Query psy11391
Match_columns 112
No_of_seqs 105 out of 193
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 17:13:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11391.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11391hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08292 RNA_pol_Rbc25: RNA po 100.0 1E-39 2.3E-44 233.8 6.7 99 2-107 21-121 (122)
2 KOG3297|consensus 100.0 4.8E-36 1E-40 228.2 8.5 100 2-108 99-199 (202)
3 PTZ00162 DNA-directed RNA poly 99.6 3.2E-16 7E-21 118.0 6.3 73 2-105 99-171 (176)
4 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.5 3.6E-14 7.7E-19 96.1 6.4 66 2-103 19-88 (88)
5 TIGR00448 rpoE DNA-directed RN 99.5 5.7E-14 1.2E-18 105.0 7.1 78 2-108 99-176 (179)
6 PRK08563 DNA-directed RNA poly 99.4 5.1E-13 1.1E-17 99.9 5.8 78 1-107 98-175 (187)
7 COG1095 RPB7 DNA-directed RNA 99.1 7.5E-11 1.6E-15 90.0 5.8 78 2-108 99-176 (183)
8 KOG3298|consensus 96.0 0.026 5.6E-07 42.9 6.2 71 4-105 95-170 (170)
9 cd04460 S1_RpoE S1_RpoE: RpoE, 92.6 0.19 4.2E-06 33.6 3.7 72 8-108 22-94 (99)
10 TIGR02866 CoxB cytochrome c ox 84.8 1.3 2.8E-05 33.6 3.6 32 28-59 98-135 (201)
11 PF02918 Pertussis_S2S3: Pertu 83.5 1.1 2.4E-05 31.9 2.5 41 41-96 64-104 (109)
12 TIGR01433 CyoA cytochrome o ub 79.7 2.4 5.2E-05 33.1 3.4 32 28-59 122-157 (226)
13 PRK09750 hypothetical protein; 79.4 2 4.3E-05 27.8 2.4 21 86-110 3-23 (64)
14 TIGR01432 QOXA cytochrome aa3 77.8 2.6 5.7E-05 32.4 3.1 32 28-59 113-148 (217)
15 MTH00051 COX2 cytochrome c oxi 77.5 3.5 7.6E-05 32.3 3.8 18 41-58 144-161 (234)
16 PF00116 COX2: Cytochrome C ox 77.1 2.1 4.6E-05 30.1 2.3 18 41-58 46-63 (120)
17 MTH00047 COX2 cytochrome c oxi 76.2 3.1 6.7E-05 31.9 3.1 32 28-59 89-134 (194)
18 MTH00154 COX2 cytochrome c oxi 75.4 4.2 9E-05 31.7 3.7 19 41-59 140-158 (227)
19 MTH00038 COX2 cytochrome c oxi 73.7 4.8 0.0001 31.4 3.7 19 41-59 140-158 (229)
20 MTH00140 COX2 cytochrome c oxi 73.6 4.6 9.9E-05 31.4 3.5 18 41-58 140-157 (228)
21 PRK10525 cytochrome o ubiquino 71.5 5 0.00011 33.1 3.4 33 28-60 134-170 (315)
22 MTH00139 COX2 cytochrome c oxi 71.0 6 0.00013 30.7 3.6 19 41-59 140-158 (226)
23 MTH00117 COX2 cytochrome c oxi 70.6 5.6 0.00012 31.0 3.4 19 41-59 140-158 (227)
24 MTH00185 COX2 cytochrome c oxi 70.3 6.2 0.00014 30.9 3.6 19 41-59 140-158 (230)
25 MTH00076 COX2 cytochrome c oxi 70.1 6.2 0.00013 30.8 3.6 19 41-59 140-158 (228)
26 MTH00129 COX2 cytochrome c oxi 69.8 6 0.00013 30.9 3.4 19 41-59 140-158 (230)
27 MTH00168 COX2 cytochrome c oxi 68.9 6.1 0.00013 30.7 3.3 19 41-59 140-158 (225)
28 MTH00023 COX2 cytochrome c oxi 68.6 6.5 0.00014 30.9 3.4 19 41-59 151-169 (240)
29 MTH00008 COX2 cytochrome c oxi 67.7 5.1 0.00011 31.3 2.6 17 41-57 140-156 (228)
30 PF06688 DUF1187: Protein of u 61.9 8.4 0.00018 24.8 2.3 20 87-110 1-20 (61)
31 MTH00080 COX2 cytochrome c oxi 61.5 9.7 0.00021 29.9 3.2 19 41-59 143-161 (231)
32 MTH00098 COX2 cytochrome c oxi 59.1 7.8 0.00017 30.3 2.2 19 41-59 140-158 (227)
33 cd04454 S1_Rrp4_like S1_Rrp4_l 53.1 24 0.00053 22.3 3.5 16 44-59 50-65 (82)
34 MTH00027 COX2 cytochrome c oxi 53.0 16 0.00034 29.3 3.1 19 41-59 174-192 (262)
35 cd05791 S1_CSL4 S1_CSL4: CSL4, 49.2 27 0.00059 23.3 3.4 34 43-105 59-92 (92)
36 COG1622 CyoA Heme/copper-type 44.8 30 0.00066 27.5 3.5 31 28-58 120-154 (247)
37 cd05688 S1_RPS1_repeat_ec3 S1_ 44.3 30 0.00066 20.3 2.8 16 44-59 44-59 (68)
38 PRK15266 subtilase cytotoxin s 43.2 18 0.00039 26.7 1.8 49 40-104 86-134 (135)
39 PRK15265 subtilase cytotoxin s 43.1 14 0.00031 27.2 1.3 23 41-63 83-105 (134)
40 cd00164 S1_like S1_like: Ribos 42.5 31 0.00066 19.5 2.5 17 43-59 40-56 (65)
41 smart00316 S1 Ribosomal protei 41.5 34 0.00075 19.7 2.7 17 43-59 45-61 (72)
42 cd04471 S1_RNase_R S1_RNase_R: 41.1 52 0.0011 20.2 3.6 43 11-59 29-72 (83)
43 PRK04163 exosome complex RNA-b 37.2 57 0.0012 25.4 3.9 18 42-59 109-126 (235)
44 PF00975 Thioesterase: Thioest 36.5 12 0.00027 27.1 0.2 13 85-97 66-78 (229)
45 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 34.2 59 0.0013 20.5 3.1 16 44-59 54-69 (86)
46 cd05691 S1_RPS1_repeat_ec6 S1_ 33.8 47 0.001 19.9 2.5 17 44-60 44-60 (73)
47 cd05708 S1_Rrp5_repeat_sc12 S1 32.5 57 0.0012 19.7 2.7 17 43-59 46-62 (77)
