Query 028570
Match_columns 207
No_of_seqs 98 out of 100
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 13:35:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028570.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028570hhsearch_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 6.9E-63 1.5E-67 424.2 10.4 188 5-206 1-193 (220)
2 PF05757 PsbQ: Oxygen evolving 100.0 7.6E-60 1.6E-64 403.6 3.9 172 35-206 3-175 (202)
3 PLN02999 photosystem II oxygen 100.0 4.8E-42 1E-46 290.0 9.0 133 50-206 30-163 (190)
4 PLN02956 PSII-Q subunit 100.0 3.5E-30 7.5E-35 218.3 12.1 86 121-206 74-159 (185)
5 TIGR03042 PS_II_psbQ_bact phot 99.9 9.2E-22 2E-26 161.4 7.8 77 130-206 39-115 (142)
6 PLN00042 photosystem II oxygen 88.2 0.82 1.8E-05 41.6 4.7 35 48-83 38-72 (260)
7 PRK11546 zraP zinc resistance 71.9 58 0.0013 27.2 10.1 37 160-197 64-100 (143)
8 PF13801 Metal_resist: Heavy-m 61.5 11 0.00024 27.4 3.3 44 158-202 60-103 (125)
9 PF13413 HTH_25: Helix-turn-he 57.5 15 0.00032 26.0 3.3 52 125-176 9-62 (62)
10 TIGR01042 V-ATPase_V1_A V-type 51.6 72 0.0016 32.4 8.0 79 117-199 497-590 (591)
11 cd07625 BAR_Vps17p The Bin/Amp 50.7 13 0.00027 33.1 2.4 98 92-199 10-107 (230)
12 PF11221 Med21: Subunit 21 of 49.9 70 0.0015 26.0 6.5 33 127-182 62-94 (144)
13 PF10399 UCR_Fe-S_N: Ubiquitin 45.6 25 0.00054 23.5 2.7 17 58-74 6-22 (41)
14 COG5420 Uncharacterized conser 38.3 49 0.0011 24.8 3.5 44 161-205 17-60 (71)
15 PF05082 Rop-like: Rop-like; 37.9 45 0.00097 24.7 3.2 44 161-205 13-56 (66)
16 PRK14864 putative biofilm stre 35.4 95 0.0021 24.6 5.0 16 127-142 60-75 (104)
17 COG3181 Uncharacterized protei 34.2 77 0.0017 29.7 5.0 58 94-158 230-290 (319)
18 PF10518 TAT_signal: TAT (twin 30.1 46 0.001 20.0 1.9 14 62-75 3-16 (26)
19 TIGR02811 formate_TAT formate 29.3 74 0.0016 23.1 3.2 13 60-72 8-20 (66)
20 PF01093 Clusterin: Clusterin; 29.0 99 0.0021 30.2 4.9 55 132-202 14-70 (436)
21 PF08454 RIH_assoc: RyR and IP 28.8 2.3E+02 0.005 22.2 6.1 63 140-202 10-80 (109)
22 PF12805 FUSC-like: FUSC-like 27.5 1.6E+02 0.0035 25.9 5.7 73 131-204 210-282 (284)
23 PF08988 DUF1895: Protein of u 27.2 1.7E+02 0.0038 21.4 4.9 52 144-196 2-54 (68)
24 PRK09706 transcriptional repre 25.2 1E+02 0.0022 24.1 3.6 32 171-202 90-121 (135)
25 PF14425 Imm3: Immunity protei 24.8 2.9E+02 0.0064 22.4 6.2 77 124-202 22-109 (117)
26 COG1426 Predicted transcriptio 24.0 94 0.002 28.2 3.6 58 124-181 14-73 (284)
27 PF11521 TFIIE-A_C-term: C-ter 22.9 92 0.002 23.9 2.8 33 167-199 49-84 (86)
28 PRK12750 cpxP periplasmic repr 22.4 3.1E+02 0.0068 23.1 6.2 20 176-195 133-152 (170)
29 cd08332 CARD_CASP2 Caspase act 22.2 2.9E+02 0.0063 20.8 5.4 51 145-201 12-62 (90)
30 KOG0177 20S proteasome, regula 22.1 85 0.0018 27.8 2.8 31 114-144 138-168 (200)
31 PF14304 CSTF_C: Transcription 22.0 73 0.0016 22.0 1.9 23 175-197 20-42 (46)
32 PF06248 Zw10: Centromere/kine 21.2 4E+02 0.0086 26.2 7.5 66 130-195 13-85 (593)
33 smart00073 HPT Histidine Phosp 21.2 2.8E+02 0.0061 19.1 4.9 33 132-164 4-36 (87)
34 PF01627 Hpt: Hpt domain; Int 21.0 2.8E+02 0.006 18.8 6.4 29 136-164 7-38 (90)
35 PF06971 Put_DNA-bind_N: Putat 20.5 3E+02 0.0065 19.0 4.8 46 129-174 4-50 (50)
36 PRK14140 heat shock protein Gr 20.4 3.1E+02 0.0068 23.8 5.9 23 183-205 81-103 (191)
37 PF05960 DUF885: Bacterial pro 20.3 3E+02 0.0065 26.2 6.3 43 155-197 142-191 (549)
No 1
>PLN02729 PSII-Q subunit
Probab=100.00 E-value=6.9e-63 Score=424.20 Aligned_cols=188 Identities=28% Similarity=0.416 Sum_probs=176.7
Q ss_pred hHHhhcccCCCcccccccccccccCCCcccCCCCCccccccceeEEeec-c-cCCCcchhhHHHHHHHHHHHhhhhhhhh
Q 028570 5 MASMAGLRGSSHSQAVLEGSFQLSGPNRLNAPSNSRVAVARPGFTVRAQ-Q-ASNEPETSRRAMLGLVAAGVASGSFVQA 82 (207)
Q Consensus 5 ma~ma~l~g~s~~~~~~~~~~~~~g~~r~~~~~~~~~~~~~~g~~vra~-~-~~~~~~~sRRa~lgl~aa~la~~~~~~~ 82 (207)
|||+++|+|.+ +++ |.+++|+|.+|. +.++...|+.|+.+ | |+++.|++||++|||+++|+++++|+++
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 89999999888777 3 6678999999999999999999999999
Q ss_pred hhhcccCcccCCC-CCCCCCCCCCCCC--CCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhcChhHHH
