hHhhhh
Confidence 887776
No 58
>PRK14144 heat shock protein GrpE; Provisional
Probab=29.20 E-value=4.1e+02 Score=23.65 Aligned_cols=51 Identities=20% Similarity=0.321 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCCh---HHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKST---PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~---~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
..+-...+++++|+.-+++|+.|...... .....=++-+.+.|..+|.+.|
T Consensus 89 ~~~~a~~~~~~~LLpV~DnLerAl~~~~~~~~~~i~~Gv~mi~k~l~~~L~k~G 142 (199)
T PRK14144 89 AHKYGVEKLISALLPVVDSLEQALQLADKNSDPSMHEGLELTMKLFLDALQKFD 142 (199)
T ss_pred HHHHHHHHHHHHHhhHHhHHHHHHHcccccchhHHHHHHHHHHHHHHHHHHHCC
Confidence 34455677899999999999999864221 2334455566666777766654
No 59
>COG5057 LAG1 Phosphotyrosyl phosphatase activator [Cell division and chromosome partitioning / Signal transduction mechanisms]
Probab=29.04 E-value=59 Score=31.24 Aligned_cols=41 Identities=20% Similarity=0.305 Sum_probs=25.7
Q ss_pred HHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhh
Q 026780 192 TGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKV 232 (233)
Q Consensus 192 a~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l 232 (233)
+..+++.|-+||.+++.+..++...-|...+..+..||++|
T Consensus 31 y~ri~~fi~~l~~sik~~~~~d~~~~~Sssv~~m~~vL~ri 71 (353)
T COG5057 31 YARIYNFILDLDESIKGCSDSDYHSEQSSSVNHMMNVLDRI 71 (353)
T ss_pred HHHHHHHHHHHHHHhcCCCCCcccchhHHHHHHHHHHHHHH
Confidence 45566666666666666666655555666666666666654
No 60
>PRK14161 heat shock protein GrpE; Provisional
Probab=28.91 E-value=3.9e+02 Score=23.24 Aligned_cols=53 Identities=17% Similarity=0.161 Sum_probs=34.9
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhcCChH------HHHHHHHHHHHHHHHHHhhhC
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTP------EAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~------~a~~~Y~~tv~~LdevLa~l~ 233 (233)
..-.+-...+++++|+.-+++|+.|....... ....=.+-|.+.|..+|.+.|
T Consensus 61 ~~~~~~a~~~~~~~LLpv~DnlerAl~~~~~~~~~~~~~~~~Gv~mi~k~l~~vL~~~G 119 (178)
T PRK14161 61 DEAKDYAIATFAKELLNVSDNLSRALAHKPANSDVEVTNIIAGVQMTKDELDKVFHKHH 119 (178)
T ss_pred HHHHHHHHHHHHHHHhhHHhHHHHHHhcCccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 44455667788999999999999998754321 222334455666666766654
No 61
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=28.40 E-value=1.5e+02 Score=26.54 Aligned_cols=33 Identities=15% Similarity=0.236 Sum_probs=25.0
Q ss_pred CCCcccccccccCCCCHHHHHHHHHHHHHHHHH
Q 026780 113 DLDLPLKERFFIQPLSPAQAAERAKASAKDILN 145 (233)
Q Consensus 113 dl~l~lk~rf~~q~ls~~ea~~RIkesA~~L~~ 145 (233)
|+....+-.||.++=.|++.+..+.++-++...