48 cd04452 S1_IF2_alpha S1_IF2_al 31.9 58 0.0013 19.8 2.7 16 44-59 49-64 (76)
49 cd05705 S1_Rrp5_repeat_hs14 S1 29.6 59 0.0013 20.5 2.5 17 43-59 49-65 (74)
50 PRK09521 exosome complex RNA-b 29.5 1.1E+02 0.0024 22.7 4.3 16 44-59 118-133 (189)
51 PF14326 DUF4384: Domain of un 29.4 45 0.00098 21.5 1.9 14 45-58 3-16 (83)
52 PF00575 S1: S1 RNA binding do 28.8 58 0.0012 19.8 2.3 18 42-59 46-63 (74)
53 cd05687 S1_RPS1_repeat_ec1_hs1 28.5 64 0.0014 19.4 2.4 16 44-59 44-59 (70)
54 KOG3400|consensus 28.3 1.3E+02 0.0029 22.4 4.4 57 6-66 5-71 (143)
55 COG3319 Thioesterase domains o 27.8 37 0.0008 27.1 1.5 16 82-97 62-77 (257)
56 cd05692 S1_RPS1_repeat_hs4 S1_ 27.8 63 0.0014 18.7 2.3 16 44-59 44-59 (69)
57 PF08206 OB_RNB: Ribonuclease 27.7 9.1 0.0002 23.5 -1.6 14 5-18 17-30 (58)
58 cd05698 S1_Rrp5_repeat_hs6_sc5 27.3 61 0.0013 19.5 2.2 16 44-59 44-59 (70)
59 cd05697 S1_Rrp5_repeat_hs5 S1_ 26.5 74 0.0016 19.2 2.5 17 43-59 43-59 (69)
60 cd05686 S1_pNO40 S1_pNO40: pNO 25.1 83 0.0018 19.4 2.6 17 43-59 47-63 (73)
61 cd05706 S1_Rrp5_repeat_sc10 S1 24.5 83 0.0018 19.1 2.4 16 44-59 47-62 (73)
62 cd04472 S1_PNPase S1_PNPase: P 24.2 81 0.0018 18.4 2.3 16 44-59 44-59 (68)
63 PF01835 A2M_N: MG2 domain; I 23.8 63 0.0014 20.9 1.9 18 42-59 8-25 (99)
64 PRK15458 tagatose 6-phosphate 23.7 35 0.00077 29.5 0.8 23 82-110 78-100 (426)
65 TIGR03834 EAGR_box EAGR box. T 23.1 59 0.0013 17.9 1.3 11 22-33 8-18 (28)
66 cd05685 S1_Tex S1_Tex: The C-t 22.9 92 0.002 18.0 2.3 17 43-59 43-59 (68)
67 cd05690 S1_RPS1_repeat_ec5 S1_ 22.7 1.1E+02 0.0024 18.1 2.8 17 43-59 44-60 (69)
68 PRK15267 subtilase cytotoxin s 22.3 53 0.0011 24.4 1.3 24 40-63 88-111 (141)
69 cd05707 S1_Rrp5_repeat_sc11 S1 22.2 97 0.0021 18.6 2.4 17 43-59 43-59 (68)
70 TIGR02810 agaZ_gatZ D-tagatose 22.0 43 0.00093 29.0 0.9 23 82-110 74-96 (420)
71 KOG3409|consensus 21.9 1.7E+02 0.0037 22.8 4.1 13 45-57 123-135 (193)
72 PF12306 PixA: Inclusion body 21.6 1.3E+02 0.0028 22.4 3.3 18 41-58 58-75 (172)
73 cd05704 S1_Rrp5_repeat_hs13 S1 21.3 86 0.0019 19.5 2.0 16 44-59 48-63 (72)
74 cd04461 S1_Rrp5_repeat_hs8_sc7 21.0 96 0.0021 19.5 2.3 17 43-59 57-73 (83)
No 1
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=100.00 E-value=1e-39 Score=233.83 Aligned_cols=99 Identities=45% Similarity=0.882 Sum_probs=66.7
Q ss_pred eeecCcceeeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCC--CCCCCC
Q psy11391 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHD--GAPGSE 79 (112)
Q Consensus 2 vslgFFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~--~~~~~~ 79 (112)
||||||||||||+++||+||.||+++|+|+|+|+ ++++||||.|++|||||++++|+|+.|..+..+++ .....+
T Consensus 21 vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~---~~~~l~~d~ge~IRFRV~~~~f~d~~p~~~~~~~~~~~~~~~~ 97 (122)
T PF08292_consen 21 VSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYD---EEQELFFDIGEEIRFRVESEIFPDVPPTPPPSAEASGEEEEEE 97 (122)
T ss_dssp EEECCEEEEEEECCCC-TTEEEECCCTEEEEEES---SSEEEEE-TT-EEEEEEEEEEE---------------------
T ss_pred EEecccccEEECHHHCCCCCccCccCCEEEEECC---CCceeEccCCCEEEEEEeEEEEecCCCCCcccccccccccccc
Confidence 8999999999999999999999999999999995 25899999999999999999999999998763321 112234
Q ss_pred CCCCCCCeEEEeccceeeeCCCCceeee
Q psy11391 80 VDTPKIPYSYGYYSLAVLRTQLLSPVRF 107 (112)
Q Consensus 80 ~~~~~~Py~I~~~~~gs~~~~GLGpv~W 107 (112)
..++++||+|+ |||+++||||++|
T Consensus 98 ~~~~~~Py~I~----gs~~~~GLG~~sW 121 (122)
T PF08292_consen 98 EDEPKPPYQII----GSINEDGLGLVSW 121 (122)
T ss_dssp ------SEEEE----EEB-STT-EEGGG
T ss_pred cccCCCCeEEE----EEecCCCCccccc
Confidence 67889999999 9999999999999
No 2
>KOG3297|consensus
Probab=100.00 E-value=4.8e-36 Score=228.16 Aligned_cols=100 Identities=39% Similarity=0.748 Sum_probs=88.1
Q ss_pred eeecCcceeeeCCCCCCCCCCCCcccceEEEeccCCCC-ceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCC
Q psy11391 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGD-KHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEV 80 (112)
Q Consensus 2 vslgFFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~-~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~ 80 (112)
||||||||||||+++||+||+|++++|+|+|+|+.||+ +++||||.|+.|||||+++.|.|++|.+...+. + .++.
