Query 030036
Match_columns 184
No_of_seqs 98 out of 104
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:31:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02956 PSII-Q subunit 100.0 1.5E-64 3.2E-69 419.7 18.0 184 1-184 1-185 (185)
2 PLN02999 photosystem II oxygen 100.0 6.5E-44 1.4E-48 295.9 13.9 112 73-184 78-189 (190)
3 PLN02729 PSII-Q subunit 100.0 1.4E-43 3E-48 299.4 12.2 123 61-184 90-219 (220)
4 PF05757 PsbQ: Oxygen evolving 100.0 8.6E-44 1.9E-48 299.5 6.3 124 61-184 74-201 (202)
5 TIGR03042 PS_II_psbQ_bact phot 100.0 5.7E-33 1.2E-37 223.3 14.6 108 77-184 27-141 (142)
6 PF06248 Zw10: Centromere/kine 60.3 62 0.0013 31.1 8.9 96 84-179 15-140 (593)
7 PF12185 IR1-M: Nup358/RanBP2 57.2 4 8.7E-05 29.4 0.3 14 13-26 21-35 (64)
8 PF12729 4HB_MCP_1: Four helix 56.1 80 0.0017 23.3 10.0 132 40-172 3-146 (181)
9 PF05082 Rop-like: Rop-like; 46.0 59 0.0013 23.5 4.9 44 114-158 14-57 (66)
10 COG5420 Uncharacterized conser 41.6 67 0.0015 23.5 4.5 46 113-159 17-62 (71)
11 PF01322 Cytochrom_C_2: Cytoch 41.5 69 0.0015 24.1 5.0 41 136-176 73-113 (122)
12 PF06971 Put_DNA-bind_N: Putat 40.5 99 0.0021 20.9 5.0 46 81-126 4-50 (50)
13 CHL00102 rps20 ribosomal prote 40.4 66 0.0014 24.5 4.6 44 138-181 26-69 (93)
14 KOG0412 Golgi transport comple 39.2 1.4E+02 0.0031 30.6 7.9 85 82-171 111-217 (773)
15 COG0233 Frr Ribosome recycling 37.3 2.7E+02 0.0058 23.9 9.8 42 47-89 76-117 (187)
16 cd02682 MIT_AAA_Arch MIT: doma 30.4 75 0.0016 23.2 3.4 24 159-182 18-41 (75)
17 PF08281 Sigma70_r4_2: Sigma-7 30.2 1.5E+02 0.0032 18.8 4.8 52 122-176 1-53 (54)
18 TIGR00029 S20 ribosomal protei 30.2 1.3E+02 0.0027 22.6 4.7 30 152-181 33-62 (87)
19 PRK11546 zraP zinc resistance 28.3 1.1E+02 0.0023 25.2 4.3 65 74-155 39-106 (143)
20 PRK00239 rpsT 30S ribosomal pr 27.4 1.5E+02 0.0033 22.1 4.7 29 154-182 35-63 (88)
21 PF11221 Med21: Subunit 21 of 26.4 71 0.0015 25.4 2.9 16 122-137 82-97 (144)
22 PF12662 cEGF: Complement Clr- 25.1 49 0.0011 19.3 1.3 14 19-32 2-15 (24)
23 PF12805 FUSC-like: FUSC-like 24.9 2E+02 0.0043 24.8 5.7 46 132-178 233-278 (284)
24 KOG4519 Phosphomevalonate kina 24.4 1.4E+02 0.0031 28.5 4.8 66 95-160 247-330 (459)
25 PRK14704 anaerobic ribonucleos 24.4 1.2E+02 0.0025 30.2 4.5 133 17-153 83-231 (618)
26 PLN03184 chloroplast Hsp70; Pr 24.2 4.6E+02 0.01 26.0 8.6 73 103-182 560-632 (673)
27 TIGR00496 frr ribosome recycli 23.9 4.2E+02 0.0091 22.0 9.1 50 47-97 65-114 (176)
28 PF14276 DUF4363: Domain of un 23.9 2.2E+02 0.0047 21.4 5.1 39 142-180 23-61 (121)
29 PF13324 GCIP: Grap2 and cycli 23.9 4E+02 0.0086 23.1 7.4 89 92-181 44-139 (275)
30 PRK00083 frr ribosome recyclin 23.9 4.3E+02 0.0094 22.1 9.8 50 47-97 74-123 (185)
31 KOG2607 CDK5 activator-binding 23.8 5.2E+02 0.011 25.3 8.5 61 113-174 147-210 (505)
32 PRK14140 heat shock protein Gr 23.1 4.7E+02 0.01 22.2 7.7 48 136-183 82-133 (191)
33 PF05960 DUF885: Bacterial pro 23.0 3.3E+02 0.0071 25.4 7.1 68 108-175 143-233 (549)
34 PF05957 DUF883: Bacterial pro 22.1 3.1E+02 0.0068 19.8 5.7 64 117-181 6-69 (94)
35 PF09210 DUF1957: Domain of un 22.1 1.6E+02 0.0034 22.6 4.0 30 77-106 49-78 (102)
36 PF14276 DUF4363: Domain of un 22.0 3.5E+02 0.0075 20.3 7.7 81 93-180 30-110 (121)
37 PF01649 Ribosomal_S20p: Ribos 21.9 3.3E+02 0.0072 20.0 5.9 34 149-182 29-62 (84)
38 PF09976 TPR_21: Tetratricopep 20.8 3.8E+02 0.0081 20.2 7.0 73 97-174 70-145 (145)
39 TIGR03752 conj_TIGR03752 integ 20.8 5.1E+02 0.011 25.3 7.9 60 85-146 65-124 (472)
40 PF13413 HTH_25: Helix-turn-he 20.7 1.3E+02 0.0028 20.7 3.0 52 77-128 9-62 (62)
41 PRK07417 arogenate dehydrogena 20.7 2.5E+02 0.0054 24.0 5.4 41 84-125 237-277 (279)
No 1
>PLN02956 PSII-Q subunit
Probab=100.00 E-value=1.5e-64 Score=419.67 Aligned_cols=184 Identities=56% Similarity=0.867 Sum_probs=181.2
Q ss_pred CCcccccccCCCCCCCcceeeecCccccccCCCcccccccchhhHHHHHHHHHHHhhh-hhhccccccccceeeeecCCC
Q 030036 1 MALKPLVSKCTLPHLYPTFMCYQQPAFRSKGMPQNVLQCNISRRIGVIAVTASTMLAR-EAIFREDIANAFEFRMVAPDQ 79 (184)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rr~~~~~~~~~~~~~~-~~~~~~~~a~~~~~rf~~ppl 79 (184)
|||++.+.+.|++|++|+||||.||+|.+++|++++...+++||+|++|+|+++++++ ++.++++.|++|||||++|+.