T Consensus 199 d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~ 231 (274)
T PF03401_consen 199 DIVFGSWRGLFAPKGTPDEIVDKLADAIKKALE 231 (274)
T ss_dssp TG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT
T ss_pred ceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhC
Confidence 566667788899999999999999998877763
No 62
>PRK14148 heat shock protein GrpE; Provisional
Probab=28.36 E-value=4.2e+02 Score=23.45 Aligned_cols=52 Identities=21% Similarity=0.300 Sum_probs=34.1
Q ss_pred hhhHHHHHHHHHHHHHhhhhhHHHHhcCCh-H---HHHHHHHHHHHHHHHHHhhhC
Q 026780 182 KDEKQSLKNLTGKLFQTIGNLDHAAKIKST-P---EAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 182 kd~Kk~l~~La~kLF~~le~LD~AaR~Kn~-~---~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.-.+-...+++++|+.-+++|+.|...... . .-..=++-+.+.|..+|.+.|
T Consensus 83 ~~~~~a~~~~~~~LLpV~DnlerAl~~~~~~~~~~~l~~Gv~mi~k~l~~vL~k~G 138 (195)
T PRK14148 83 NARKFGIEKFAKELLPVIDSIEQALKHEVKLEEAIAMKEGIELTAKMLVDILKKNG 138 (195)
T ss_pred HHHHHHHHHHHHHHhhHHhHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 344455668899999999999999875322 2 223344456666667766654
No 63
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=27.69 E-value=2.8e+02 Score=21.22 Aligned_cols=108 Identities=10% Similarity=0.116 Sum_probs=59.5
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHH-HHHHHhhhCC---hhHHHHHHhhhhhhHHHHHHHHHhc-CChhhHHHHHHH---H
Q 026780 121 RFFIQPLSPAQAAERAKASAKDIL-NVKELIDKKA---WPYVQNDLRLRASYLRYDLNTIISA-KPKDEKQSLKNL---T 192 (233)
Q Consensus 121 rf~~q~ls~~ea~~RIkesA~~L~-~lk~lIdkks---W~~vr~~LRlka~~Lr~DL~tliss-kPkd~Kk~l~~L---a 192 (233)
.+|-..+.+-..+..++....++. .+..++-..+ =......++.....+..-+..+-.. ..+++|+.+.++ .
T Consensus 39 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (181)
T PF12729_consen 39 EIYENNLPSIELLNDIRSNLQRIRRALRRYLLATDPEERQEIEKEIDEARAEIDEALEEYEKLILSPEEKQLLEEFKEAW 118 (181)
T ss_pred HHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 345555666667777777777776 5666663322 2222223333333333334444333 234455544443 4
Q ss_pred HHHHHhhhhhHHHHhcCChHHHHHHHHHHH-HHHHHH
Q 026780 193 GKLFQTIGNLDHAAKIKSTPEAEKYYAETV-STLNDV 228 (233)
Q Consensus 193 ~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv-~~Ldev 228 (233)
+.+.+..+++=..++.++..++...|..-. ..++++
T Consensus 119 ~~y~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 155 (181)
T PF12729_consen 119 KAYRKLRDQVIELAKSGDNDEARAILNGEARPAFDEL 155 (181)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHhHHHHHHHH
Confidence 566666677777888899888877776544 444444
No 64
>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]
Probab=27.10 E-value=2e+02 Score=24.53 Aligned_cols=58 Identities=19% Similarity=0.225 Sum_probs=30.7
Q ss_pred HHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcC--ChHHHHHHHHHHHHHHHHHH
Q 026780 171 YDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIK--STPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 171 ~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~K--n~~~a~~~Y~~tv~~LdevL 229 (233)
.|+++||.++|.++--+-..|.+ +...=++.+..+.++ =+.+.++...+..+.|.++.
T Consensus 70 kqId~LIdsLP~~~~~~e~Ql~~-i~kLq~en~e~~~el~~~v~~~e~Ll~~vq~~le~~a 129 (139)
T KOG1510|consen 70 KQIDTLIDSLPGEEGSAEAQLEK-IKKLQEENEEVALELEELVSKGEKLLEQVQSLLEDIA 129 (139)
T ss_pred HHHHHHHHhCCCcccCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999998654222222222 333334444444332 34455666666666665553
No 65
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=26.72 E-value=6.4e+02 Score=25.88 Aligned_cols=49 Identities=18% Similarity=0.167 Sum_probs=31.5
Q ss_pred CChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhh
Q 026780 153 KAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGN 201 (233)
Q Consensus 153 ksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~ 201 (233)
+...+.+|.|..-...+|.-|..+-...++++|+.+.++-+++.+-+++
T Consensus 564 ~~~~eakN~lEs~iy~~r~~l~e~~~~~s~~ere~i~~~l~~~~~WL~~ 612 (663)
T PTZ00400 564 KELVDAKNEAETLIYSVEKQLSDLKDKISDADKDELKQKITKLRSTLSS 612 (663)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHHHHhc
Confidence 3444566666655555555554433345888889998888888777764
No 66
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.19 E-value=1.3e+02 Score=28.70 Aligned_cols=56 Identities=14% Similarity=0.151 Sum_probs=40.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHH---HHHHHhhhCChhH
Q 026780 95 PPPPSGGLPGTLNSDEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDIL---NVKELIDKKAWPY 157 (233)
Q Consensus 95 ~P~ps~~~~Gt~~~~eardl~l~lk~rf~~q~ls~~ea~~RIkesA~~L~---~lk~lIdkksW~~ 157 (233)
|=.|+...-|.. .-...+..||.++-.|.|-..++.+..+.++ ++++.+++.+|..