T Consensus 99 vtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f~d~~p~~~~~~~-t--~~e~ 175 (202)
T KOG3297|consen 99 VTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESFVDVSPEGNSTAI-T--GAED 175 (202)
T ss_pred EEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecccccCcccccccc-c--cccc
Confidence 78999999999999999999999999999999998877 589999999999999999999999998732221 1 1235
Q ss_pred CCCCCCeEEEeccceeeeCCCCceeeee
Q psy11391 81 DTPKIPYSYGYYSLAVLRTQLLSPVRFQ 108 (112)
Q Consensus 81 ~~~~~Py~I~~~~~gs~~~~GLGpv~W~ 108 (112)
.++.+||+|+ |||+++||||++|=
T Consensus 176 ~e~~~py~l~----gs~~~~GLG~lsWW 199 (202)
T KOG3297|consen 176 PEKESPYTLL----GSMNEDGLGPLSWW 199 (202)
T ss_pred cccCCCeEEE----EEecCCCCccchhh
Confidence 5678899999 99999999999993
No 3
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=99.64 E-value=3.2e-16 Score=117.95 Aligned_cols=73 Identities=10% Similarity=0.239 Sum_probs=64.5
Q ss_pred eeecCcceeeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCC
Q psy11391 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVD 81 (112)
Q Consensus 2 vslgFFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~ 81 (112)
|++|||| ||||.++||+++.||++++.|+|..+ +++++++.|+.|||||.++.|...
T Consensus 99 v~~Gp~~-ifI~~~~l~~~~~fd~~~~~~~~~~~----~~~~~i~~g~~VR~rV~~v~~~~~------------------ 155 (176)
T PTZ00162 99 AQAGPLK-AFVSRSAIPPDFVYDSDSAYPCYISS----DGQIQIKPNTEVRLRLQGVRYDAS------------------ 155 (176)
T ss_pred EEeeCeE-EEEcHHHCCCccEECCCCCcceEecC----CCcEEECCCCEEEEEEEEEEecCC------------------
Confidence 7899999 99999999999999999999999932 247999999999999999996542
Q ss_pred CCCCCeEEEeccceeeeCCCCcee
Q psy11391 82 TPKIPYSYGYYSLAVLRTQLLSPV 105 (112)
Q Consensus 82 ~~~~Py~I~~~~~gs~~~~GLGpv 105 (112)
-..++ |+|++++||++
T Consensus 156 ----~~~~i----~T~~~~~LG~~ 171 (176)
T PTZ00162 156 ----NLFAI----ATINSDYLGPI 171 (176)
T ss_pred ----CcEEE----EEecCCCcCcc
Confidence 04778 99999999997
No 4
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=99.51 E-value=3.6e-14 Score=96.14 Aligned_cols=66 Identities=12% Similarity=0.279 Sum_probs=55.3
Q ss_pred eeec----CcceeeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCC
Q psy11391 2 VTLG----FFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPG 77 (112)
Q Consensus 2 vslg----FFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~ 77 (112)
|++| ||++++||++++++| +++.|+|..+ ++++++.|+.|||||.+++|. ..
T Consensus 19 v~~Gpl~~f~~~~~ip~~~~~~~-----~~~~~~~~~~-----~~~~i~~g~~VR~rV~~v~~~-~~------------- 74 (88)
T cd04462 19 AEVGPLSIFISRHLIPSDMEFDP-----NASPPCFTSN-----EDIVIKKDTEVRLKIIGTRVD-AT------------- 74 (88)
T ss_pred EEEcCceEEEEeeecCccceECC-----cCCCCeEeCC-----CcEEECCCCEEEEEEEEEEEc-cC-------------
Confidence 6888 999999999999877 6688999732 479999999999999999973 20
Q ss_pred CCCCCCCCCeEEEeccceeeeCCCCc
Q psy11391 78 SEVDTPKIPYSYGYYSLAVLRTQLLS 103 (112)
Q Consensus 78 ~~~~~~~~Py~I~~~~~gs~~~~GLG 103 (112)
-+..+ |+|++++||
T Consensus 75 --------~~~~i----gt~~~~~LG 88 (88)
T cd04462 75 --------DIFAI----GTIKDDYLG 88 (88)
T ss_pred --------ceEEE----EEccCCCCC
Confidence 15667 999999998
No 5
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=99.50 E-value=5.7e-14 Score=104.97 Aligned_cols=78 Identities=22% Similarity=0.367 Sum_probs=68.3
Q ss_pred eeecCcceeeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCC
Q psy11391 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVD 81 (112)
Q Consensus 2 vslgFFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~ 81 (112)
|+||||+++++|.+++++++.||++++.|+|.- .+.+|+.|+.|||||.++.|.+..|
T Consensus 99 V~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~------~~~~~~~Gd~VrvrV~~v~~~~~~~---------------- 156 (179)
T TIGR00448 99 VSLGPFDGLFHVSQVTDDYCYYDPKESALIGKE------TKKVLDEGDKVRARIVALSLKDRRP---------------- 156 (179)
T ss_pred EEeCCceEEEEcHHhCCCceEEccccceEEEcc------CCeEEcCCCEEEEEEEEEEccCCCC----------------
Confidence 688999999999999999999999999999952 3689999999999999999876532
Q ss_pred CCCCCeEEEeccceeeeCCCCceeeee
Q psy11391 82 TPKIPYSYGYYSLAVLRTQLLSPVRFQ 108 (112)
Q Consensus 82 ~~~~Py~I~~~~~gs~~~~GLGpv~W~ 108 (112)
..-+|. +||+++|||++.|-
T Consensus 157 ---~~~~I~----lt~k~~~LG~~~w~ 176 (179)
T TIGR00448 157 ---EGSKIG----LTMRQPLLGKLEWI 176 (179)
T ss_pred ---CcceEE----EEeccCcCCccccc
Confidence 124578 99999999999995
No 6
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=99.39 E-value=5.1e-13 Score=99.92 Aligned_cols=78 Identities=17% Similarity=0.260 Sum_probs=67.6
Q ss_pred CeeecCcceeeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCC
Q psy11391 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEV 80 (112)
Q Consensus 1 ~vslgFFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~ 80 (112)
.|+||||+.++.+.+++++++.||+++++|+|+- ...+++.|+.|||||.++.+.+..|.