Q 028570 83 VLADATPIKVGPP-PPPSGGLPGTLNS--DEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQ 159 (207)
Q Consensus 83 ~~A~~~~i~~~p~-P~ps~~~~Gt~~~--~eardl~l~lkerf~~~~ls~~eAa~RIkesA~~L~~lk~lIdkksW~yv~ 159 (207)
++||+++||++|| |||| |+|+ ||..++|.|||||||+||++|+||++|||++|++|++||+|||+++|+|||
T Consensus 72 ~~A~~~~i~~~~P~P~ps-----t~n~~~~e~~gtRsfLKerfy~~~l~p~~aa~RiK~sA~dLl~vKdLId~~sW~yVq 146 (220)
T PLN02729 72 SLAEDNGFWLDGPLPVPS-----VDNKIVNEKTGTRSFLKKGIYMADIGTKGRMYRVKKYAFDLLALEDLIGPDTLNYVR 146 (220)
T ss_pred HHhcccCceeCCCCCCCc-----cccccccccchHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHhhCcchHHHHH
Confidence 9999999999888 8888 4554 777777779999999999999999999999999999999999999999999
Q ss_pred HHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhcccccC
Q 028570 160 NDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNVSFFS 206 (207)
Q Consensus 160 ~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~LD~Aa 206 (207)
+|||+|++||||||++||+++|+++||+|++|+|+||++|++||||+
T Consensus 147 ~~LRLKAsyL~yDL~tvIsskP~~eKk~L~~LankLFdn~~eLD~Aa 193 (220)
T PLN02729 147 KYLRLKSTFMYYDFDKLISAAPVDDKQPLTDLANRLFDNFEKLEDAS 193 (220)
T ss_pred HHHHHHHHHHHHHHHHHhccCChhhhHHHHHHHHHHHhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999997
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=7.6e-60 Score=403.60 Aligned_cols=172 Identities=63% Similarity=0.973 Sum_probs=82.4
Q ss_pred CCCCCccccccceeEEeecccCCCcchhhHHHHH-HHHHHHhhhhhhhhhhhcccCcccCCCCCCCCCCCCCCCCCCCCC
Q 028570 35 APSNSRVAVARPGFTVRAQQASNEPETSRRAMLG-LVAAGVASGSFVQAVLADATPIKVGPPPPPSGGLPGTLNSDEPRD 113 (207)
Q Consensus 35 ~~~~~~~~~~~~g~~vra~~~~~~~~~sRRa~lg-l~aa~la~~~~~~~~~A~~~~i~~~p~P~ps~~~~Gt~~~~eard 113 (207)
+.++.++.+.+.+++|||++++++.+++||++|| |+++++++++++++++|+.+||++++||||+++++||+|+||+||
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 3455577778888999999988889999999999 999999999999999998999999999999999999999999999
Q ss_pred CCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHH
Q 028570 114 LDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTG 193 (207)
Q Consensus 114 l~l~lkerf~~~~ls~~eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~ 193 (207)
++||||+|||+|+++|+||++|||+++++|+.||+|||+++|+|||+|||+|++||||||++||++||+++||+|++|+|
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 HHhhhhhcccccC
Q 028570 194 KLFQTIGNVSFFS 206 (207)
Q Consensus 194 kLF~~le~LD~Aa 206 (207)
+||++||+||||+
T Consensus 163 ~lf~~ie~LD~Aa 175 (202)
T PF05757_consen 163 KLFDNIEELDYAA 175 (202)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999996
No 3
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=100.00 E-value=4.8e-42 Score=290.03 Aligned_cols=133 Identities=25% Similarity=0.452 Sum_probs=118.0
Q ss_pred EeecccCCCcchhhHHHHH-HHHHHHhhhhhhhhhhhcccCcccCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCC
Q 028570 50 VRAQQASNEPETSRRAMLG-LVAAGVASGSFVQAVLADATPIKVGPPPPPSGGLPGTLNSDEPRDLDLPLKERFFIQPLS 128 (207)
Q Consensus 50 vra~~~~~~~~~sRRa~lg-l~aa~la~~~~~~~~~A~~~~i~~~p~P~ps~~~~Gt~~~~eardl~l~lkerf~~~~ls 128 (207)
|.++-+..+..++||.++. |++++++++++. |+....+||| |+|||||||+||++
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 4555444567789999888 999998755522 3444456666 47999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhcccccC
Q 028570 129 PAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNVSFFS 206 (207)
Q Consensus 129 ~~eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~LD~Aa 206 (207)
|+||++|||++|++|++||+|||+++|+|||+|||++++||||||+++|+++|+++|++|++|+++|||||++|||||
T Consensus 86 peeAaaRiK~sA~dLl~vK~LId~~aW~YVq~~LRlkasyLryDL~tiIsskP~~eK~~L~~LankLFdnvt~LDyAA 163 (190)
T PLN02999 86 PEDAAARIKQTAEGLRDMREMLDHMSWRYVIFYIRLKQAYLSQDLTNAMNILPESRRNDYVQAANELVENMSELDYYV 163 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHhcCCHhhhHHHHHHHHHHhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999997
No 4
>PLN02956 PSII-Q subunit
Probab=99.97 E-value=3.5e-30 Score=218.31 Aligned_cols=86 Identities=30% Similarity=0.522 Sum_probs=84.6
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhh
Q 028570 121 RFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIG 200 (207)