T Consensus 231 pdvPT~~E~G~~-------~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s~e~~~~~~~~~~~~ 289 (319)
T COG3181 231 PDVPTLKEQGYD-------VVMSIWRGVFAPAGTPDEIIAKLSAALKKALASPEWQKRLKELGLVP 289 (319)
T ss_pred CCCCChHhcCCc-------eeeeeeeEEEeCCCCCHHHHHHHHHHHHHHhcCHHHHHHHHhcCCCC
Confidence 344666655663 3356678889999999999999999988887 4555666666654
No 67
>PRK13411 molecular chaperone DnaK; Provisional
Probab=25.86 E-value=7.3e+02 Score=25.39 Aligned_cols=72 Identities=13% Similarity=-0.006 Sum_probs=38.5
Q ss_pred ChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 026780 154 AWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLS 230 (233)
Q Consensus 154 sW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa 230 (233)
.+.+.+|.|..-...+|.-|...-..+++++|+.+.+.-+++.+-|++ +. .+..+-++.+++....++.++.
T Consensus 526 ~~~eakN~lEs~iy~~r~~l~~~~~~~~~~er~~i~~~l~~~~~wL~~-~~----~~~~~~~~~~~el~~~~~~i~~ 597 (653)
T PRK13411 526 QLIELKNQADSLLYSYESTLKENGELISEELKQRAEQKVEQLEAALTD-PN----ISLEELKQQLEEFQQALLAIGA 597 (653)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHhc-CC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 334455555544444444443322234788888888888888887765 11 2344444444444444444443
No 68
>PRK07502 cyclohexadienyl dehydrogenase; Validated
Probab=25.83 E-value=1.6e+02 Score=26.47 Aligned_cols=66 Identities=15% Similarity=0.297 Sum_probs=53.0
Q ss_pred hhhhhhHHHHHHHHHhcCCh-------hhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 163 RLRASYLRYDLNTIISAKPK-------DEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 163 Rlka~~Lr~DL~tlisskPk-------d~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
+...+-+ .|+..|.++-|. .-|+.+.+.-++|-+.++++=.+.+++|..+-+++++++...-+.+.