T Consensus 98 ~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~------~~~~i~~Gd~VrvrV~~v~~~~~~~~-------------- 157 (187)
T PRK08563 98 FVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKE------SKRVLKVGDVVRARIVAVSLKERRPR-------------- 157 (187)
T ss_pred EEEEeCceEEEEcHHcCCCceEEccccceEEEcc------CCeEEcCCCEEEEEEEEEEcccCCCC--------------
Confidence 3789999999999999999999999999999983 36899999999999999997654321
Q ss_pred CCCCCCeEEEeccceeeeCCCCceeee
Q psy11391 81 DTPKIPYSYGYYSLAVLRTQLLSPVRF 107 (112)
Q Consensus 81 ~~~~~Py~I~~~~~gs~~~~GLGpv~W 107 (112)
..+|. +||+++|||+++|
T Consensus 158 -----~~~I~----ls~~~~~LG~~~w 175 (187)
T PRK08563 158 -----GSKIG----LTMRQPGLGKLEW 175 (187)
T ss_pred -----CCEEE----EEecCCCCCcHHH
Confidence 14888 9999999999998
No 7
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=99.14 E-value=7.5e-11 Score=90.00 Aligned_cols=78 Identities=19% Similarity=0.230 Sum_probs=68.2
Q ss_pred eeecCcceeeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCC
Q psy11391 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVD 81 (112)
Q Consensus 2 vslgFFdDI~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~ 81 (112)
|++| +.|++||.+.+++. .++.+++.|.|..+ +++++++.|+.|||||+++.+....|.
T Consensus 99 V~ig-p~dglvh~sqi~dd-~~~~d~~~~~~~g~----~tk~~i~~gd~VR~RIv~~s~~~~~~~--------------- 157 (183)
T COG1095 99 VRIG-PLDGLVHVSQIMDD-YIDYDEKNKVLIGE----ETKRVLKVGDKVRARIVGVSLKSRRPR--------------- 157 (183)
T ss_pred EEec-cccccccHhhccCc-ccccCcccceeeec----ccceEEecCCEEEEEEEEEecccCccc---------------
Confidence 6777 78899999999999 99999999999997 378999999999999999998877651
Q ss_pred CCCCCeEEEeccceeeeCCCCceeeee
Q psy11391 82 TPKIPYSYGYYSLAVLRTQLLSPVRFQ 108 (112)
Q Consensus 82 ~~~~Py~I~~~~~gs~~~~GLGpv~W~ 108 (112)
-=.|. ++|+++|||.+.|-
T Consensus 158 ----~~~I~----lTmrq~~LGklew~ 176 (183)
T COG1095 158 ----ESKIG----LTMRQPGLGKLEWI 176 (183)
T ss_pred ----cceEE----EEeccccCCcchhh
Confidence 13577 99999999999994
No 8
>KOG3298|consensus
Probab=95.97 E-value=0.026 Score=42.93 Aligned_cols=71 Identities=18% Similarity=0.341 Sum_probs=52.3
Q ss_pred ecCcce-----eeeCCCCCCCCCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCC
Q psy11391 4 LGFFED-----ILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGS 78 (112)
Q Consensus 4 lgFFdD-----I~IP~~~L~~ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~ 78 (112)
+|||=+ +|+-.|+.|+--.||+.++-= .|..+|+ + -+..|.+|||+|...+|...
T Consensus 95 ~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P--~f~~~d~-s--~I~~~~~VR~kiigtr~~~~--------------- 154 (170)
T KOG3298|consen 95 MGVFARSGPLEVFYSSHLKPPDYEFDPGENPP--NFQTEDE-S--VIQKGVEVRLKIIGTRVDET--------------- 154 (170)
T ss_pred eeEEEeccceEeeeecccCCCCcccCCCCCCC--ccccccc-c--eeeeCcEEEEEEEEEEEeee---------------
Confidence 466654 588999999999999987741 1332222 2 68899999999999996433
Q ss_pred CCCCCCCCeEEEeccceeeeCCCCcee
Q psy11391 79 EVDTPKIPYSYGYYSLAVLRTQLLSPV 105 (112)
Q Consensus 79 ~~~~~~~Py~I~~~~~gs~~~~GLGpv 105 (112)
++--+ ||+.++=|||+
T Consensus 155 -------~i~al----gtl~~D~LG~i 170 (170)
T KOG3298|consen 155 -------EIFAL----GTLKGDYLGPI 170 (170)
T ss_pred -------eEEEE----EEecCcccccC
Confidence 34444 99999999985
No 9
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=92.59 E-value=0.19 Score=33.62 Aligned_cols=72 Identities=18% Similarity=0.242 Sum_probs=43.4
Q ss_pred ceeeeCCCCCCC-CCCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCCCCCCC
Q psy11391 8 EDILIPPEGLQQ-PSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPKIP 86 (112)
Q Consensus 8 dDI~IP~~~L~~-ps~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~~~~~P 86 (112)
-+.++|...|.. ...|++....|+=.. ..-.|..|+.|+++|.+..-....|+ .
T Consensus 22 v~G~v~~~~l~~~~~~~~~~~~~~~~~~------~~~~~~~Gd~v~vkI~~vd~~~~~~~-----------------~-- 76 (99)
T cd04460 22 VDGLLHISQIMDDYISYDPKNKRLIGEE------TKRVLKVGDVVRARIVAVSLKERRPR-----------------E-- 76 (99)
T ss_pred eEEEEEEEEccCCceEechhheeecccC------cCCEECCCCEEEEEEEEEeHHHCcCC-----------------C--
Confidence 455677666643 233455444443222 23567999999999988871111000 1
Q ss_pred eEEEeccceeeeCCCCceeeee
Q psy11391 87 YSYGYYSLAVLRTQLLSPVRFQ 108 (112)
Q Consensus 87 y~I~~~~~gs~~~~GLGpv~W~ 108 (112)
.+|. -|+.+.+|||+.|-
T Consensus 77 ~~i~----ls~k~~~~g~~~~~ 94 (99)
T cd04460 77 SKIG----LTMRQPGLGKLEWI 94 (99)
T ss_pred ceEE----EEEecCCCCcHHHh
Confidence 2344 46999999999994
No 10
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=84.79 E-value=1.3 Score=33.56 Aligned_cols=32 Identities=28% Similarity=0.675 Sum_probs=25.4
Q ss_pred ceEEEeccCCCC------ceeeeeCCCCeEEEEEceEE
Q psy11391 28 QVWVWEFDNEGD------KHDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 28 ~~W~W~~~~ed~------~~~l~~d~ge~IRFRV~~~~ 59 (112)
+.|.|.++..+. .++|.+-.|++|||++.+..