Q Consensus 121 rf~~~~ls~~eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le 200 (207)
|||+|+++||||++|||++|++|++||+||++++|+|||||||+|++||+|||++||++||+++||++++|+++||++|+
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 cccccC
Q 028570 201 NVSFFS 206 (207)
Q Consensus 201 ~LD~Aa 206 (207)
+|||||
T Consensus 154 ~LD~AA 159 (185)
T PLN02956 154 KLDYAA 159 (185)
T ss_pred HHHHHH
Confidence 999997
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=99.86 E-value=9.2e-22 Score=161.35 Aligned_cols=77 Identities=13% Similarity=0.226 Sum_probs=74.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhcccccC
Q 028570 130 AQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNVSFFS 206 (207)
Q Consensus 130 ~eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~LD~Aa 206 (207)
++-+.+|.+.+++|.+|+.||++++|++|||+||+++|+||+||++||++||+++||++++|+++||+++++||+||
T Consensus 39 ~~~~~~i~~~~~r~~eLk~lI~kk~W~~vrn~irgp~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA 115 (142)
T TIGR03042 39 QRQAEGIEAAKDRLPELASLVAKEDWVFTRNLIHGPMGEVRREMTYLNQSLLPKDQKEALALAKELKDDLEKLDEAA 115 (142)
T ss_pred HHHHHHHHHHHHhhHHHHHHHhhcchHHHHHHHhccHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 45588999999999999999999999999999999999999999999999999999999999999999999999997
No 6
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=88.21 E-value=0.82 Score=41.59 Aligned_cols=35 Identities=40% Similarity=0.527 Sum_probs=21.5
Q ss_pred eEEeecccCCCcchhhHHHHHHHHHHHhhhhhhhhh
Q 028570 48 FTVRAQQASNEPETSRRAMLGLVAAGVASGSFVQAV 83 (207)
Q Consensus 48 ~~vra~~~~~~~~~sRRa~lgl~aa~la~~~~~~~~ 83 (207)
++||+|.++. ...|||..|.+++..++.++-+..+
T Consensus 38 ~~~~~~~~~~-~~~srr~~l~~~~ga~a~~~~~~pa 72 (260)
T PLN00042 38 VVCRAQEEDN-SAVSRRAALALLAGAAAAGAKVSPA 72 (260)
T ss_pred eeeecccccc-ccccHHHHHHHHHHHHHhhcccCch
Confidence 9999986543 4468888776665444434434333
No 7
>PRK11546 zraP zinc resistance protein; Provisional
Probab=71.91 E-value=58 Score=27.25 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=23.7
Q ss_pred HHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhh
Q 028570 160 NDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQ 197 (207)
Q Consensus 160 ~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~ 197 (207)
..||.+.---+.+|+.|.++-+.|++ .+..|++++.+
T Consensus 64 ~~LRqqL~aKr~ELnALl~~~~pD~~-kI~aL~kEI~~ 100 (143)
T PRK11546 64 SALRQQLVSKRYEYNALLTANPPDSS-KINAVAKEMEN 100 (143)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHH
Confidence 35666777778999999999444444 34444444443
No 8
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=61.50 E-value=11 Score=27.41 Aligned_cols=44 Identities=20% Similarity=0.342 Sum_probs=31.0
Q ss_pred HHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhcc
Q 028570 158 VQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNV 202 (207)
Q Consensus 158 v~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~L 202 (207)
-...+|....-++.+|..++.+-+.|.. .+..+.+++.+.-.++
T Consensus 60 ~~~~~r~~~~~~r~~l~~ll~~~~~D~~-~i~a~~~~~~~~~~~l 103 (125)
T PF13801_consen 60 EMRALRQELRAARQELRALLAAPPPDEA-AIEALLEEIREAQAEL 103 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCSSS-HH-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHH
Confidence 3456777778899999999999766666 5777766666555444
No 9
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=57.48 E-value=15 Score=25.99 Aligned_cols=52 Identities=25% Similarity=0.279 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH-hhh-cChhHHHHHhhhhhhhhHhHHHHH
Q 028570 125 QPLSPAQAAERAKASAKDILNVKEL-IDK-KAWPYVQNDLRLRASYLRYDLNTI 176 (207)
Q Consensus 125 ~~ls~~eAa~RIkesA~~L~~lk~l-Idk-ksW~yv~~~LRlka~~Lr~DL~tl 176 (207)
.++|.++.....+=...-|..++.. .+. ..+.|++.|||.=+.+|.-|-+.|
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 5689999999999888888888764 333 368999999999999999887654
No 10
>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=51.56 E-value=72 Score=32.38 Aligned_cols=79 Identities=18% Similarity=0.262 Sum_probs=46.6
Q ss_pred ccccccccCC--------CCHHHHHHHHHHHHHHHHHHHHHhhhc-------ChhHHHHHhhhhhhhhHhHHHHHHhcCC