T Consensus 1 mal~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rr~~~~~~~~~~~~~~~~~~~~~~~a~~f~~~~~~p~~ 80 (185)
T PLN02956 1 MALRLAVQALSATHLSPAFICCLKPTFPSKGNTSRRPLRSISRRRGALAAVAGVLLAQLEASFNVAIAFGFDLRLTAPER 80 (185)
T ss_pred CCcccccccccchhcCCcccccCCCCCCccccccCCCccchhhHHHHHHHHHHHHHhhhccccchhhccccceeecCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999 567999999999999999999
Q ss_pred CHHHHHHHHHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHHh
Q 030036 80 TVEQAESGIRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAAR 159 (184)
Q Consensus 80 ~~~eA~~RIke~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr 159 (184)
+||||++|||++|++|++||+||++++|+|||||||||+|||||||++||+++|++||+++++|+++||++|++||+|||
T Consensus 81 speeA~ar~k~~A~~l~~LK~LI~k~~W~yvrn~LRgp~s~Lr~DL~~Ii~slpp~Drk~a~~La~~LFd~l~~LD~AAR 160 (185)
T PLN02956 81 TVEEAESGVRGHAENLLRVKALIESESWKEAQKALRRSASNLKQDLYAIIQAKPGKDRPQLRRLYSDLFNSVTKLDYAAR 160 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHccHHHHHHHHHHHHHhcCHhHhHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCChHHHHHHHHHHHHHHHHHHhhC
Q 030036 160 DKDVSRVHQCYENVVVALDSILSRL 184 (184)
Q Consensus 160 ~Kn~~~A~~~Y~~tv~~LdevLa~i 184 (184)
.||.++|++||++|+++||+||++|
T Consensus 161 ~kd~~~a~k~Y~~tva~lD~Vl~~i 185 (185)
T PLN02956 161 DKDETRVWEYYENIVASLDDIFSRI 185 (185)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999987
No 2
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=100.00 E-value=6.5e-44 Score=295.93 Aligned_cols=112 Identities=25% Similarity=0.404 Sum_probs=110.8
Q ss_pred eeecCCCCHHHHHHHHHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchH
Q 030036 73 RMVAPDQTVEQAESGIRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVT 152 (184)
Q Consensus 73 rf~~ppl~~~eA~~RIke~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le 152 (184)
|||+||++|+||++|||++|++|++||+|||+++|+||+||||++++||||||+++|+++|+++|+++++|+++|||+|+
T Consensus 78 rfy~p~lspeeAaaRiK~sA~dLl~vK~LId~~aW~YVq~~LRlkasyLryDL~tiIsskP~~eK~~L~~LankLFdnvt 157 (190)
T PLN02999 78 KYFMPGLSPEDAAARIKQTAEGLRDMREMLDHMSWRYVIFYIRLKQAYLSQDLTNAMNILPESRRNDYVQAANELVENMS 157 (190)
T ss_pred hccCCCCCHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHhcCCHhhhHHHHHHHHHHhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhcCChHHHHHHHHHHHHHHHHHHhhC
Q 030036 153 KLDYAARDKDVSRVHQCYENVVVALDSILSRL 184 (184)
Q Consensus 153 ~LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa~i 184 (184)
+||||||+||++++++||++||++||||++.+
T Consensus 158 ~LDyAAR~K~~~eae~yY~~Tv~slddVl~~l 189 (190)
T PLN02999 158 ELDYYVRTPKVYESYLYYEKTLKSIDNVVELL 189 (190)
T ss_pred HHHHHHhcCChHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999864
No 3
>PLN02729 PSII-Q subunit
Probab=100.00 E-value=1.4e-43 Score=299.43 Aligned_cols=123 Identities=22% Similarity=0.354 Sum_probs=120.2
Q ss_pred hccc-----ccccccee--eeecCCCCHHHHHHHHHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCC
Q 030036 61 IFRE-----DIANAFEF--RMVAPDQTVEQAESGIRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKP 133 (184)
Q Consensus 61 ~~~~-----~~a~~~~~--rf~~ppl~~~eA~~RIke~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P 133 (184)
+.|+ ++||+| | |||+||++|++|++|||++|++|++||+|||+++|+||++|||++++||||||+++|+++|
T Consensus 90 t~n~~~~e~~gtRsf-LKerfy~~~l~p~~aa~RiK~sA~dLl~vKdLId~~sW~yVq~~LRLKAsyL~yDL~tvIsskP 168 (220)
T PLN02729 90 VDNKIVNEKTGTRSF-LKKGIYMADIGTKGRMYRVKKYAFDLLALEDLIGPDTLNYVRKYLRLKSTFMYYDFDKLISAAP 168 (220)
T ss_pred cccccccccchHHHH-HHhcccCCCCCHHHHHHHHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4577 999999 7 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHHHHHhhC
Q 030036 134 ATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALDSILSRL 184 (184)
Q Consensus 134 ~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa~i 184 (184)
+++|+++++||++||++|++||||||+||++++++||++|+++|||||++|
T Consensus 169 ~~eKk~L~~LankLFdn~~eLD~AaR~Ks~~eae~yY~~Tv~aLdeVl~k~ 219 (220)
T PLN02729 169 VDDKQPLTDLANRLFDNFEKLEDASKRKNLSETESSYKDTKTLLQEVMDRM 219 (220)
T ss_pred hhhhHHHHHHHHHHHhhHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999986
No 4
>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=8.6e-44 Score=299.51 Aligned_cols=124 Identities=36% Similarity=0.590 Sum_probs=102.0
Q ss_pred hcccccccccee----eeecCCCCHHHHHHHHHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCC
Q 030036 61 IFREDIANAFEF----RMVAPDQTVEQAESGIRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATE 136 (184)
Q Consensus 61 ~~~~~~a~~~~~----rf~~ppl~~~eA~~RIke~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~ 136 (184)
+.++++||||+| |||+||++|+|+++||++++++|++|++||++++|+||++|||+++|||||||++||+++|+++
T Consensus 74 ~~~~~~aRd~~l~lk~rf~~~~l~~~ea~~Rik~sa~~L~~lk~lIdk~sW~~v~~~LRlka~~Lr~DL~~liss~p~~~ 153 (202)
T PF05757_consen 74 TNNSDGARDFDLPLKERFYIQPLSPEEAAARIKESAKRLLSLKELIDKKSWPYVRNYLRLKAGYLRYDLNTLISSKPKDE 153 (202)
T ss_dssp --------------TT--EE----CCCHHHHHHHHHHHHCCCHHHHHTT-HHHHHHHHHCCCCCHHHHHHHHHCCS-HHH
T ss_pred ccccccccccccchhhceecCCCCHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHhHHHHHHHHHHHhCCHHH
Confidence 456899999987 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHHHHHhhC
Q 030036 137 RPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALDSILSRL 184 (184)
Q Consensus 137 Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa~i 184 (184)
||++++|+++||++||+||+|+|+||++++++||++|+++||+||++|
T Consensus 154 kk~l~~La~~lf~~ie~LD~Aar~K~~~~a~~~Y~~t~~~Ldevla~l 201 (202)