T Consensus 98 ~qw~W~f~Y~~~~~~~~~~~~l~vp~g~~v~~~~ts~D 135 (201)
T TIGR02866 98 HQWYWSFDYPESRRGFTTVNELVVPAGTPVRLQVTSKD 135 (201)
T ss_pred EEeEEEEEcCCcCCCccccCEEEEEcCCEEEEEEEeCc
Confidence 469998765443 36899999999999999843
No 11
>PF02918 Pertussis_S2S3: Pertussis toxin, subunit 2 and 3, C-terminal domain; InterPro: IPR020063 A large group of bacterial exotoxins are referred to as "A/B toxins", essentially because they are formed from two subunits []. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit []. Bordetella pertussis is the causative agent of whooping cough, and is a Gram-negative aerobic coccus. Its major virulence factor is the pertussis toxin, an A/B exotoxin that mediates both colonisation and toxaemic stages of the the disease [, ]. Recombinant, inactive forms of the 5 subunits that make up the toxin have proven to be good vaccines. The S2 and S3 subunits of the toxin form part of the "B" moiety. They are responsible for binding the whole toxin to host cells prior to invasion, and are classed as adhesins []. S2 attaches to a host receptor called lactosylceramide. It has also been speculated that the S3 unit may preferentially bind phagocytes. The crystal structure of pertussis toxin has been determined to 2.9A resolution []. The catalytic A-subunit (S1) shares structural similarity with other ADP-ribosylating bacterial toxins, although differences in the C-terminal portion explain its unique activation mechanism. Despite its heterogeneous subunit composition, the structure of the cell-binding B-oligomer (S2, S3, two copies of S4, and S5) resembles the symmetrical B-pentamers of the cholera and shiga toxin families, but it interacts differently with the A-subunit and there is virtually no sequence similarity between B-subunits of the different toxins. Two peripheral domains that are unique to the pertussis toxin B-oligomer share structural similarity with a calcium-dependent eukaryotic lectin, and reveal possible receptor-binding sites.; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1BCP_H 1PRT_H 1PTO_B.
Probab=83.45 E-value=1.1 Score=31.93 Aligned_cols=41 Identities=15% Similarity=0.154 Sum_probs=27.8
Q ss_pred eeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCCCCCCCeEEEecccee
Q psy11391 41 HDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPKIPYSYGYYSLAV 96 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~~~~~Py~I~~~~~gs 96 (112)
.++|+-.|..||.-|..++|.+.. ....++.|.|+|.|.++
T Consensus 64 ~~~~y~tGl~VRVhV~k~~~~~~~---------------~~~tf~a~aL~gissCn 104 (109)
T PF02918_consen 64 LYYFYSTGLAVRVHVSKDEWYYPA---------------FDATFSAYALTGISSCN 104 (109)
T ss_dssp HHHHHHCT-EEEEEEEEEEEE--S---------------TT-SS-EEEEEEEEE--
T ss_pred HHHHHHcCcEEEEEEecccccChh---------------hhcCcchheeeeeeecC
Confidence 478899999999999999999884 22346789999766544
No 12
>TIGR01433 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant.
Probab=79.70 E-value=2.4 Score=33.12 Aligned_cols=32 Identities=22% Similarity=0.454 Sum_probs=25.9
Q ss_pred ceEEEeccCCCC----ceeeeeCCCCeEEEEEceEE
Q psy11391 28 QVWVWEFDNEGD----KHDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 28 ~~W~W~~~~ed~----~~~l~~d~ge~IRFRV~~~~ 59 (112)
+.|.|.|+..+. .++|.+-.|..|||++.+..
T Consensus 122 ~QW~W~f~Yp~~~~~~~nel~lP~g~pV~~~ltS~D 157 (226)
T TIGR01433 122 LDWKWLFIYPEQGIATVNEIAFPVNTPINFKITSNS 157 (226)
T ss_pred EeceEEEEcCCCCccccceEEEECCCEEEEEEEECc
Confidence 369998776442 37999999999999999865
No 13
>PRK09750 hypothetical protein; Provisional
Probab=79.39 E-value=2 Score=27.84 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=19.5
Q ss_pred CeEEEeccceeeeCCCCceeeeeee
Q psy11391 86 PYSYGYYSLAVLRTQLLSPVRFQHV 110 (112)
Q Consensus 86 Py~I~~~~~gs~~~~GLGpv~W~~~ 110 (112)
-|.|+ |.|.-.|=+|+.|-|.
T Consensus 3 kY~I~----Ati~KpGg~P~~W~r~ 23 (64)
T PRK09750 3 MYKIT----ATIEKEGGTPTNWTRY 23 (64)
T ss_pred eeEEE----EEEECCCCCccceeEe
Confidence 59999 9999999999999885
No 14
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b).
Probab=77.84 E-value=2.6 Score=32.38 Aligned_cols=32 Identities=19% Similarity=0.385 Sum_probs=26.0
Q ss_pred ceEEEeccCCCC----ceeeeeCCCCeEEEEEceEE
Q psy11391 28 QVWVWEFDNEGD----KHDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 28 ~~W~W~~~~ed~----~~~l~~d~ge~IRFRV~~~~ 59 (112)
+.|.|.|+..++ .++|.+-.|..|||++.+-.
T Consensus 113 ~qw~W~~~Yp~~~~~~~n~l~iP~g~~v~~~ltS~D 148 (217)
T TIGR01432 113 ADWKWFFSYPDEHIETVNYLNIPKDRPVLFKLQSAD 148 (217)
T ss_pred EeeeEEEEeCCCCcceeCcEEEECCCEEEEEEECCc
Confidence 469999876443 26899999999999999864
No 15
>MTH00051 COX2 cytochrome c oxidase subunit II; Provisional
Probab=77.54 E-value=3.5 Score=32.31 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=16.0
Q ss_pred eeeeeCCCCeEEEEEceE
Q psy11391 41 HDLFMDPGDKIKFRVTSE 58 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~ 58 (112)
++|.+-.|..|||+|.+.
T Consensus 144 n~lvlP~~~~v~~~itS~ 161 (234)
T MTH00051 144 NRLIVPIQTQVRVLVTAA 161 (234)
T ss_pred eEEEEecCcEEEEEEEeC
Confidence 578899999999999985
No 16
>PF00116 COX2: Cytochrome C oxidase subunit II, periplasmic domain This family corresponds to chains b and o.; InterPro: IPR002429 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c.; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0016020 membrane; PDB: 3OMN_D 3OMA_B 3OMI_D 3OM3_B 3EHB_B 1AR1_B 1QLE_B 3HB3_B 2IWK_B 2IWF_A ....