Q 028570 117 PLKERFFIQP--------LSPAQAAERAKASAKDILNVKELIDKK-------AWPYVQNDLRLRASYLRYDLNTIISAKP 181 (207)
Q Consensus 117 ~lkerf~~~~--------ls~~eAa~RIkesA~~L~~lk~lIdkk-------sW~yv~~~LRlka~~Lr~DL~tlIsskP 181 (207)
++++.|.+|+ .+++++...++.--.=-..-+..|++. +|..+++.+. -++.++..+=-..|
T Consensus 497 ~i~e~FLqQ~a~~~~d~~~~~~kt~~~L~~i~~~~~~~~~~~~~~~~~~~ki~~~~i~~~~~----~~~~~~~~~k~~~~ 572 (591)
T TIGR01042 497 LIKEDFLQQNGYTPYDRFCPFYKTVGMMRNMIAFYDLARQAVERTAQDDNKITWSIIKESLG----DLLYRLSSMKFEDP 572 (591)
T ss_pred HHHHHhCCCCCCCCccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCccccccHHHHHHHHH----HHHHHHHHhcCCCc
Confidence 4568888888 455555555444332222334444433 2888775431 22333333322347
Q ss_pred hhhhHHHHHHHHHHhhhh
Q 028570 182 KDEKQSLKNLTGKLFQTI 199 (207)
Q Consensus 182 kdqKk~l~~La~kLF~~l 199 (207)
++..+.+.++.+||++.|
T Consensus 573 ~~~~~~~~~~~~kl~~ei 590 (591)
T TIGR01042 573 SDGEAKIKADYEKLNEDM 590 (591)
T ss_pred cchHHHHHHHHHHHHHhh
Confidence 888889999999999986
No 11
>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=50.72 E-value=13 Score=33.08 Aligned_cols=98 Identities=11% Similarity=0.110 Sum_probs=70.1
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHh
Q 028570 92 VGPPPPPSGGLPGTLNSDEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRY 171 (207)
Q Consensus 92 ~~p~P~ps~~~~Gt~~~~eardl~l~lkerf~~~~ls~~eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~ 171 (207)
.-|||+|-..+..++ |+=..||+.-.....++.++-.+.++|-.-...+.++-=..-..+-+...+.++.
T Consensus 10 ~~~p~d~~~el~~~r----------p~vk~~y~~~~~l~~~~~~lvk~rr~La~~~~dfg~~l~~Ls~~E~~~~L~~a~~ 79 (230)
T cd07625 10 FAPPYDEYTELAEFR----------PLVKSIYLTAQDLQEKLLRVSKARKQLSLEEADFGQKLIQLSVEETHHGLGNLYE 79 (230)
T ss_pred cCcCCCCCHHHHHhh----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHH
Confidence 468888888876665 8888899999999999999999999998666666555555555556667777888
Q ss_pred HHHHHHhcCChhhhHHHHHHHHHHhhhh
Q 028570 172 DLNTIISAKPKDEKQSLKNLTGKLFQTI 199 (207)
Q Consensus 172 DL~tlIsskPkdqKk~l~~La~kLF~~l 199 (207)
.|-.++.....=+-.+.......|.+.+
T Consensus 80 kLg~v~~~v~dl~~~QA~~d~~tl~d~L 107 (230)
T cd07625 80 KFGKVLTAVGDIDSIQATVDMATLYDGL 107 (230)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 8888888865333334444444444444
No 12
>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=49.93 E-value=70 Score=25.96 Aligned_cols=33 Identities=24% Similarity=0.331 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCCh
Q 028570 127 LSPAQAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPK 182 (207)
Q Consensus 127 ls~~eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPk 182 (207)
.++++-...+++.|.+|.. --+++..||++||.
T Consensus 62 ~~~~~~~~~~~elA~dIi~-----------------------kakqIe~LIdsLPg 94 (144)
T PF11221_consen 62 DPPEEFEENIKELATDIIR-----------------------KAKQIEYLIDSLPG 94 (144)
T ss_dssp --HHHHHHHHHHHHHHHHH-----------------------HHHHHHHHHHHSTT
T ss_pred CChhhHHHHHHHHHHHHHH-----------------------HHHHHHHHHHhCCC
Confidence 5788889999999998874 24678889999885
No 13
>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=45.62 E-value=25 Score=23.52 Aligned_cols=17 Identities=24% Similarity=0.474 Sum_probs=9.8
Q ss_pred CcchhhHHHHHHHHHHH
Q 028570 58 EPETSRRAMLGLVAAGV 74 (207)
Q Consensus 58 ~~~~sRRa~lgl~aa~l 74 (207)
+.+.+||-+|.++++++
T Consensus 6 ~~~~~RRdFL~~at~~~ 22 (41)
T PF10399_consen 6 PVDPTRRDFLTIATSAV 22 (41)
T ss_dssp ----HHHHHHHHHHHHH
T ss_pred CCCchHHHHHHHHHHHH
Confidence 35679999998766443
No 14
>COG5420 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=38.27 E-value=49 Score=24.76 Aligned_cols=44 Identities=16% Similarity=0.261 Sum_probs=39.1
Q ss_pred HhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhccccc
Q 028570 161 DLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNVSFF 205 (207)
Q Consensus 161 ~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~LD~A 205 (207)
-|..++|..+-||..|...+|.+-- ++-+.|.+-|.-+.+||.+
T Consensus 17 kLqsrAg~akm~LhDLAEgLP~~wt-ei~~VA~kt~~~yaeLD~~ 60 (71)
T COG5420 17 KLQSRAGQAKMELHDLAEGLPVKWT-EIMAVAEKTFEAYAELDAA 60 (71)
T ss_pred HHHHHHHHHHhhHHHHhccCCccHH-HHHHHHHHHHHHHHHHHHH