T PF05757_consen 154 KKALTDLANKLFDNIEELDYAARSKDVPEAEKYYADTVKALDEVLAKL 201 (202)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHCCH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999975
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=100.00 E-value=5.7e-33 Score=223.28 Aligned_cols=108 Identities=19% Similarity=0.311 Sum_probs=103.0
Q ss_pred CCCCHHHHHHHHHHHHHhHH-------HHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhh
Q 030036 77 PDQTVEQAESGIRYHAQSLL-------HVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFN 149 (184)
Q Consensus 77 ppl~~~eA~~RIke~A~~L~-------~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~ 149 (184)
||+|+.+.+++|+.++++|. +|+.+|++++|++|||+||||+|+||+||++||+++|++|||++++|+++||+
T Consensus 27 p~tysp~~l~~i~~~~~~i~~~~~r~~eLk~lI~kk~W~~vrn~irgp~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~ 106 (142)
T TIGR03042 27 PPTYSPAQLAQIQRQAEGIEAAKDRLPELASLVAKEDWVFTRNLIHGPMGEVRREMTYLNQSLLPKDQKEALALAKELKD 106 (142)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhcchHHHHHHHhccHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHH
Confidence 99999999998888888864 46899999999999999999999999999999999999999999999999999
Q ss_pred chHhHHHHHhcCChHHHHHHHHHHHHHHHHHHhhC
Q 030036 150 GVTKLDYAARDKDVSRVHQCYENVVVALDSILSRL 184 (184)
Q Consensus 150 ~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa~i 184 (184)
++++||+||+.||.++|+++|++++++||+|++.|
T Consensus 107 ~L~~LD~AA~~kd~~~a~k~Y~~av~~~dafl~~~ 141 (142)
T TIGR03042 107 DLEKLDEAARLQDGPQAQKAYQKAAADFDAYLDLL 141 (142)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999865
No 6
>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=60.26 E-value=62 Score=31.10 Aligned_cols=96 Identities=19% Similarity=0.263 Sum_probs=58.6
Q ss_pred HHHHHHHHHHhHH-HHHHhhhhcC-----hHHHHHHHhhchhhhHHHHHHHhhc-CCCCChHHHHHHHHh----------
Q 030036 84 AESGIRYHAQSLL-HVKALLESES-----WSEVQKALRASSASLKQDIYTLINN-KPATERPQLRKLYSD---------- 146 (184)
Q Consensus 84 A~~RIke~A~~L~-~lk~lIdkks-----W~~Vrn~LRlka~~Lr~DL~~lIss-~P~d~Kk~l~~La~~---------- 146 (184)
.+.|+.....++. +|.++|++++ |-.-...|..++..|..|++.+.++ .+..-++.+.+.+.+
T Consensus 15 ~I~~L~~~i~~~k~eV~~~I~~~y~df~~~~~~~~~L~~~~~~l~~eI~d~l~~~~~~~i~~~l~~a~~e~~~L~~eL~~ 94 (593)
T PF06248_consen 15 SISRLSRRIEELKEEVHSMINKKYSDFSPSLQSAKDLIERSKSLAREINDLLQSEIENEIQPQLRDAAEELQELKRELEE 94 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555553 4666676665 6666777888888899999777776 454455555444333
Q ss_pred ------HhhchH-------hHHHHHhcCChHHHHHHHHHHHHHHHH
Q 030036 147 ------LFNGVT-------KLDYAARDKDVSRVHQCYENVVVALDS 179 (184)
Q Consensus 147 ------LF~~le-------~LD~AAr~Kn~~~A~~~Y~~tv~~Lde 179 (184)
+..++. +++.|...|+...|...-+++-..|++
T Consensus 95 ~~~~l~~L~~L~~i~~~l~~~~~al~~~~~~~Aa~~L~~~~~~L~~ 140 (593)
T PF06248_consen 95 NEQLLEVLEQLQEIDELLEEVEEALKEGNYLDAADLLEELKSLLDD 140 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh
Confidence 233444 444555666666666666666666665
No 7
>PF12185 IR1-M: Nup358/RanBP2 E3 ligase domain; InterPro: IPR022011 This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with PF00638 from PFAM, PF00641 from PFAM, PF00160 from PFAM. There are two conserved sequence motifs: TFFC and EDF. Nup358/RanBP2 is a nucleoporin involved in ubiquitination of many different protein targets from various cellular pathways. It complexes with Ubc9, SUMO-1 and RanGAP1 to perform this function. This is the ligase domain which binds to Ubc9. ; PDB: 3UIO_D 3UIP_D 3UIN_D 1Z5S_D.
Probab=57.19 E-value=4 Score=29.44 Aligned_cols=14 Identities=50% Similarity=1.125 Sum_probs=10.1
Q ss_pred CCCCcceeeecC-cc
Q 030036 13 PHLYPTFMCYQQ-PA 26 (184)
Q Consensus 13 ~~~~~~~~~~~~-~~ 26 (184)
.+|+|||.|+.. |-
T Consensus 21 L~LPpTFfcy~~~pd 35 (64)
T PF12185_consen 21 LQLPPTFFCYKNKPD 35 (64)
T ss_dssp TT--TTGGGGGGSSS
T ss_pred cCCCCcEEEeecCCC
Confidence 579999999987 75
No 8
>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=56.13 E-value=80 Score=23.33 Aligned_cols=132 Identities=9% Similarity=0.028 Sum_probs=59.3
Q ss_pred cchhhHHHHHHHHHHHhhhh---hhccccccccceeeeecCCCCHHHHHHHHHHHHHhHH-HHHHhhhhcChHHHHHHHh
Q 030036 40 NISRRIGVIAVTASTMLARE---AIFREDIANAFEFRMVAPDQTVEQAESGIRYHAQSLL-HVKALLESESWSEVQKALR 115 (184)
Q Consensus 40 ~~~rr~~~~~~~~~~~~~~~---~~~~~~~a~~~~~rf~~ppl~~~eA~~RIke~A~~L~-~lk~lIdkksW~~Vrn~LR 115 (184)
++++|+.+.-++..+++..- ++.+....++--=.+|--.+.+-..+..++....++. .+..++-..+= .-+..++
T Consensus 3 ~I~~KL~~~f~~~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 81 (181)
T PF12729_consen 3 SIRTKLILGFGLIILLLLIVGIVGLYSLSQINQNVEEIYENNLPSIELLNDIRSNLQRIRRALRRYLLATDP-EERQEIE 81 (181)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhhcCCH-HHHHHHH
Confidence 57778774433333222222 2222222111111344444445555666666655553 34444444221 1122233
Q ss_pred hchhhhHHH----HHHHhhc-CCCCChHHHH---HHHHhHhhchHhHHHHHhcCChHHHHHHHHH
Q 030036 116 ASSASLKQD----IYTLINN-KPATERPQLR---KLYSDLFNGVTKLDYAARDKDVSRVHQCYEN 172 (184)
Q Consensus 116 lka~~Lr~D----L~~lIss-~P~d~Kk~l~---~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~ 172 (184)
......+.+ +..+-.. ..+++|+.+. +..+++.+..+++=..++.++..+|...|..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~a~~~~~~ 146 (181)
T PF12729_consen 82 KEIDEARAEIDEALEEYEKLILSPEEKQLLEEFKEAWKAYRKLRDQVIELAKSGDNDEARAILNG 146 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 323333333 3333222 2333443333 3334555555666667788888777665543
No 9
>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=46.03 E-value=59 Score=23.50 Aligned_cols=44 Identities=18% Similarity=0.314 Sum_probs=38.6