Probab=77.07 E-value=2.1 Score=30.09 Aligned_cols=18 Identities=33% Similarity=0.756 Sum_probs=16.0
Q ss_pred eeeeeCCCCeEEEEEceE
Q psy11391 41 HDLFMDPGDKIKFRVTSE 58 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~ 58 (112)
++|.+..|.+|||++.+.
T Consensus 46 ~~l~lp~g~~v~~~ltS~ 63 (120)
T PF00116_consen 46 NELVLPAGQPVRFHLTSE 63 (120)
T ss_dssp SEEEEETTSEEEEEEEES
T ss_pred ceecccccceEeEEEEcC
Confidence 578999999999999983
No 17
>MTH00047 COX2 cytochrome c oxidase subunit II; Provisional
Probab=76.16 E-value=3.1 Score=31.90 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=23.8
Q ss_pred ceEEEeccCCCCc--------------eeeeeCCCCeEEEEEceEE
Q psy11391 28 QVWVWEFDNEGDK--------------HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 28 ~~W~W~~~~ed~~--------------~~l~~d~ge~IRFRV~~~~ 59 (112)
+.|.|.|...+++ ++|.+-.|..|||++.+..
T Consensus 89 ~QW~W~f~Yp~~~~~~s~~~~~~~~~~~~l~lp~g~~v~~~ltS~D 134 (194)
T MTH00047 89 HQWYWSYEYSFGGSYDSFMTDDIFGVDKPLRLVYGVPYHLLVTSSD 134 (194)
T ss_pred hheeEEEEcCCCcccccccchhhhccCceEEEeCCCEEEeeeecCc
Confidence 3699987753321 4688888999999999865
No 18
>MTH00154 COX2 cytochrome c oxidase subunit II; Provisional
Probab=75.36 E-value=4.2 Score=31.75 Aligned_cols=19 Identities=16% Similarity=0.261 Sum_probs=16.4
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+--
T Consensus 140 n~l~lP~~~~v~~~~tS~D 158 (227)
T MTH00154 140 NRLVLPMNTQIRILITAAD 158 (227)
T ss_pred ceEEEecCCEEEEEEEcCc
Confidence 5789999999999998854
No 19
>MTH00038 COX2 cytochrome c oxidase subunit II; Provisional
Probab=73.69 E-value=4.8 Score=31.39 Aligned_cols=19 Identities=21% Similarity=0.179 Sum_probs=15.9
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+.-
T Consensus 140 n~lvlP~~~~v~~~~tS~D 158 (229)
T MTH00038 140 NRLVLPYQTPIRVLVSSAD 158 (229)
T ss_pred ceEEEecCeEEEEEEEECC
Confidence 5788888899999998865
No 20
>MTH00140 COX2 cytochrome c oxidase subunit II; Provisional
Probab=73.58 E-value=4.6 Score=31.37 Aligned_cols=18 Identities=22% Similarity=0.189 Sum_probs=15.9
Q ss_pred eeeeeCCCCeEEEEEceE
Q psy11391 41 HDLFMDPGDKIKFRVTSE 58 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~ 58 (112)
++|.+-.|..|||++.+.
T Consensus 140 n~l~lP~~~~v~~~~ts~ 157 (228)
T MTH00140 140 NRLVLPYSVDTRVLVTSA 157 (228)
T ss_pred CeEEEeeCcEEEEEEEcC
Confidence 578999999999999994
No 21
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional
Probab=71.49 E-value=5 Score=33.11 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=26.2
Q ss_pred ceEEEeccCCCC----ceeeeeCCCCeEEEEEceEEe
Q psy11391 28 QVWVWEFDNEGD----KHDLFMDPGDKIKFRVTSELF 60 (112)
Q Consensus 28 ~~W~W~~~~ed~----~~~l~~d~ge~IRFRV~~~~F 60 (112)
..|.|.|...|. .++|.+-.|..|||++.+..-
T Consensus 134 ~QW~W~f~YP~~gi~t~NeL~iP~g~pV~f~lTS~DV 170 (315)
T PRK10525 134 MDWKWFFIYPEQGIATVNEIAFPANVPVYFKVTSNSV 170 (315)
T ss_pred EeeeEEEEcCCCCceeeccEEEecCCEEEEEEEEchh
Confidence 359998865443 279999999999999998753
No 22
>MTH00139 COX2 cytochrome c oxidase subunit II; Provisional
Probab=70.97 E-value=6 Score=30.69 Aligned_cols=19 Identities=16% Similarity=0.162 Sum_probs=15.6
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+--
T Consensus 140 n~l~lP~~~~v~~~~tS~D 158 (226)
T MTH00139 140 NRLVLPYKSNIRALITAAD 158 (226)
T ss_pred ceEEEecCCEEEEEEecCc
Confidence 5788888899999998754
No 23
>MTH00117 COX2 cytochrome c oxidase subunit II; Provisional
Probab=70.63 E-value=5.6 Score=30.99 Aligned_cols=19 Identities=21% Similarity=0.333 Sum_probs=16.2
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+.-
T Consensus 140 n~lvlP~~~~v~~~~tS~D 158 (227)
T MTH00117 140 HRMVIPMESPIRILITAED 158 (227)
T ss_pred ceEEEecCceEEEEEEecc
Confidence 5788899999999998864
No 24
>MTH00185 COX2 cytochrome c oxidase subunit II; Provisional
Probab=70.28 E-value=6.2 Score=30.86 Aligned_cols=19 Identities=21% Similarity=0.301 Sum_probs=16.3
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||+|.+..
T Consensus 140 n~lvlP~~~~v~~~~tS~D 158 (230)
T MTH00185 140 HRMVVPMESPIRVLITAED 158 (230)
T ss_pred CeEEEecCCEEEEEEEcCc
Confidence 5788889999999998865
No 25
>MTH00076 COX2 cytochrome c oxidase subunit II; Provisional
Probab=70.14 E-value=6.2 Score=30.81 Aligned_cols=19 Identities=16% Similarity=0.244 Sum_probs=16.5
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||+|.+..
T Consensus 140 n~l~lP~~~~v~~~~tS~D 158 (228)
T MTH00076 140 NRMVVPMESPIRMLITAED 158 (228)
T ss_pred ceEEEecCCEEEEEEEecc
Confidence 5888999999999998865
No 26
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional
Probab=69.79 E-value=6 Score=30.91 Aligned_cols=19 Identities=21% Similarity=0.300 Sum_probs=16.4
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+..