Confidence 4667899999999999999998766 8999999999999999965
No 15
>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=37.94 E-value=45 Score=24.69 Aligned_cols=44 Identities=14% Similarity=0.269 Sum_probs=39.0
Q ss_pred HhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhccccc
Q 028570 161 DLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNVSFF 205 (207)
Q Consensus 161 ~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~LD~A 205 (207)
-|..+++.+.-||-.|...+|-+-. .+-++|.+.|+-+.+||.|
T Consensus 13 KL~~~A~~~kmdLHDLaEdLP~~w~-~i~~vA~~ty~a~~~l~~a 56 (66)
T PF05082_consen 13 KLNRKATQAKMDLHDLAEDLPTNWE-EIPEVAQKTYDAYAELDEA 56 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHCTTTTGG-GHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHccchhHH-HHHHHHHHHHHHHHHHHHH
Confidence 3778899999999999999998777 8999999999999888764
No 16
>PRK14864 putative biofilm stress and motility protein A; Provisional
Probab=35.39 E-value=95 Score=24.63 Aligned_cols=16 Identities=31% Similarity=0.320 Sum_probs=12.0
Q ss_pred CCHHHHHHHHHHHHHH
Q 028570 127 LSPAQAAERAKASAKD 142 (207)
Q Consensus 127 ls~~eAa~RIkesA~~ 142 (207)
-+|.|+...|.+-|++
T Consensus 60 gsp~d~~~~La~KAda 75 (104)
T PRK14864 60 GSPDDAEREIQAKANA 75 (104)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 4788888888777664
No 17
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.24 E-value=77 Score=29.66 Aligned_cols=58 Identities=14% Similarity=0.127 Sum_probs=42.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCHHHHHHHHHHHHHHHH---HHHHHhhhcChhHH
Q 028570 94 PPPPPSGGLPGTLNSDEPRDLDLPLKERFFIQPLSPAQAAERAKASAKDIL---NVKELIDKKAWPYV 158 (207)
Q Consensus 94 p~P~ps~~~~Gt~~~~eardl~l~lkerf~~~~ls~~eAa~RIkesA~~L~---~lk~lIdkksW~yv 158 (207)
.|=.|....-|.. .-.....+||.++-.|.|...++.+..+.++ ++++.+++.+|...
T Consensus 230 ~pdvPT~~E~G~~-------~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s~e~~~~~~~~~~~~~ 290 (319)
T COG3181 230 LPDVPTLKEQGYD-------VVMSIWRGVFAPAGTPDEIIAKLSAALKKALASPEWQKRLKELGLVPS 290 (319)
T ss_pred CCCCCChHhcCCc-------eeeeeeeEEEeCCCCCHHHHHHHHHHHHHHhcCHHHHHHHHhcCCCCc
Confidence 3446666666663 3356689999999999999999999888887 46666666666543
No 18
>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=30.12 E-value=46 Score=19.97 Aligned_cols=14 Identities=50% Similarity=0.382 Sum_probs=9.3
Q ss_pred hhHHHHHHHHHHHh
Q 028570 62 SRRAMLGLVAAGVA 75 (207)
Q Consensus 62 sRRa~lgl~aa~la 75 (207)
|||.+|-..++..+
T Consensus 3 sRR~fLk~~~a~~a 16 (26)
T PF10518_consen 3 SRRQFLKGGAAAAA 16 (26)
T ss_pred cHHHHHHHHHHHHH
Confidence 89998875553333
No 19
>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=29.31 E-value=74 Score=23.14 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=8.5
Q ss_pred chhhHHHHHHHHH
Q 028570 60 ETSRRAMLGLVAA 72 (207)
Q Consensus 60 ~~sRRa~lgl~aa 72 (207)
..+||-+|-++.+
T Consensus 8 ~~sRR~Flk~lg~ 20 (66)
T TIGR02811 8 DPSRRDLLKGLGV 20 (66)
T ss_pred CccHHHHHHHHHH
Confidence 3589997664443
No 20
>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=28.96 E-value=99 Score=30.23 Aligned_cols=55 Identities=15% Similarity=0.270 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcC--ChhhhHHHHHHHHHHhhhhhcc
Q 028570 132 AAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAK--PKDEKQSLKNLTGKLFQTIGNV 202 (207)
Q Consensus 132 Aa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIssk--PkdqKk~l~~La~kLF~~le~L 202 (207)
.=.-||.+-.++-.||.++++.. .+-..|+.+| -+++|+.+.+|+++....|++-
T Consensus 14 vdeEik~Al~GvKqMK~~Mek~e----------------eeh~~Lm~tL~k~kk~KeeAl~l~~e~e~kLee~ 70 (436)
T PF01093_consen 14 VDEEIKNALNGVKQMKTMMEKTE----------------EEHKELMKTLEKSKKEKEEALKLANEVEEKLEEE 70 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888888889999998764 3445566663 4889999999999999988763
No 21
>PF08454 RIH_assoc: RyR and IP3R Homology associated; InterPro: IPR013662 This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1, 4, 5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels []. There seems to be no known function for this domain []. Also see the IP3-binding domain IPR000699 from INTERPRO and IPR003608 from INTERPRO.