Q ss_pred HhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHH
Q 030036 114 LRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAA 158 (184)
Q Consensus 114 LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AA 158 (184)
|..++|.+..||-.|..-||.+=. .+-.++.+.|+-+.++|.|=
T Consensus 14 L~~~A~~~kmdLHDLaEdLP~~w~-~i~~vA~~ty~a~~~l~~ak 57 (66)
T PF05082_consen 14 LNRKATQAKMDLHDLAEDLPTNWE-EIPEVAQKTYDAYAELDEAK 57 (66)
T ss_dssp HHHHHHHHHHHHHHHHHCTTTTGG-GHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHccchhHH-HHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999888544 89999999999999998764
No 10
>COG5420 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=41.59 E-value=67 Score=23.48 Aligned_cols=46 Identities=20% Similarity=0.324 Sum_probs=40.2
Q ss_pred HHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHHh
Q 030036 113 ALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAAR 159 (184)
Q Consensus 113 ~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr 159 (184)
-|..++|.++.||..+...+|.+ .-++-+.+.+-|.-+.+||.+-+
T Consensus 17 kLqsrAg~akm~LhDLAEgLP~~-wtei~~VA~kt~~~yaeLD~~k~ 62 (71)
T COG5420 17 KLQSRAGQAKMELHDLAEGLPVK-WTEIMAVAEKTFEAYAELDAAKR 62 (71)
T ss_pred HHHHHHHHHHhhHHHHhccCCcc-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 36678999999999999999984 55899999999999999998755
No 11
>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=41.54 E-value=69 Score=24.10 Aligned_cols=41 Identities=15% Similarity=0.288 Sum_probs=36.1
Q ss_pred ChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHH
Q 030036 136 ERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVA 176 (184)
Q Consensus 136 ~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~ 176 (184)
+......++..+-.....|..|++.+|...+...|.+.-.+
T Consensus 73 ~~~~F~~~~~~~~~aa~~L~~aa~~~d~~~~~~a~~~v~~~ 113 (122)
T PF01322_consen 73 DPEDFKQLAQAFQKAAAALAAAAKSGDLAAIKAAFGEVGKS 113 (122)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999886543
No 12
>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=40.48 E-value=99 Score=20.88 Aligned_cols=46 Identities=20% Similarity=0.205 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhHHHHHHh-hhhcChHHHHHHHhhchhhhHHHHH
Q 030036 81 VEQAESGIRYHAQSLLHVKAL-LESESWSEVQKALRASSASLKQDIY 126 (184)
Q Consensus 81 ~~eA~~RIke~A~~L~~lk~l-IdkksW~~Vrn~LRlka~~Lr~DL~ 126 (184)
|+.++.|+-.|..-|..+++- ++.=+-.+....+.......|.||+
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 466789999999988888663 6777788999999999999999985
No 13
>CHL00102 rps20 ribosomal protein S20
Probab=40.38 E-value=66 Score=24.46 Aligned_cols=44 Identities=9% Similarity=0.273 Sum_probs=24.6
Q ss_pred HHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 030036 138 PQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALDSIL 181 (184)
Q Consensus 138 k~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevL 181 (184)
..++.+.+++...++..|.-...+|..+|+..|.++.+.||...
T Consensus 26 S~~rT~iKk~~~ai~~~~~~~~~~d~~~a~~~l~~a~s~iDkaa 69 (93)
T CHL00102 26 SSVKTLIKKYLKNLEDYKTSPNSNNKKKVQETLSSVYSKIDKAV 69 (93)
T ss_pred HHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444443333334677777777777777777654
No 14
>KOG0412 consensus Golgi transport complex COD1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.21 E-value=1.4e+02 Score=30.58 Aligned_cols=85 Identities=20% Similarity=0.327 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHhHHHHHHh----------hhhcChHHHHHHHhhchhhhHHHHHHHhhc-----CCCCCh-------HH
Q 030036 82 EQAESGIRYHAQSLLHVKAL----------LESESWSEVQKALRASSASLKQDIYTLINN-----KPATER-------PQ 139 (184)
Q Consensus 82 ~eA~~RIke~A~~L~~lk~l----------IdkksW~~Vrn~LRlka~~Lr~DL~~lIss-----~P~d~K-------k~ 139 (184)
.-|.+|+.++-....+|.++ |+.++|--....||+=.+. |-..+-+. .|.++- ++
T Consensus 111 Dla~~Rv~~clq~v~dvrdlk~C~~gv~~Al~seDyE~AA~~IhRflsl---D~~~i~~~~~~~~~~ts~i~~~~~~L~~ 187 (773)
T KOG0412|consen 111 DLAQNRVNECLQRVDDVRDLKNCIEGVDTALESEDYEKAATHIHRFLSL---DQALIESRFAKQVVPTSEISDPYETLKE 187 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhc---CHHHHhhhhhhccCCchhhhhHHHHHHH
Confidence 34678888888877777555 8999999999999875443 54433333 122211 12
Q ss_pred HHHHHHhHhhchHhHHHHHhcCChHHHHHHHH
Q 030036 140 LRKLYSDLFNGVTKLDYAARDKDVSRVHQCYE 171 (184)
Q Consensus 140 l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~ 171 (184)
+++=-..||. ++++.|+|.+|.++.+.+++
T Consensus 188 a~e~L~~l~~--~~f~eA~r~~D~~ei~RffK 217 (773)
T KOG0412|consen 188 AKERLSKLFK--ERFTEAVRKQDLKEITRFFK 217 (773)
T ss_pred HHHHHHHHHH--HHHHHHHhcccHHHHHHHHH
Confidence 2222223333 57899999999999988764
No 15
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=37.35 E-value=2.7e+02 Score=23.92 Aligned_cols=42 Identities=14% Similarity=0.216 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhhhhhccccccccceeeeecCCCCHHHHHHHHH
Q 030036 47 VIAVTASTMLAREAIFREDIANAFEFRMVAPDQTVEQAESGIR 89 (184)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~a~~~~~rf~~ppl~~~eA~~RIk 89 (184)
.+.+|-.+++++.+-+|+.-.+.. +|+.+||++.|--..-+|
T Consensus 76 ~~~~IekaI~~snLglnP~~dG~~-IRv~~P~lTeErRkelvK 117 (187)
T COG0233 76 MVKAIEKAILASNLGLNPNNDGNV-IRVPLPPLTEERRKELVK 117 (187)
T ss_pred hHHHHHHHHHHcCCCCCcCcCCCe-EEecCCCCCHHHHHHHHH
Confidence 355788889999887776554444 899999999875544444
No 16
>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=30.44 E-value=75 Score=23.24 Aligned_cols=24 Identities=13% Similarity=0.340 Sum_probs=21.3
Q ss_pred hcCChHHHHHHHHHHHHHHHHHHh
Q 030036 159 RDKDVSRVHQCYENVVVALDSILS 182 (184)
Q Consensus 159 r~Kn~~~A~~~Y~~tv~~LdevLa 182 (184)
+.++..+|..||++++..|-.++.