T Consensus 217 ~~~~~gf-rd~tRia~~~~~~w~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~d~~~l~~~~~~~~~~r~~~~ 289 (307)
T PRK07502 217 KYSASGF-RDFTRIAASDPTMWRDVFLHNKDAVLEMLGRFTEDLAALQRAIRWGDGDALFDLFTRTRAIRRGII 289 (307)
T ss_pred Hhccccc-ccccccccCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 3334433 568888887777 56677888889999999999999999999999999999888777653
No 69
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=25.67 E-value=4.5e+02 Score=22.94 Aligned_cols=52 Identities=23% Similarity=0.360 Sum_probs=33.1
Q ss_pred hhhHHHHHHHHHHHHHhhhhhHHHHhc-CChHHH----HHHHHHHHHHHHHHHhhhC
Q 026780 182 KDEKQSLKNLTGKLFQTIGNLDHAAKI-KSTPEA----EKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 182 kd~Kk~l~~La~kLF~~le~LD~AaR~-Kn~~~a----~~~Y~~tv~~LdevLa~l~ 233 (233)
+..+-.+.+++.+|..-+++|+.|... ++.... .+=++-|...|.++|.+.|
T Consensus 79 ~~~k~a~e~~~~dlLpviDnlerAl~~~~~~~d~~~~l~~Gvem~~~~l~~~L~k~G 135 (193)
T COG0576 79 EAKKYAIEKFAKDLLPVIDNLERALEAAEDDKDPEKALLEGVEMTLDQLLDALEKLG 135 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 345567788899999999999999655 222222 2334555555666665543
No 70
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=25.60 E-value=56 Score=19.86 Aligned_cols=15 Identities=47% Similarity=0.328 Sum_probs=10.1
Q ss_pred hhhHHHHHHHHHHHh
Q 026780 61 TSRRAMLGLVAAGVA 75 (233)
Q Consensus 61 ~sRRa~lgl~a~~l~ 75 (233)
.|||.+|-..++..+
T Consensus 2 ~sRR~fLk~~~a~~a 16 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAA 16 (26)
T ss_pred CcHHHHHHHHHHHHH
Confidence 489998875554443
No 71
>PRK14163 heat shock protein GrpE; Provisional
Probab=25.46 E-value=5e+02 Score=23.40 Aligned_cols=47 Identities=15% Similarity=0.302 Sum_probs=33.9
Q ss_pred hHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 184 EKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 184 ~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.+-...++.++|+.-+++|+.|....+ ...-++-+.+.|..+|.+.|
T Consensus 85 ~~~a~~~~~~~LLpVlDnLerAl~~~~---l~~Gv~mi~k~l~~~L~k~G 131 (214)
T PRK14163 85 KEIAVANLLSELLPVLDDVGRAREHGE---LVGGFKSVAESLETTVAKLG 131 (214)
T ss_pred HHHHHHHHHHHHhhhHhHHHHHHhchh---HHHHHHHHHHHHHHHHHHCC
Confidence 344566788999999999999987642 33445666777777777654
No 72
>PF12805 FUSC-like: FUSC-like inner membrane protein yccS
Probab=25.37 E-value=3.3e+02 Score=24.42 Aligned_cols=91 Identities=21% Similarity=0.175 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhCChhHHHHHHhhhhhhHHHHHHHHHh----cCChhhHHHHHHHHHHHHHhhhhhHHHHhc
Q 026780 133 AERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIIS----AKPKDEKQSLKNLTGKLFQTIGNLDHAAKI 208 (233)
Q Consensus 133 ~~RIkesA~~L~~lk~lIdkksW~~vr~~LRlka~~Lr~DL~tlis----skPkd~Kk~l~~La~kLF~~le~LD~AaR~ 208 (233)
-+++-.+-.+...+.+..+ =+++...+|.-..-+-.++..+.. .+|-..+..+.....++-+.++.+-.. ..
T Consensus 185 ~E~~~as~~~y~~l~~~f~---~~~~l~~~~~~l~~~a~~l~~ia~ai~~~~~~~~~~~l~~~l~~l~~~l~~~~~~-~~ 260 (284)
T PF12805_consen 185 FERALASHYDYEELREQFK---HSDVLFRFQRLLEQLAQALRQIAQAILRGRPYHHRNRLKRALEALEESLEFLRQQ-DQ 260 (284)
T ss_pred HHHHHhccccHHHHHHHhc---CChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHh-cC
Confidence 3344444334444444332 233333333333334444444332 234334455555555555555554444 33
Q ss_pred CChHHHHHHHHHHHHHHHH
Q 026780 209 KSTPEAEKYYAETVSTLND 227 (233)
Q Consensus 209 Kn~~~a~~~Y~~tv~~Lde 227 (233)
....++.....+....|.+
T Consensus 261 ~~~~~~~~~l~~l~~~l~~ 279 (284)
T PF12805_consen 261 PENREALLALRNLLDNLRN 279 (284)
T ss_pred ccCHHHHHHHHHHHHHHHH
Confidence 4444444444444444443
No 73
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=25.32 E-value=1.8e+02 Score=28.42 Aligned_cols=99 Identities=9% Similarity=0.073 Sum_probs=50.5
Q ss_pred CCcccccc---cccCCCCHHHHHHHHHHHHHHH----H--HHHHHh--hhCChhHHHHHHhhhhhhHH--HHHHHHHhcC
Q 026780 114 LDLPLKER---FFIQPLSPAQAAERAKASAKDI----L--NVKELI--DKKAWPYVQNDLRLRASYLR--YDLNTIISAK 180 (233)
Q Consensus 114 l~l~lk~r---f~~q~ls~~ea~~RIkesA~~L----~--~lk~lI--dkksW~~vr~~LRlka~~Lr--~DL~tlissk 180 (233)
+--++++| |.+.++++++...+++.-+++. . .++.++ -..++..+.+.|-.-..|.. .+...|....