Probab=28.78 E-value=2.3e+02 Score=22.23 Aligned_cols=63 Identities=21% Similarity=0.177 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhhcChhHHHHHhhhhhh-h----hHhHHHHHHhcC---ChhhhHHHHHHHHHHhhhhhcc
Q 028570 140 AKDILNVKELIDKKAWPYVQNDLRLRAS-Y----LRYDLNTIISAK---PKDEKQSLKNLTGKLFQTIGNV 202 (207)
Q Consensus 140 A~~L~~lk~lIdkksW~yv~~~LRlka~-~----Lr~DL~tlIssk---PkdqKk~l~~La~kLF~~le~L 202 (207)
...++.+=.++=+..-...|+|||.+-. + |=.++-.+...+ .++--+...++....|+++.++
T Consensus 10 ~~~ilr~LQLlCEghn~~lQnylR~Q~~~~~s~nlV~~~~~ll~~l~~~~~~~~~~~~~~~~q~~~tL~E~ 80 (109)
T PF08454_consen 10 IQRILRFLQLLCEGHNLDLQNYLRQQPNNKNSYNLVSETVDLLDSLQEFGKDINSDNIELIIQCFDTLTEF 80 (109)
T ss_pred HHHHHHHHHHHHCcCCHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 4556666667777888999999999888 3 333333444444 4555567777888888888764
No 22
>PF12805 FUSC-like: FUSC-like inner membrane protein yccS
Probab=27.46 E-value=1.6e+02 Score=25.88 Aligned_cols=73 Identities=11% Similarity=0.063 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhcccc
Q 028570 131 QAAERAKASAKDILNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGNVSF 204 (207)
Q Consensus 131 eAa~RIkesA~~L~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~LD~ 204 (207)
....=+++.++++..+..-|..+....-.+.++....-+..-+..+......+.+ +..-.-+.|+++++++|.
T Consensus 210 ~~~~~l~~~a~~l~~ia~ai~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~~~~-~~~~~l~~l~~~l~~i~~ 282 (284)
T PF12805_consen 210 RFQRLLEQLAQALRQIAQAILRGRPYHHRNRLKRALEALEESLEFLRQQDQPENR-EALLALRNLLDNLRNIDR 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHhcCccCH-HHHHHHHHHHHHHHHHHh
Confidence 3455566777777888888887777777777777777777777777777222233 344445678888888774
No 23
>PF08988 DUF1895: Protein of unknown function (DUF1895); InterPro: IPR015081 The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The function of this protein is, as yet, unknown. ; PDB: 1ZW0_B 2P58_A 2UWJ_E 2Q1K_D 3PH0_B.
Probab=27.16 E-value=1.7e+02 Score=21.45 Aligned_cols=52 Identities=10% Similarity=0.061 Sum_probs=42.4
Q ss_pred HHHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhc-CChhhhHHHHHHHHHHh
Q 028570 144 LNVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISA-KPKDEKQSLKNLTGKLF 196 (207)
Q Consensus 144 ~~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIss-kPkdqKk~l~~La~kLF 196 (207)
-+|++.+.. +|++-..-|+.+.-....+++..... +.+++=+.+...++.+-
T Consensus 2 T~LE~~L~~-~~~~~~~~i~~~L~~a~~~vkr~L~~G~~P~eyQq~q~~~~Aie 54 (68)
T PF08988_consen 2 TNLEQRLSN-ASGEEARAIEQQLRQAQSQVKRKLDRGGTPQEYQQLQQQYDAIE 54 (68)
T ss_dssp CHHHHHHTC-TSHHHHHHHHHHHHHHHHHHHHHHTCTSSHHHHHHHHHHHHHHH
T ss_pred chHHHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 368888888 99999999999999999999999998 65666657777766543
No 24
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=25.16 E-value=1e+02 Score=24.11 Aligned_cols=32 Identities=13% Similarity=0.200 Sum_probs=22.7
Q ss_pred hHHHHHHhcCChhhhHHHHHHHHHHhhhhhcc
Q 028570 171 YDLNTIISAKPKDEKQSLKNLTGKLFQTIGNV 202 (207)
Q Consensus 171 ~DL~tlIsskPkdqKk~l~~La~kLF~~le~L 202 (207)
.+|-.+...+|+++++.+.+..+...+.+++|
T Consensus 90 ~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~ 121 (135)
T PRK09706 90 KELLELFDALPESEQDAQLSEMRARVENFNKL 121 (135)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677788888888887777777666654
No 25
>PF14425 Imm3: Immunity protein Imm3
Probab=24.76 E-value=2.9e+02 Score=22.45 Aligned_cols=77 Identities=16% Similarity=0.208 Sum_probs=48.7
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHh---------hhcCh--hHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHH
Q 028570 124 IQPLSPAQAAERAKASAKDILNVKELI---------DKKAW--PYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLT 192 (207)
Q Consensus 124 ~~~ls~~eAa~RIkesA~~L~~lk~lI---------dkksW--~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La 192 (207)
..+.|..+|++|+-.--+.|-.+++.| =..+- .-....+..... .+|+..+-..+..++++.|....
T Consensus 22 ~~d~s~~eaiar~~~eye~lg~~EkiIv~~~igEi~l~~~~i~~~~~~~i~~~L~--~~~~~~~~~eLt~eE~~dL~~R~ 99 (117)
T PF14425_consen 22 NEDRSYSEAIARTFDEYENLGETEKIIVDTAIGEILLSHNKIFVGQKEGITKRLS--QFDFEEVKGELTQEEKEDLSQRI 99 (117)
T ss_pred HccCCHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHhhcchHHhhHHHHHHHHHH--hcChHHHHhHhhHHHHHHHHHHH
Confidence 456799999999876656665566555 11111 112222222221 24555555668899999999999
Q ss_pred HHHhhhhhcc
Q 028570 193 GKLFQTIGNV 202 (207)
Q Consensus 193 ~kLF~~le~L 202 (207)
++..+.+++.