T Consensus 18 ~~gr~~eAi~~Y~~aIe~L~q~~~ 41 (75)
T cd02682 18 KEGNAEDAITNYKKAIEVLSQIVK 41 (75)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999988874
No 17
>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=30.18 E-value=1.5e+02 Score=18.82 Aligned_cols=52 Identities=13% Similarity=0.165 Sum_probs=30.4
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHHhcC-ChHHHHHHHHHHHHH
Q 030036 122 KQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAARDK-DVSRVHQCYENVVVA 176 (184)
Q Consensus 122 r~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr~K-n~~~A~~~Y~~tv~~ 176 (184)
|..+...++.+|+.+|..+. -..++.+.-=+=|...+ +...+...+..+.+.
T Consensus 1 r~~l~~~l~~L~~~~r~i~~---l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFL---LRYFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHH---HHHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH---HHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 56788899999998874333 23456665555555555 666666776666554
No 18
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=30.17 E-value=1.3e+02 Score=22.59 Aligned_cols=30 Identities=17% Similarity=0.237 Sum_probs=20.0
Q ss_pred HhHHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 030036 152 TKLDYAARDKDVSRVHQCYENVVVALDSIL 181 (184)
Q Consensus 152 e~LD~AAr~Kn~~~A~~~Y~~tv~~LdevL 181 (184)
-++..|+..+|..+|...|.++.+.||...
T Consensus 33 Kk~~~ai~~~d~~~a~~~l~~a~s~iDkaa 62 (87)
T TIGR00029 33 KKVYAAIAAGDKDKAQEAFKEAAKKLDRAA 62 (87)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345555666777777777777777777654
No 19
>PRK11546 zraP zinc resistance protein; Provisional
Probab=28.31 E-value=1.1e+02 Score=25.17 Aligned_cols=65 Identities=20% Similarity=0.174 Sum_probs=40.9
Q ss_pred eecCCCCHHHHHHH---HHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhc
Q 030036 74 MVAPDQTVEQAESG---IRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNG 150 (184)
Q Consensus 74 f~~ppl~~~eA~~R---Ike~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~ 150 (184)
=+..+++||.+... .+++..+. ..||.+.-.-+.+|+.+.++-++|++ .+++|++|+.+=
T Consensus 39 ~~~~~LT~EQQa~~q~I~~~f~~~t----------------~~LRqqL~aKr~ELnALl~~~~pD~~-kI~aL~kEI~~L 101 (143)
T PRK11546 39 QNAAPLTTEQQAAWQKIHNDFYAQT----------------SALRQQLVSKRYEYNALLTANPPDSS-KINAVAKEMENL 101 (143)
T ss_pred cccccCCHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHHH
Confidence 35567888877443 12233332 34666667778899999888666554 677777776665
Q ss_pred hHhHH
Q 030036 151 VTKLD 155 (184)
Q Consensus 151 le~LD 155 (184)
-.+|+
T Consensus 102 r~kL~ 106 (143)
T PRK11546 102 RQSLD 106 (143)
T ss_pred HHHHH
Confidence 54444
No 20
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=27.37 E-value=1.5e+02 Score=22.12 Aligned_cols=29 Identities=14% Similarity=0.153 Sum_probs=19.2
Q ss_pred HHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 030036 154 LDYAARDKDVSRVHQCYENVVVALDSILS 182 (184)
Q Consensus 154 LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa 182 (184)
+..|+..+|..+|...|..+.+.||....
T Consensus 35 ~~~ai~~~~~~~a~~~~~~a~s~iDka~~ 63 (88)
T PRK00239 35 VEAAIAAGDKEAAEEALKAAQSKIDKAAS 63 (88)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 44455567777777777777777776543
No 21
>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=26.35 E-value=71 Score=25.39 Aligned_cols=16 Identities=31% Similarity=0.407 Sum_probs=12.8
Q ss_pred HHHHHHHhhcCCCCCh
Q 030036 122 KQDIYTLINNKPATER 137 (184)
Q Consensus 122 r~DL~~lIss~P~d~K 137 (184)
-+++.+||++||+.+.
T Consensus 82 akqIe~LIdsLPg~~~ 97 (144)
T PF11221_consen 82 AKQIEYLIDSLPGIEV 97 (144)
T ss_dssp HHHHHHHHHHSTTSSS
T ss_pred HHHHHHHHHhCCCCCC
Confidence 4688999999998544
No 22
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=25.13 E-value=49 Score=19.33 Aligned_cols=14 Identities=14% Similarity=0.467 Sum_probs=11.7
Q ss_pred eeeecCccccccCC
Q 030036 19 FMCYQQPAFRSKGM 32 (184)
Q Consensus 19 ~~~~~~~~~~~~~~ 32 (184)
|+|-|.|-|+...+
T Consensus 2 y~C~C~~Gy~l~~d 15 (24)
T PF12662_consen 2 YTCSCPPGYQLSPD 15 (24)
T ss_pred EEeeCCCCCcCCCC
Confidence 79999999997654
No 23
>PF12805 FUSC-like: FUSC-like inner membrane protein yccS
Probab=24.94 E-value=2e+02 Score=24.84 Aligned_cols=46 Identities=15% Similarity=0.214 Sum_probs=21.1
Q ss_pred CCCCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHH
Q 030036 132 KPATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALD 178 (184)
Q Consensus 132 ~P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~Ld 178 (184)
.|....+.+.....++-+.++.+-.. ......++...-.+...-|.
T Consensus 233 ~~~~~~~~l~~~l~~l~~~l~~~~~~-~~~~~~~~~~~l~~l~~~l~ 278 (284)
T PF12805_consen 233 RPYHHRNRLKRALEALEESLEFLRQQ-DQPENREALLALRNLLDNLR 278 (284)
T ss_pred CCCCCchHHHHHHHHHHHHHHHHHHh-cCccCHHHHHHHHHHHHHHH
Confidence 44444445555555555555554444 33333444444444444333
No 24
>KOG4519 consensus Phosphomevalonate kinase [Lipid transport and metabolism]
Probab=24.41 E-value=1.4e+02 Score=28.45 Aligned_cols=66 Identities=15% Similarity=0.182 Sum_probs=47.2
Q ss_pred HHHHHHhhhhcChHHHHHHHhhchhhh---------------HHHHHHHhhc-CCCCCh--HHHHHHHHhHhhchHhHHH
Q 030036 95 LLHVKALLESESWSEVQKALRASSASL---------------KQDIYTLINN-KPATER--PQLRKLYSDLFNGVTKLDY 156 (184)
Q Consensus 95 L~~lk~lIdkksW~~Vrn~LRlka~~L---------------r~DL~~lIss-~P~d~K--k~l~~La~~LF~~le~LD~ 156 (184)
+.++...+.|+.|..++..-++|.++= -+-..+---+ .|++.| +.+-+++.+|-+.+.+||.