T Consensus 140 n~lvlP~~~~v~~~~tS~D 158 (230)
T MTH00129 140 HRMVVPVESPIRVLVSAED 158 (230)
T ss_pred ceEEEecCcEEEEEEEeCc
Confidence 5788999999999998865
No 27
>MTH00168 COX2 cytochrome c oxidase subunit II; Provisional
Probab=68.87 E-value=6.1 Score=30.71 Aligned_cols=19 Identities=32% Similarity=0.303 Sum_probs=15.9
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+.-
T Consensus 140 n~l~lP~~~~v~~~~tS~D 158 (225)
T MTH00168 140 NRLVLPMDSKIRVLVTSAD 158 (225)
T ss_pred ceEEEecCCEEEEEEEeCC
Confidence 5788888999999998864
No 28
>MTH00023 COX2 cytochrome c oxidase subunit II; Validated
Probab=68.60 E-value=6.5 Score=30.93 Aligned_cols=19 Identities=16% Similarity=0.198 Sum_probs=16.2
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+.-
T Consensus 151 n~lvlP~~~~v~~~~tS~D 169 (240)
T MTH00023 151 NRLVVPINTHVRILVTGAD 169 (240)
T ss_pred ceEEEecCCEEEEEEEcCC
Confidence 5788889999999998864
No 29
>MTH00008 COX2 cytochrome c oxidase subunit II; Validated
Probab=67.66 E-value=5.1 Score=31.29 Aligned_cols=17 Identities=18% Similarity=0.223 Sum_probs=15.3
Q ss_pred eeeeeCCCCeEEEEEce
Q psy11391 41 HDLFMDPGDKIKFRVTS 57 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~ 57 (112)
++|.+-.|..|||+|.+
T Consensus 140 n~lvlP~~~~v~~~~tS 156 (228)
T MTH00008 140 NRAVLPMQTEIRVLVTA 156 (228)
T ss_pred ceEEEecCCEEEEEEEe
Confidence 57888889999999999
No 30
>PF06688 DUF1187: Protein of unknown function (DUF1187); InterPro: IPR009572 This family consists of several short, hypothetical bacterial proteins of around 62 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi. The function of this family is unknown.
Probab=61.91 E-value=8.4 Score=24.85 Aligned_cols=20 Identities=20% Similarity=0.290 Sum_probs=18.5
Q ss_pred eEEEeccceeeeCCCCceeeeeee
Q psy11391 87 YSYGYYSLAVLRTQLLSPVRFQHV 110 (112)
Q Consensus 87 y~I~~~~~gs~~~~GLGpv~W~~~ 110 (112)
|+|+ |.|--.|=.||.|-+.
T Consensus 1 YkIt----AtI~KpG~~Pv~W~ry 20 (61)
T PF06688_consen 1 YKIT----ATIIKPGNTPVNWTRY 20 (61)
T ss_pred CceE----EEEEcCCCCCeeeEEe
Confidence 8899 9999999999999874
No 31
>MTH00080 COX2 cytochrome c oxidase subunit II; Provisional
Probab=61.50 E-value=9.7 Score=29.92 Aligned_cols=19 Identities=21% Similarity=0.263 Sum_probs=15.3
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||+|.+.-
T Consensus 143 n~l~lP~~~~v~~~itS~D 161 (231)
T MTH00080 143 NRCVLPCDTNIRFCITSSD 161 (231)
T ss_pred CceEeecCcEEEEEEEeCc
Confidence 4567888999999998865
No 32
>MTH00098 COX2 cytochrome c oxidase subunit II; Validated
Probab=59.14 E-value=7.8 Score=30.26 Aligned_cols=19 Identities=16% Similarity=0.188 Sum_probs=16.4
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+..
T Consensus 140 n~lvlP~~~~v~~~~tS~D 158 (227)
T MTH00098 140 NRVVLPMEMPIRMLISSED 158 (227)
T ss_pred ceEEecCCCEEEEEEEECc
Confidence 5788999999999998865
No 33
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=53.15 E-value=24 Score=22.29 Aligned_cols=16 Identities=38% Similarity=0.372 Sum_probs=13.8
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
.+..|+.|++||.+..
T Consensus 50 ~~~~GD~i~~~V~~~~ 65 (82)
T cd04454 50 SLQPGDLILAKVISLG 65 (82)
T ss_pred cCCCCCEEEEEEEEeC
Confidence 3689999999999876
No 34
>MTH00027 COX2 cytochrome c oxidase subunit II; Provisional
Probab=53.01 E-value=16 Score=29.35 Aligned_cols=19 Identities=11% Similarity=0.239 Sum_probs=15.5
Q ss_pred eeeeeCCCCeEEEEEceEE
Q psy11391 41 HDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~ 59 (112)
++|.+-.|..|||++.+--
T Consensus 174 n~lvlP~~~~v~~~ltS~D 192 (262)
T MTH00027 174 NRLILPVDTNVRVLITAAD 192 (262)
T ss_pred ceEEEeeCcEEEEEEEcCc
Confidence 4788888899999998754
No 35
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=49.16 E-value=27 Score=23.27 Aligned_cols=34 Identities=24% Similarity=0.257 Sum_probs=25.8
Q ss_pred eeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCCCCCCCeEEEeccceeeeCCCCcee
Q psy11391 43 LFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPKIPYSYGYYSLAVLRTQLLSPV 105 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~~~~~Py~I~~~~~gs~~~~GLGpv 105 (112)
-+|..|+-||=||.+.. + ..+|.++ +++.+||.|
T Consensus 59 ~~f~~GDiV~AkVis~~------------~-----------~~~~~Ls------t~~~~lGVv 92 (92)
T cd05791 59 KCFRPGDIVRAKVISLG------------D-----------ASSYYLS------TAENELGVV 92 (92)
T ss_pred hhcCCCCEEEEEEEEcC------------C-----------CCCcEEE------ecCCCCccC
Confidence 36799999999998765 0 1357777 889999864
No 36
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=44.85 E-value=30 Score=27.51 Aligned_cols=31 Identities=26% Similarity=0.577 Sum_probs=24.8
Q ss_pred ceEEEeccCCCC----ceeeeeCCCCeEEEEEceE
Q psy11391 28 QVWVWEFDNEGD----KHDLFMDPGDKIKFRVTSE 58 (112)
Q Consensus 28 ~~W~W~~~~ed~----~~~l~~d~ge~IRFRV~~~ 58 (112)
..|.|.+...+. .++|.+-.|..|||++.+-
T Consensus 120 ~qw~W~f~Yp~~~~~t~n~l~lPv~~~V~f~ltS~ 154 (247)
T COG1622 120 YQWKWLFIYPDYGIATVNELVLPVGRPVRFKLTSA 154 (247)
T ss_pred EEEEEEEEccCcCccccceEEEeCCCeEEEEEEec
Confidence 368887765442 3789999999999999986
No 37
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=44.33 E-value=30 Score=20.30 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=14.5
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
.|.+|+.|+++|.++.