T Consensus 100 nkVL~~l~~~ 109 (117)
T PF14425_consen 100 NKVLDGLEKV 109 (117)
T ss_pred HHHHHHHhcC
Confidence 9999998864
No 26
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=24.05 E-value=94 Score=28.21 Aligned_cols=58 Identities=21% Similarity=0.212 Sum_probs=44.9
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHH-h-hhcChhHHHHHhhhhhhhhHhHHHHHHhcCC
Q 028570 124 IQPLSPAQAAERAKASAKDILNVKEL-I-DKKAWPYVQNDLRLRASYLRYDLNTIISAKP 181 (207)
Q Consensus 124 ~~~ls~~eAa~RIkesA~~L~~lk~l-I-dkksW~yv~~~LRlka~~Lr~DL~tlIsskP 181 (207)
..+||.+|.+.+++=.-.-|..||+. + .--.=.|+|-|||.=+.||..|-+.++...+
T Consensus 14 ~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~~~ 73 (284)
T COG1426 14 EKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQAFE 73 (284)
T ss_pred HcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHHHHHHHhh
Confidence 35789999988887777667676653 1 1122479999999999999999999999844
No 27
>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=22.91 E-value=92 Score=23.94 Aligned_cols=33 Identities=12% Similarity=0.365 Sum_probs=26.7
Q ss_pred hhhHhHHH---HHHhcCChhhhHHHHHHHHHHhhhh
Q 028570 167 SYLRYDLN---TIISAKPKDEKQSLKNLTGKLFQTI 199 (207)
Q Consensus 167 ~~Lr~DL~---tlIsskPkdqKk~l~~La~kLF~~l 199 (207)
-|-+-+++ .||+..-.++|..+..+..++|.+|
T Consensus 49 ~~~~~eVtq~p~LV~qMT~~EKEaYi~v~Q~~f~~m 84 (86)
T PF11521_consen 49 PYPYSEVTQRPELVAQMTPEEKEAYIQVGQEMFSHM 84 (86)
T ss_dssp EEEHHHHHH-HHHHHHS-HHHHHHHHHHHHHHCST-
T ss_pred EeehhhcCcchHHHHHcCHHHHHHHHHHHHHHHHHh
Confidence 35566777 8998899999999999999999886
No 28
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=22.39 E-value=3.1e+02 Score=23.08 Aligned_cols=20 Identities=15% Similarity=0.301 Sum_probs=12.7
Q ss_pred HHhcCChhhhHHHHHHHHHH
Q 028570 176 IISAKPKDEKQSLKNLTGKL 195 (207)
Q Consensus 176 lIsskPkdqKk~l~~La~kL 195 (207)
+++-|.++||..|.++-++-
T Consensus 133 ~~~vLTpEQRak~~e~~~~r 152 (170)
T PRK12750 133 MLSILTPEQKAKFQELQQER 152 (170)
T ss_pred HHHhCCHHHHHHHHHHHHHH
Confidence 45556777777777766544
No 29
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=22.21 E-value=2.9e+02 Score=20.75 Aligned_cols=51 Identities=20% Similarity=0.147 Sum_probs=37.0
Q ss_pred HHHHHhhhcChhHHHHHhhhhhhhhHhHHHHHHhcCChhhhHHHHHHHHHHhhhhhc
Q 028570 145 NVKELIDKKAWPYVQNDLRLRASYLRYDLNTIISAKPKDEKQSLKNLTGKLFQTIGN 201 (207)
Q Consensus 145 ~lk~lIdkksW~yv~~~LRlka~~Lr~DL~tlIsskPkdqKk~l~~La~kLF~~le~ 201 (207)
....++.+-.-.+|..||-.+ +-|-.++..-|.+.|-.+.+ +.+|++-+.+
T Consensus 12 ~r~~Lv~~l~~~~v~~~L~~~-gvlt~~~~~~I~~~~t~~~k-----~~~Lld~L~~ 62 (90)
T cd08332 12 NRVKLAKELVLDELLIHLLQK-DILTDSMAESIMAKPTSFSQ-----NVALLNLLPK 62 (90)
T ss_pred hHHHHHHHCCHHHHHHHHHHc-CCCCHHHHHHHHcCCCcHHH-----HHHHHHHHHH
Confidence 344556666777888888886 88999999999998865554 5566665544
No 30
>KOG0177 consensus 20S proteasome, regulatory subunit beta type PSMB2/PRE1 [Posttranslational modification, protein turnover, chaperones]
Probab=22.13 E-value=85 Score=27.84 Aligned_cols=31 Identities=13% Similarity=0.294 Sum_probs=26.4
Q ss_pred CCcccccccccCCCCHHHHHHHHHHHHHHHH
Q 028570 114 LDLPLKERFFIQPLSPAQAAERAKASAKDIL 144 (207)
Q Consensus 114 l~l~lkerf~~~~ls~~eAa~RIkesA~~L~ 144 (207)
+-+.+=||+|-++++.+||..-+|.|-.+|-
T Consensus 138 f~~sIlDr~Y~pdmt~eea~~lmkKCv~El~ 168 (200)
T KOG0177|consen 138 FCLSILDRYYKPDMTIEEALDLMKKCVLELK 168 (200)
T ss_pred hhHHHHHhhhCCCCCHHHHHHHHHHHHHHHH
Confidence 3445569999999999999999999988874
No 31
>PF14304 CSTF_C: Transcription termination and cleavage factor C-terminal; PDB: 2J8P_A.
Probab=21.99 E-value=73 Score=22.05 Aligned_cols=23 Identities=30% Similarity=0.508 Sum_probs=17.2
Q ss_pred HHHhcCChhhhHHHHHHHHHHhh
Q 028570 175 TIISAKPKDEKQSLKNLTGKLFQ 197 (207)
Q Consensus 175 tlIsskPkdqKk~l~~La~kLF~ 197 (207)
.-|+.+|.++|.....|-..|-.