T Consensus 247 ~~el~~~V~k~~W~~~~~~f~LP~~~~L~mGd~~gGSsTp~mV~kVk~Wq~s~~pe~~k~~~~lddansr~~~~l~kl~~ 326 (459)
T KOG4519|consen 247 LNELIGTVLKGKWDNKRTEFSLPPLMNLFMGDGSGGSSTPSMVGKVKKWQMSDPPEARKNWQNLDDANSRLETKLNKLSK 326 (459)
T ss_pred hHHHHHHhhhhhcccccccccCCceeeeeeecCCCCCCcHHHHHHHHHHhhcCChhHhhhhcchhhHHHHHHhhhhhhhH
Confidence 346788899999999999999998752 2222222223 455455 5777888899998999888
Q ss_pred HHhc
Q 030036 157 AARD 160 (184)
Q Consensus 157 AAr~ 160 (184)
-+++
T Consensus 327 l~~~ 330 (459)
T KOG4519|consen 327 LAKD 330 (459)
T ss_pred hhhh
Confidence 8877
No 25
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.38 E-value=1.2e+02 Score=30.21 Aligned_cols=133 Identities=14% Similarity=0.145 Sum_probs=71.3
Q ss_pred cceeeecCcc--ccccCCCcccccccchhhHHHHHHHHHHHhhhhhhcccccccccee---eeecCCCCHHHHHHHHHHH
Q 030036 17 PTFMCYQQPA--FRSKGMPQNVLQCNISRRIGVIAVTASTMLAREAIFREDIANAFEF---RMVAPDQTVEQAESGIRYH 91 (184)
Q Consensus 17 ~~~~~~~~~~--~~~~~~~~~~~~~~~~rr~~~~~~~~~~~~~~~~~~~~~~a~~~~~---rf~~ppl~~~eA~~RIke~ 91 (184)
+++.||+-+. +...|-.-..-...-.+++.+.+++++-++++. .+..+++.-+ -.|+.|-=-..-..-++.+
T Consensus 83 ~~~~C~~~dl~~lL~~Gf~~g~~~~~ppk~~~ta~~~~~~~~~~~---q~~~~Ggqa~~~~d~~lAPyv~~~~~~~l~~~ 159 (618)
T PRK14704 83 GTTTCSQIPLAQMLANGFHTGHGHMRQPQDIKSALALSSIIFQAN---QNMQHGGQSFALFDVDLAPYVRKTVERHKKRL 159 (618)
T ss_pred CCCccccccHHHHHhcCcCCCCceeCCCCCHHHHHHHHHHHHHHH---HhhhhcCeeHHHHHHHhhhHHHHhHHHHHHHH
Confidence 4678998765 222222212235566788887666665555542 3344555444 2333331100001111111
Q ss_pred HHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHH-hh----------cCCCCChHHHHHHHHhHhhchHh
Q 030036 92 AQSLLHVKALLESESWSEVQKALRASSASLKQDIYTL-IN----------NKPATERPQLRKLYSDLFNGVTK 153 (184)
Q Consensus 92 A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~l-Is----------s~P~d~Kk~l~~La~~LF~~le~ 153 (184)
.+.... .+.|.+-+|..+.+.+.--.-.+-|.||++ .+ ++.-+-.++.+.+.+.|++-+.+
T Consensus 160 ~~~~~~-~~~~~~~a~~~~~~ev~qa~Q~f~y~lNt~~sr~ggQ~PFt~it~g~~~~~e~~~i~~a~l~v~~e 231 (618)
T PRK14704 160 QSYPLT-KEQIEEFAWKETENDTYQACEAFIHNSNSMHSRGGGQVPFISINYGTDTSKEGRLLIKQLLKATQA 231 (618)
T ss_pred HHhhcc-HHHHHHHHHHHHHHHHHHHHHhheeeeccccccCCCCCCeEEEEeCCCCCHHHHHHHHHHHHHHHh
Confidence 111111 233677788889999988888888899988 43 12334445777777777765543
No 26
>PLN03184 chloroplast Hsp70; Provisional
Probab=24.21 E-value=4.6e+02 Score=25.97 Aligned_cols=73 Identities=8% Similarity=0.130 Sum_probs=41.7
Q ss_pred hhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 030036 103 ESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALDSILS 182 (184)
Q Consensus 103 dkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa 182 (184)
....+.+.+|.+..-.-.++.-+...-...++++|.++.++-+++-+-|+. .+..+.+..|++....++.+..
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 344445555544433333333332222246777888888887777766653 3556666667776666666554
No 27
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=23.93 E-value=4.2e+02 Score=21.96 Aligned_cols=50 Identities=10% Similarity=0.069 Sum_probs=33.0
Q ss_pred HHHHHHHHHhhhhhhccccccccceeeeecCCCCHHHHHHHHHHHHHhHHH
Q 030036 47 VIAVTASTMLAREAIFREDIANAFEFRMVAPDQTVEQAESGIRYHAQSLLH 97 (184)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~a~~~~~rf~~ppl~~~eA~~RIke~A~~L~~ 97 (184)
.+.++..++..+..-+|+. ..+-.+|+-+||++.|--.+=++...+....
T Consensus 65 ~~~~I~kAI~~s~lglnP~-~dg~~Iri~iP~lT~E~RkelvK~~k~~~E~ 114 (176)
T TIGR00496 65 NINAIEKAIQRSDLGLNPN-NDGSVIRVNFPPLTEERRKELVKHAKKIAEQ 114 (176)
T ss_pred hHHHHHHHHHHCCCCCCcc-cCCCEEEecCCCCCHHHHHHHHHHHHHHHHH
Confidence 4567888888888777774 2333579999999887655555544443333
No 28
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=23.90 E-value=2.2e+02 Score=21.42 Aligned_cols=39 Identities=10% Similarity=0.101 Sum_probs=27.9
Q ss_pred HHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHHHH
Q 030036 142 KLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALDSI 180 (184)
Q Consensus 142 ~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~Ldev 180 (184)
..+.++-+.++.++.++..+|-.+|++.+++..+.-+..
T Consensus 23 ~~~~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~ 61 (121)
T PF14276_consen 23 NSTDSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKN 61 (121)
T ss_pred hHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhh
Confidence 445666677777788888888888887777777665543
No 29
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=23.89 E-value=4e+02 Score=23.06 Aligned_cols=89 Identities=15% Similarity=0.190 Sum_probs=45.0
Q ss_pred HHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhh-------cCCCCChHHHHHHHHhHhhchHhHHHHHhcCChH
Q 030036 92 AQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLIN-------NKPATERPQLRKLYSDLFNGVTKLDYAARDKDVS 164 (184)
Q Consensus 92 A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIs-------s~P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~ 164 (184)
...|..+=-.+-.+.++-.++.||...-.+-.-+..++. +..+++++.....++.+++.-+.|-...++ |..