T Consensus 164 l~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~~~It~~~V~~l~ 243 (451)
T PRK06305 164 IPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGLFPKSLDPDSVAKAL 243 (451)
T ss_pred cchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHH
Confidence 43457777 6888999999988888765542 1 122222 12344444444432221100 0111111101
Q ss_pred ChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHH
Q 026780 181 PKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVS 223 (233)
Q Consensus 181 Pkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~ 223 (233)
+ ...=+++-+|-.|++.+|..++...|.+...
T Consensus 244 ~-----------~~~~~~vf~L~~ai~~~d~~~al~~l~~L~~ 275 (451)
T PRK06305 244 G-----------LLSQDSLYTLDEAITTQNYAQALEPVTDAMN 275 (451)
T ss_pred C-----------CCCHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 1 1111234455568888888888888766554
No 74
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=24.71 E-value=3.3e+02 Score=24.22 Aligned_cols=66 Identities=15% Similarity=0.136 Sum_probs=52.0
Q ss_pred hhhhhhHHHHHHHHHhcCCh-------hhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 026780 163 RLRASYLRYDLNTIISAKPK-------DEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVL 229 (233)
Q Consensus 163 Rlka~~Lr~DL~tlisskPk-------d~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevL 229 (233)
+.-.+- ++|+.+|.++=|. .-|+.+.+.-.+|-+.+++|=.+.+++|..+-++.++++...-++++
T Consensus 206 ~~~~~g-frd~tRia~~~p~~w~~i~~~N~~~i~~~l~~~~~~l~~~~~~l~~~d~~~l~~~~~~~~~~r~~~~ 278 (279)
T PRK07417 206 NLASSG-FADTSRVGGGNPELGVMMAEYNRAALLRSLASYRQSLDQLEELIEQENWSALEQKLEQTQELRPNFL 278 (279)
T ss_pred hhccCc-ccccccccCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhh
Confidence 344443 4488888877664 45677888889999999999999999999999999998887776654
No 75
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=24.37 E-value=1.4e+02 Score=23.73 Aligned_cols=32 Identities=16% Similarity=0.223 Sum_probs=25.0
Q ss_pred HHHHHHHhcCChhhHHHHHHHHHHHHHhhhhh
Q 026780 171 YDLNTIISAKPKDEKQSLKNLTGKLFQTIGNL 202 (233)
Q Consensus 171 ~DL~tlisskPkd~Kk~l~~La~kLF~~le~L 202 (233)
.+|-.+...+|+++++.+.+..+...+.+|+|
T Consensus 90 ~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~ 121 (135)
T PRK09706 90 KELLELFDALPESEQDAQLSEMRARVENFNKL 121 (135)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45666788889888888888888877777765
No 76
>cd00446 GrpE GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent.