T Consensus 20 eQI~~LPp~qR~~I~~Lr~ql~~ 42 (46)
T PF14304_consen 20 EQINALPPDQRQQILQLRQQLMR 42 (46)
T ss_dssp HHHHTS-HHHHTHHHHHHHHHH-
T ss_pred HHHHhCCHHHHHHHHHHHHHHHh
Confidence 35888999999999988877643
No 32
>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=21.23 E-value=4e+02 Score=26.15 Aligned_cols=66 Identities=18% Similarity=0.286 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHHH-HHHHHhhhcC-----hhHHHHHhhhhhhhhHhHHHHHHhc-CChhhhHHHHHHHHHH
Q 028570 130 AQAAERAKASAKDIL-NVKELIDKKA-----WPYVQNDLRLRASYLRYDLNTIISA-KPKDEKQSLKNLTGKL 195 (207)
Q Consensus 130 ~eAa~RIkesA~~L~-~lk~lIdkks-----W~yv~~~LRlka~~Lr~DL~tlIss-kPkdqKk~l~~La~kL 195 (207)
+..+.++.+..+++. ++.++|++++ |-.--..|-.+..-|..|++.+.+. .+.+-+..+.+.++++
T Consensus 13 ~~~I~~L~~~i~~~k~eV~~~I~~~y~df~~~~~~~~~L~~~~~~l~~eI~d~l~~~~~~~i~~~l~~a~~e~ 85 (593)
T PF06248_consen 13 RKSISRLSRRIEELKEEVHSMINKKYSDFSPSLQSAKDLIERSKSLAREINDLLQSEIENEIQPQLRDAAEEL 85 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHH
Confidence 344556666666665 6777887776 6677788888999999999888877 6655565666655543
No 33
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=21.20 E-value=2.8e+02 Score=19.13 Aligned_cols=33 Identities=12% Similarity=0.140 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcChhHHHHHhhh
Q 028570 132 AAERAKASAKDILNVKELIDKKAWPYVQNDLRL 164 (207)
Q Consensus 132 Aa~RIkesA~~L~~lk~lIdkksW~yv~~~LRl 164 (207)
+..-+.+..+.|..++..++...|..+...+|.
T Consensus 4 ~~~f~~~~~~~l~~l~~~~~~~~~~~l~~~~H~ 36 (87)
T smart00073 4 LAEFLQSLEEGLLELEKALDAQDVNEIFRAAHT 36 (87)
T ss_pred HHHHHHHHHHHHHHHHhCcCHhHHHHHHHHHHh
Confidence 344566777788888888888899999887764
No 34
>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=21.02 E-value=2.8e+02 Score=18.81 Aligned_cols=29 Identities=7% Similarity=0.314 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHh---hhcChhHHHHHhhh
Q 028570 136 AKASAKDILNVKELI---DKKAWPYVQNDLRL 164 (207)
Q Consensus 136 IkesA~~L~~lk~lI---dkksW~yv~~~LRl 164 (207)
+.+..+.+..|+..+ +...|+.++..+|.
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 356677788899999 89999999998775
No 35
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=20.46 E-value=3e+02 Score=18.96 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HhhhcChhHHHHHhhhhhhhhHhHHH
Q 028570 129 PAQAAERAKASAKDILNVKE-LIDKKAWPYVQNDLRLRASYLRYDLN 174 (207)
Q Consensus 129 ~~eAa~RIkesA~~L~~lk~-lIdkksW~yv~~~LRlka~~Lr~DL~ 174 (207)
|+-++.|+-.+-.-|..|++ =++.=+=.+....+.......|.||+
T Consensus 4 p~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 4 PKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccCC
Confidence 35678888888887777766 45666788899999999999999985
No 36
>PRK14140 heat shock protein GrpE; Provisional
Probab=20.42 E-value=3.1e+02 Score=23.78 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=15.3
Q ss_pred hhhHHHHHHHHHHhhhhhccccc
Q 028570 183 DEKQSLKNLTGKLFQTIGNVSFF 205 (207)
Q Consensus 183 dqKk~l~~La~kLF~~le~LD~A 205 (207)
-.+-...++.++|+.-+|+|+.|
T Consensus 81 ~~~~a~~~~~~~LLpvlDnLerA 103 (191)
T PRK14140 81 AEKYRAQSLASDLLPALDNFERA 103 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445566777777777777766
No 37
>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=20.35 E-value=3e+02 Score=26.18 Aligned_cols=43 Identities=14% Similarity=0.156 Sum_probs=33.0
Q ss_pred hhHHHHHhhhhhh------hhHhHHHHHHh-cCChhhhHHHHHHHHHHhh
Q 028570 155 WPYVQNDLRLRAS------YLRYDLNTIIS-AKPKDEKQSLKNLTGKLFQ 197 (207)
Q Consensus 155 W~yv~~~LRlka~------~Lr~DL~tlIs-skPkdqKk~l~~La~kLF~ 197 (207)
..-+...++.-.. +|..++...+. .+++++++.++.-+.+.++
T Consensus 142 ~e~~i~q~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~~l~~~~~~ai~ 191 (549)
T PF05960_consen 142 VERAIAQLRGFIDADPEESFLYEDFPERLAASLSEEQKEALIAQAREAIE 191 (549)
T ss_dssp HHHHHHHHHHHCSS-GGCTCHHHHHHHHHCCCS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHccCcccchHHHHHHHhccccCChhHHHHHHHHHHHHHH
Confidence 3456677777666 89999999998 6889999888887777666
Done!