T Consensus 44 l~~l~~~~~~~~~~~G~tL~~~i~~~v~~lv~~~~~L~~~~~~~~~s~~~~~~~~~~~~tG~VWeaCd~l~~lp~~-n~~ 122 (275)
T PF13324_consen 44 LLGLLSLYHGLPKGQGPTLRKEIRSAVKSLVDSSIQLVEELVSAYGSSSQSEKNEVLQSTGRVWEACDQLKKLPKD-NKV 122 (275)
T ss_dssp HHHHHHHHTTS-GGG-HHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHTTTTS-SS-HHH
T ss_pred HHHHHHHHhhCcHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcccCccchhHHHHhHHHHHHHHHHHhhhh-hHH
Confidence 333444444466777888888888887777655554433 334667788889999999999999776664 555
Q ss_pred HHHHHHHHHHHHHHHHH
Q 030036 165 RVHQCYENVVVALDSIL 181 (184)
Q Consensus 165 ~A~~~Y~~tv~~LdevL 181 (184)
.+.+.-.+....+++.+
T Consensus 123 av~~~~~~~~~lvkDa~ 139 (275)
T PF13324_consen 123 AVLRRLKQSRDLVKDAL 139 (275)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55555555555554443
No 30
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=23.88 E-value=4.3e+02 Score=22.08 Aligned_cols=50 Identities=10% Similarity=0.102 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhhhhhccccccccceeeeecCCCCHHHHHHHHHHHHHhHHH
Q 030036 47 VIAVTASTMLAREAIFREDIANAFEFRMVAPDQTVEQAESGIRYHAQSLLH 97 (184)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~a~~~~~rf~~ppl~~~eA~~RIke~A~~L~~ 97 (184)
.+-.|..++..+.+-+|+.. .+-.+|+-+|+++.|--.+=++...+....
T Consensus 74 ~i~~I~kAI~~s~lgl~P~~-dg~~Iri~iP~lT~E~R~elvK~~k~~~E~ 123 (185)
T PRK00083 74 MLKAIEKAIRASDLGLNPSN-DGTVIRLPIPPLTEERRKELVKQVKKEAEE 123 (185)
T ss_pred HHHHHHHHHHHCCCCCCccc-CCCEEEecCCCCCHHHHHHHHHHHHHHHHH
Confidence 45678888888887677744 344589999999987665555544444333
No 31
>KOG2607 consensus CDK5 activator-binding protein [Signal transduction mechanisms]
Probab=23.77 E-value=5.2e+02 Score=25.33 Aligned_cols=61 Identities=16% Similarity=0.141 Sum_probs=49.5
Q ss_pred HHhhchhhhHHHHHHHhhcC---CCCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHH
Q 030036 113 ALRASSASLKQDIYTLINNK---PATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVV 174 (184)
Q Consensus 113 ~LRlka~~Lr~DL~~lIss~---P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv 174 (184)
++-.+++..|-++...++.+ ...-|.++.+++++|=..|-++-.++-.+ ...|-.||++-+
T Consensus 147 d~~k~aa~~r~qfe~~c~qlglkG~nvr~ElLelasdLPs~fyei~~v~i~~-i~~aiDyYqa~v 210 (505)
T KOG2607|consen 147 DIKKSAALSRTQFEDACRQLGLKGNNVRRELLELASDLPSTFYEILEVIISD-ITGAIDYYQAYV 210 (505)
T ss_pred HhCccHHHHHHHHHHHHHHhCCccchHHHHHHHHHhcCcHHHHHHHHHHHhh-hhHHHHHHHHHH
Confidence 56677888999999999883 34478899999999987777777666554 999999999888
No 32
>PRK14140 heat shock protein GrpE; Provisional
Probab=23.06 E-value=4.7e+02 Score=22.21 Aligned_cols=48 Identities=21% Similarity=0.172 Sum_probs=31.4
Q ss_pred ChHHHHHHHHhHhhchHhHHHHHhcCChHHH----HHHHHHHHHHHHHHHhh
Q 030036 136 ERPQLRKLYSDLFNGVTKLDYAARDKDVSRV----HQCYENVVVALDSILSR 183 (184)
Q Consensus 136 ~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A----~~~Y~~tv~~LdevLa~ 183 (184)
.+-...++.++|+.-+++|+.|....+.... ..-++-+.+.|.++|.+
T Consensus 82 ~~~a~~~~~~~LLpvlDnLerAl~~~~~~~~~~~i~~Gv~mi~k~l~~~L~k 133 (191)
T PRK14140 82 EKYRAQSLASDLLPALDNFERALQIEADDEQTKSLLKGVEMVHRQLLEALKK 133 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHHHHHHHHHHHHHH
Confidence 3446677889999999999999976443222 23344455556655543
No 33
>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=23.03 E-value=3.3e+02 Score=25.44 Aligned_cols=68 Identities=13% Similarity=0.144 Sum_probs=48.4
Q ss_pred HHHHHHHhhchh------hhHHHHHHHhh-cCCCCChHHHHHHHHhHhh-----chHhHHHHHhc-----------CChH
Q 030036 108 SEVQKALRASSA------SLKQDIYTLIN-NKPATERPQLRKLYSDLFN-----GVTKLDYAARD-----------KDVS 164 (184)
Q Consensus 108 ~~Vrn~LRlka~------~Lr~DL~~lIs-s~P~d~Kk~l~~La~~LF~-----~le~LD~AAr~-----------Kn~~ 164 (184)
..+...+++-.. ++..++...+. .++.++++.++.-+.+.++ .++++-...++ .+.+
T Consensus 143 e~~i~q~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~~l~~~~~~ai~~~v~pA~~~~~~~L~~~~~~~~~~~G~~~~~ 222 (549)
T PF05960_consen 143 ERAIAQLRGFIDADPEESFLYEDFPERLAASLSEEQKEALIAQAREAIEEYVIPAYERLRDFLESEYLPAANSSGLSDLP 222 (549)
T ss_dssp HHHHHHHHHHCSS-GGCTCHHHHHHHHHCCCS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTCCCCSHHSGCGST
T ss_pred HHHHHHHHHHHccCcccchHHHHHHHhccccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCcccCC
Confidence 456667777666 88899999888 6788888888888877777 78787666652 2445
Q ss_pred HHHHHHHHHHH
Q 030036 165 RVHQCYENVVV 175 (184)
Q Consensus 165 ~A~~~Y~~tv~ 175 (184)
....+|+..+.
T Consensus 223 ~G~~~Y~~~l~ 233 (549)
T PF05960_consen 223 NGKEYYERLLR 233 (549)
T ss_dssp THHHHHHHHHH
T ss_pred CcHHHHHHHHH
Confidence 66777776654
No 34
>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=22.10 E-value=3.1e+02 Score=19.80 Aligned_cols=64 Identities=8% Similarity=0.064 Sum_probs=36.7
Q ss_pred chhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHHHHHHHHHH
Q 030036 117 SSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENVVVALDSIL 181 (184)
Q Consensus 117 ka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevL 181 (184)
....|+-|+..++.+....-...+.++..++-+.++..-..+...- ..+...++++....++.+
T Consensus 6 ~l~~l~~d~~~l~~~~~~~~~~~~~~~r~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~~~~~~V 69 (94)
T PF05957_consen 6 ELEQLRADLEDLARSAADLAGEKADEARDRAEEALDDARDRAEDAA-DQAREQAREAAEQTEDYV 69 (94)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 3456777777777775544445566666666555555555444332 235555666666666554
No 35
>PF09210 DUF1957: Domain of unknown function (DUF1957); InterPro: IPR015293 This C-terminal domain is found in a set of hypothetical bacterial proteins that have a N-terminal domain related to the glycoside hydrolase family 57 family GH57 from CAZY. The exact function of this domain has not, as yet, been defined. ; PDB: 3N98_A 3N8T_A 3N92_A 1UFA_A 3P0B_A.