Probab=23.83 E-value=3.9e+02 Score=21.53 Aligned_cols=51 Identities=24% Similarity=0.312 Sum_probs=35.2
Q ss_pred hhHHHHHHHHHHHHHhhhhhHHHHhcCCh----HHHHHHHHHHHHHHHHHHhhhC
Q 026780 183 DEKQSLKNLTGKLFQTIGNLDHAAKIKST----PEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 183 d~Kk~l~~La~kLF~~le~LD~AaR~Kn~----~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
..+.....+..+|..-+++|+.|...-.. ..-.+-++-+.+.|.++|.+.|
T Consensus 29 ~~~~~~~~~~~~ll~v~D~le~a~~~~~~~~~~~~~~~g~~~i~~~l~~~L~~~G 83 (137)
T cd00446 29 ARKYAIEKFAKDLLPVLDNLERALEAAKKEEELKNLVEGVEMTLKQLLDVLEKHG 83 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 34456777889999999999999875432 2344555667777777776654
No 77
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=23.63 E-value=2.9e+02 Score=23.16 Aligned_cols=26 Identities=15% Similarity=0.417 Sum_probs=20.4
Q ss_pred HHHHHhcCChhhHHHHHHHHHHHHHh
Q 026780 173 LNTIISAKPKDEKQSLKNLTGKLFQT 198 (233)
Q Consensus 173 L~tlisskPkd~Kk~l~~La~kLF~~ 198 (233)
|+.-...+|+++|+++.+=+++.|++
T Consensus 10 L~~~L~~lp~~e~~e~l~~Y~e~f~d 35 (181)
T PF08006_consen 10 LEKYLKKLPEEEREEILEYYEEYFDD 35 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 44444567999999999999999986
No 78
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=23.49 E-value=3.1e+02 Score=21.64 Aligned_cols=47 Identities=11% Similarity=0.103 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhh
Q 026780 186 QSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKV 232 (233)
Q Consensus 186 k~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l 232 (233)
+-+.-|+..+...++..-.|...++......+-.++...|.++.+-|
T Consensus 20 ~Li~~Lyd~ai~~l~~a~~a~~~~~~~~~~~~l~ka~~Ii~~L~~~L 66 (122)
T PF02561_consen 20 QLILMLYDGAIEFLKQAKEAIEQGDIEEKNEALQKAQDIITELQSSL 66 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 56778899999999999999999999999999999999999887654
No 79
>PTZ00208 65 kDa invariant surface glycoprotein; Provisional
Probab=22.99 E-value=3.6e+02 Score=26.96 Aligned_cols=68 Identities=19% Similarity=0.290 Sum_probs=37.3
Q ss_pred CChhHHHHHHhhhhhhHHHHHHHH---Hhc-------------CChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHH
Q 026780 153 KAWPYVQNDLRLRASYLRYDLNTI---ISA-------------KPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEK 216 (233)
Q Consensus 153 ksW~~vr~~LRlka~~Lr~DL~tl---iss-------------kPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~ 216 (233)
+.=.++.+.--.-+++|..+++.| ... ++..+.+.++++..+--+.|. +..|+|++
T Consensus 55 ~~ad~l~~~T~~fa~~i~~~~dri~~wLe~l~~~~~~~dgyaklSD~d~kKvKei~ekAKd~i~--------k~LpeAkk 126 (436)
T PTZ00208 55 ERADKLKDRTQNFAGYIEFELDRLDYWLEKLNGPKHSNDGYAKLSDSDTEKVKEIFEKAKDGIA--------KQLPEAKK 126 (436)
T ss_pred hhhHHHHHHHHhHHHHHHHHHHHHHHHHHhhcCccccCCcccccCcccHHHHHHHHHHHHHHHH--------hhhhhhHH
Confidence 333444455555566666666666 222 233333444444433333222 25788888
Q ss_pred HHHHHHHHHHHH
Q 026780 217 YYAETVSTLNDV 228 (233)
Q Consensus 217 ~Y~~tv~~Ldev 228 (233)
+++++.+..++|
T Consensus 127 ~~eEaek~~~~V 138 (436)
T PTZ00208 127 AGEEAEKLHQEV 138 (436)
T ss_pred HHHHHHHHHHHH
Confidence 888888877776
No 80
>PRK14157 heat shock protein GrpE; Provisional
Probab=22.95 E-value=4.2e+02 Score=24.19 Aligned_cols=47 Identities=9% Similarity=0.313 Sum_probs=33.6
Q ss_pred hHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhhC
Q 026780 184 EKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKVG 233 (233)
Q Consensus 184 ~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l~ 233 (233)
.+-...++.++|+.-+++|+.|....+.. .-|.-+.+.|..+|.+.|