Probab=22.08 E-value=1.6e+02 Score=22.55 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHHHHHhHHHHHHhhhhcC
Q 030036 77 PDQTVEQAESGIRYHAQSLLHVKALLESES 106 (184)
Q Consensus 77 ppl~~~eA~~RIke~A~~L~~lk~lIdkks 106 (184)
-++.++.|..|++++..+...+.+.|+.+.
T Consensus 49 ~gta~~YA~~R~~~Hl~rF~~L~~~l~~~~ 78 (102)
T PF09210_consen 49 TGTAVEYARERFKEHLNRFWRLYDMLESGR 78 (102)
T ss_dssp CTTTHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 568889999999999999999988888654
No 36
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=22.03 E-value=3.5e+02 Score=20.30 Aligned_cols=81 Identities=14% Similarity=0.146 Sum_probs=52.5
Q ss_pred HhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHH
Q 030036 93 QSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYEN 172 (184)
Q Consensus 93 ~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~ 172 (184)
..+..+++.|++++|..+.+.+-.=... -.......+-. -+..+..+ +=.++.+|..++..+|.+++...-..
T Consensus 30 ~~l~~i~~~i~~~dW~~A~~~~~~l~~~-W~k~~~~~~~~--~~h~eid~----i~~sl~rl~~~i~~~dk~~~l~el~~ 102 (121)
T PF14276_consen 30 EQLEQIEEAIENEDWEKAYKETEELEKE-WDKNKKRWSIL--IEHQEIDN----IDISLARLKGYIEAKDKSESLAELAE 102 (121)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHH-HHhhchheeee--ecHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 4456789999999999998766432222 12222222211 13334443 45678899999999999998887777
Q ss_pred HHHHHHHH
Q 030036 173 VVVALDSI 180 (184)
Q Consensus 173 tv~~Ldev 180 (184)
...-++.+
T Consensus 103 lk~~i~~i 110 (121)
T PF14276_consen 103 LKELIEHI 110 (121)
T ss_pred HHHHHHHH
Confidence 76666554
No 37
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=21.91 E-value=3.3e+02 Score=20.04 Aligned_cols=34 Identities=15% Similarity=0.186 Sum_probs=25.5
Q ss_pred hchHhHHHHHhcCChHHHHHHHHHHHHHHHHHHh
Q 030036 149 NGVTKLDYAARDKDVSRVHQCYENVVVALDSILS 182 (184)
Q Consensus 149 ~~le~LD~AAr~Kn~~~A~~~Y~~tv~~LdevLa 182 (184)
..+-++..|+..+|..+|...|..+.+.||....
T Consensus 29 T~iKk~~~ai~~~~~~~a~~~l~~a~s~iDka~~ 62 (84)
T PF01649_consen 29 TAIKKFREAIEAGDKEEAKELLRKAYSAIDKAAK 62 (84)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccChHHHHHHHHHHHHHHHHHHH
Confidence 3455677788888888899999999888887654
No 38
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=20.82 E-value=3.8e+02 Score=20.23 Aligned_cols=73 Identities=12% Similarity=0.114 Sum_probs=38.7
Q ss_pred HHHHhhhhcChHHHHHHHhhchhhhHHHHH---HHhhcCCCCChHHHHHHHHhHhhchHhHHHHHhcCChHHHHHHHHHH
Q 030036 97 HVKALLESESWSEVQKALRASSASLKQDIY---TLINNKPATERPQLRKLYSDLFNGVTKLDYAARDKDVSRVHQCYENV 173 (184)
Q Consensus 97 ~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~---~lIss~P~d~Kk~l~~La~~LF~~le~LD~AAr~Kn~~~A~~~Y~~t 173 (184)
.++..+++..=+.++...|+..+.+..+.. ..+..+.....+.....+.++ .=|-+.+.++..+|...|+++
T Consensus 70 ~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~-----~Gdi~~~~g~~~~A~~~y~~A 144 (145)
T PF09976_consen 70 ALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPDEAFKALAAEL-----LGDIYLAQGDYDEARAAYQKA 144 (145)
T ss_pred HHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHH-----HHHHHHHCCCHHHHHHHHHHh
Confidence 344445544334555566666666665542 122222111122233333222 346677899999999999987
Q ss_pred H
Q 030036 174 V 174 (184)
Q Consensus 174 v 174 (184)
+
T Consensus 145 l 145 (145)
T PF09976_consen 145 L 145 (145)
T ss_pred C
Confidence 4
No 39
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=20.82 E-value=5.1e+02 Score=25.27 Aligned_cols=60 Identities=15% Similarity=0.240 Sum_probs=34.3
Q ss_pred HHHHHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHHHHHhhcCCCCChHHHHHHHHh
Q 030036 85 ESGIRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDIYTLINNKPATERPQLRKLYSD 146 (184)
Q Consensus 85 ~~RIke~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL~~lIss~P~d~Kk~l~~La~~ 146 (184)
+.+.|+...++..+.. +.+.-..=-+-||.+...+.+-+...+++...+-.++..+|.++
T Consensus 65 va~~k~~r~~~~~l~~--~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~ 124 (472)
T TIGR03752 65 VAEVKELRKRLAKLIS--ENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSE 124 (472)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence 6788888888876632 11112222235667777777777777766544444444454444
No 40
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=20.75 E-value=1.3e+02 Score=20.69 Aligned_cols=52 Identities=17% Similarity=0.077 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHHHhHHHHHHh-hhh-cChHHHHHHHhhchhhhHHHHHHH
Q 030036 77 PDQTVEQAESGIRYHAQSLLHVKAL-LES-ESWSEVQKALRASSASLKQDIYTL 128 (184)
Q Consensus 77 ppl~~~eA~~RIke~A~~L~~lk~l-Idk-ksW~~Vrn~LRlka~~Lr~DL~~l 128 (184)
.+++.++...+.+=...-|.++++- .+. .++.|++.|||.=+.+|..|-+.|
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 3566777777777677777776543 222 257899999999999988776543
No 41
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=20.74 E-value=2.5e+02 Score=24.03 Aligned_cols=41 Identities=24% Similarity=0.446 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhHHHHHHhhhhcChHHHHHHHhhchhhhHHHH
Q 030036 84 AESGIRYHAQSLLHVKALLESESWSEVQKALRASSASLKQDI 125 (184)
Q Consensus 84 A~~RIke~A~~L~~lk~lIdkksW~~Vrn~LRlka~~Lr~DL 125 (184)
-...+.++.++|..+++.|++++|..+..++. ++...|.++
T Consensus 237 i~~~l~~~~~~l~~~~~~l~~~d~~~l~~~~~-~~~~~r~~~ 277 (279)
T PRK07417 237 LLRSLASYRQSLDQLEELIEQENWSALEQKLE-QTQELRPNF 277 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHH-HHHHHHHHh
Confidence 36778888888899999999999988888876 355555443
Done!