T Consensus 122 ~~~a~~~~~~dLLpvlDnLeRAl~~~~~~---~~~~~i~k~l~~vL~k~G 168 (227)
T PRK14157 122 RQHGIIDVLTALLPALDDIDRIREHSEMD---DSFKAVAAKIDKAFEKFG 168 (227)
T ss_pred HHHHHHHHHHHHhhhhhhHHHHHhccccc---hHHHHHHHHHHHHHHHCC
Confidence 34456778899999999999998654332 235566777888877654
No 81
>PRK06214 sulfite reductase; Provisional
Probab=22.71 E-value=2.1e+02 Score=28.88 Aligned_cols=71 Identities=23% Similarity=0.259 Sum_probs=39.3
Q ss_pred cCCcchhhHHHHHHHHHHHhhchhhhhh-hh-ccCCcccCCCCCCCCCCCCCCCCCCCCCCCccccccccc-CCCCHHH
Q 026780 56 SNEPETSRRAMLGLVAAGVASGSFVQAV-LA-DATPIKVGPPPPPSGGLPGTLNSDEPRDLDLPLKERFFI-QPLSPAQ 131 (233)
Q Consensus 56 ~~~~~~sRRa~lgl~a~~l~~~~~~~~~-~a-~~~~i~~~p~P~ps~~~~Gt~~~~eardl~l~lk~rf~~-q~ls~~e 131 (233)
+.++...-|+.|.+-++++.+....++. +. ...+. .-+.|+|.....|+- =.|-.+|+.|||.+ .+.+..+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~ 81 (530)
T PRK06214 8 SAPFSEEQRAWLNGFFAGLLGPDVEGATALSPGEAPA-LLAAPPAAADDDDAP----WHDPSLPIDERMALAEGRPLPR 81 (530)
T ss_pred CCCCCHHHHHHHHHHHHHhhcccccCCcccCcccccc-ccCCCCCCCCCCCCC----CCCCCCChHHhcccCCCCcHHH
Confidence 3456678899998777777766642221 11 00111 112344444332322 25788999999998 5555444
No 82
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=22.29 E-value=1.3e+02 Score=25.35 Aligned_cols=13 Identities=15% Similarity=0.329 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHH
Q 026780 216 KYYAETVSTLNDV 228 (233)
Q Consensus 216 ~~Y~~tv~~Ldev 228 (233)
..|.....+|+++
T Consensus 101 ~Sf~~m~tAln~L 113 (145)
T PF13326_consen 101 PSFTTMYTALNAL 113 (145)
T ss_dssp HHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHH
Confidence 4566666666654
No 83
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=21.69 E-value=4.3e+02 Score=21.26 Aligned_cols=55 Identities=9% Similarity=0.073 Sum_probs=46.4
Q ss_pred HHHhcCChhhHHHHHHHHHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHhhh
Q 026780 175 TIISAKPKDEKQSLKNLTGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLSKV 232 (233)
Q Consensus 175 tlisskPkd~Kk~l~~La~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa~l 232 (233)
.+.++-|. +-+.-|+..+..++..--.|+.++|.++....-.++...|.++.+-|
T Consensus 14 ~v~tasp~---~Li~mLydg~i~~l~~a~~ai~~~d~~~~~~~i~ka~~Ii~eL~~~L 68 (124)
T TIGR00208 14 SVNTASPG---ELTLMLYNGCLKFIRLAAQAIENDDIERKNENLIKAQNIIQELNFTL 68 (124)
T ss_pred hHhcCCHH---HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 34444455 56888999999999999999999999999999999999998887644
No 84
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=21.12 E-value=1.5e+02 Score=21.24 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=36.0
Q ss_pred hHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHH--hhhhh
Q 026780 156 PYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQ--TIGNL 202 (233)
Q Consensus 156 ~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~--~le~L 202 (233)
.-+.+-|++|-|.+--++..-|.+++.++ +..|+..+|+ ++++|
T Consensus 10 ~lllRlL~rrFG~lp~~~~~~I~~l~~eq---LE~l~e~ildf~~l~dL 55 (59)
T PF14261_consen 10 RLLLRLLTRRFGELPPEIQERIQQLSLEQ---LEALAEAILDFNSLEDL 55 (59)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHcCCHHH---HHHHHHHHhCCCCHHHH
Confidence 45678899999999999999999998754 8889999976 34444
No 85
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=21.10 E-value=3.3e+02 Score=20.59 Aligned_cols=36 Identities=14% Similarity=0.207 Sum_probs=25.5
Q ss_pred HHHHHHhhhhhHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 026780 192 TGKLFQTIGNLDHAAKIKSTPEAEKYYAETVSTLNDVLS 230 (233)
Q Consensus 192 a~kLF~~le~LD~AaR~Kn~~~a~~~Y~~tv~~LdevLa 230 (233)
|.++...=-++| +.++..+|-.||++++..|-.++.
T Consensus 6 A~~~a~~AVe~D---~~gr~~eAi~~Y~~aIe~L~q~~~ 41 (75)
T cd02682 6 ARKYAINAVKAE---KEGNAEDAITNYKKAIEVLSQIVK 41 (75)
T ss_pred HHHHHHHHHHHH---hcCCHHHHHHHHHHHHHHHHHHHH
Confidence 344444333444 578899999999999999988764
No 86
>PF11521 TFIIE-A_C-term: C-terminal general transcription factor TFIIE alpha; InterPro: IPR021600 TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C-terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C-terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo []. ; PDB: 2RNR_A 2RNQ_A 2JTX_A.
Probab=20.99 E-value=1e+02 Score=23.99 Aligned_cols=32 Identities=13% Similarity=0.372 Sum_probs=25.7
Q ss_pred hHHHHHH---HHHhcCChhhHHHHHHHHHHHHHhh
Q 026780 168 YLRYDLN---TIISAKPKDEKQSLKNLTGKLFQTI 199 (233)
Q Consensus 168 ~Lr~DL~---tlisskPkd~Kk~l~~La~kLF~~l 199 (233)
|-+.+++ .||+....++|..+..+..++|.+|
T Consensus 50 ~~~~eVtq~p~LV~qMT~~EKEaYi~v~Q~~f~~m 84 (86)
T PF11521_consen 50 YPYSEVTQRPELVAQMTPEEKEAYIQVGQEMFSHM 84 (86)
T ss_dssp EEHHHHHH-HHHHHHS-HHHHHHHHHHHHHHCST-
T ss_pred eehhhcCcchHHHHHcCHHHHHHHHHHHHHHHHHh
Confidence 5556666 8999998889999999999999876
No 87
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=20.74 E-value=3.9e+02 Score=20.41 Aligned_cols=13 Identities=8% Similarity=0.087 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHH
Q 026780 132 AAERAKASAKDIL 144 (233)
Q Consensus 132 a~~RIkesA~~L~ 144 (233)
....+.+...++.
T Consensus 80 ~~~~~~~~~~~~~ 92 (181)
T PF12729_consen 80 IEKEIDEARAEID 92 (181)
T ss_pred HHHHHHHHHHHHH
Confidence 4455555555554
No 88
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=20.48 E-value=3.9e+02 Score=25.68 Aligned_cols=52 Identities=19% Similarity=0.137 Sum_probs=39.2
Q ss_pred hhCChhHHHHHHhhhhhhHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhhH
Q 026780 151 DKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNLD 203 (233)
Q Consensus 151 dkksW~~vr~~LRlka~~Lr~DL~tlisskPkd~Kk~l~~La~kLF~~le~LD 203 (233)
+.+.+..+|...=+|-|.|-.=++. +..+|.++|+.+=++.|++-+.++++=
T Consensus 21 ~~~~l~~~r~~~lgkkg~l~~~~~~-l~~l~~eer~~~G~~~n~~k~~~~~~~ 72 (339)
T PRK00488 21 DLEALEALRVKYLGKKGELTELLKG-LGKLPPEERKEAGALINELKQAIEAAL 72 (339)
T ss_pred CHHHHHHHHHHHhCCchHHHHHHHH-HhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777766777877665554 556799999999999999988777653
Done!