T Consensus 44 ~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 44 VVNVGDEVEVKVLKID 59 (68)
T ss_pred EECCCCEEEEEEEEEE
Confidence 5799999999999886
No 38
>PRK15266 subtilase cytotoxin subunit B; Provisional
Probab=43.19 E-value=18 Score=26.66 Aligned_cols=49 Identities=16% Similarity=0.219 Sum_probs=33.7
Q ss_pred ceeeeeCCCCeEEEEEceEEeeecCCCCCCCcCCCCCCCCCCCCCCCeEEEeccceeeeCCCCce
Q psy11391 40 KHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPKIPYSYGYYSLAVLRTQLLSP 104 (112)
Q Consensus 40 ~~~l~~d~ge~IRFRV~~~~F~d~~P~~p~~~e~~~~~~~~~~~~~Py~I~~~~~gs~~~~GLGp 104 (112)
..++||-.|+.||.-+....|++..=.. ....=.|+|.+-++ ..+=+||
T Consensus 86 qA~YyYtTG~~VRiYy~~nVWt~p~F~~---------------afS~naLvg~ssCs-~s~C~GP 134 (135)
T PRK15266 86 QARYFYSTGQSVRIHVQKNIWTYPLFVN---------------TFSANALVGLSSCS-ATQCFGP 134 (135)
T ss_pred hhheeEecCceEEEEEcCCcccCchhhh---------------hccccceeEEEeec-cceecCC
Confidence 3689999999999999999998863111 11223355666666 6666666
No 39
>PRK15265 subtilase cytotoxin subunit B-like protein; Provisional
Probab=43.14 E-value=14 Score=27.23 Aligned_cols=23 Identities=13% Similarity=0.405 Sum_probs=21.5
Q ss_pred eeeeeCCCCeEEEEEceEEeeec
Q psy11391 41 HDLFMDPGDKIKFRVTSELFTET 63 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~~F~d~ 63 (112)
.+.|+-.|+.||.+|+...|+|.
T Consensus 83 A~yyYtTg~~vRiy~~~nVWTdp 105 (134)
T PRK15265 83 AMYYYTTGKRIRVYYAPDVWTNN 105 (134)
T ss_pred hhheeecCCcEEEEEcCCcccCc
Confidence 57899999999999999999986
No 40
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=42.49 E-value=31 Score=19.55 Aligned_cols=17 Identities=18% Similarity=0.268 Sum_probs=15.0
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-++..|+.|++||.++.
T Consensus 40 ~~~~~G~~v~~~v~~~d 56 (65)
T cd00164 40 EVFKVGDEVEVKVLEVD 56 (65)
T ss_pred hEeCCCCEEEEEEEEEc
Confidence 46899999999999875
No 41
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=41.47 E-value=34 Score=19.69 Aligned_cols=17 Identities=29% Similarity=0.370 Sum_probs=15.0
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.|..|+.|++||.++.
T Consensus 45 ~~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 45 EVLKVGDEVKVKVLSVD 61 (72)
T ss_pred HeecCCCEEEEEEEEEe
Confidence 35799999999999987
No 42
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=41.08 E-value=52 Score=20.24 Aligned_cols=43 Identities=30% Similarity=0.331 Sum_probs=26.0
Q ss_pred eeCCCCCCCC-CCCCcccceEEEeccCCCCceeeeeCCCCeEEEEEceEE
Q psy11391 11 LIPPEGLQQP-SRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 11 ~IP~~~L~~p-s~fd~~e~~W~W~~~~ed~~~~l~~d~ge~IRFRV~~~~ 59 (112)
+|+.+.|... -.||+......... ..-.|..|+.||.||.++.
T Consensus 29 ~v~~~~l~~~~~~~d~~~~~~~~~~------~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 29 LVHVSTLGDDYYEFDEENHALVGER------TGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred EEEEEecCCCcEEEcccceEEEecc------CCCEEcCCCEEEEEEEEec
Confidence 5566666533 23444433332221 2357899999999999887
No 43
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=37.17 E-value=57 Score=25.37 Aligned_cols=18 Identities=28% Similarity=0.320 Sum_probs=14.3
Q ss_pred eeeeCCCCeEEEEEceEE
Q psy11391 42 DLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 42 ~l~~d~ge~IRFRV~~~~ 59 (112)
+-+|+.|+.|+-||.+..
T Consensus 109 ~~~~~~GDlV~akV~~i~ 126 (235)
T PRK04163 109 RKYLDIGDYIIAKVKDVD 126 (235)
T ss_pred HhhCCCCCEEEEEEEEEC
Confidence 346789999999998765
No 44
>PF00975 Thioesterase: Thioesterase domain; InterPro: IPR001031 Thioesterase domains often occur integrated in or associated with peptide synthetases which are involved in the non-ribosomal synthesis of peptide antibiotics []. Thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates.; GO: 0016788 hydrolase activity, acting on ester bonds, 0009058 biosynthetic process; PDB: 2RON_A 2K2Q_B 3LCR_B 2HFJ_B 1MNQ_A 1MN6_B 1MNA_B 2HFK_B 2H7Y_B 2H7X_A ....
Probab=36.55 E-value=12 Score=27.05 Aligned_cols=13 Identities=23% Similarity=0.378 Sum_probs=11.4
Q ss_pred CCeEEEeccceee
Q psy11391 85 IPYSYGYYSLAVL 97 (112)
Q Consensus 85 ~Py~I~~~~~gs~ 97 (112)
-||.|.|||+|++
T Consensus 66 gp~~L~G~S~Gg~ 78 (229)
T PF00975_consen 66 GPYVLAGWSFGGI 78 (229)
T ss_dssp SSEEEEEETHHHH
T ss_pred CCeeehccCccHH
Confidence 3999999999975
No 45
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=34.19 E-value=59 Score=20.54 Aligned_cols=16 Identities=38% Similarity=0.447 Sum_probs=13.7
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
++..|+.|++||.+..
T Consensus 54 ~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 54 YLDEGDLIVAEVQSVD 69 (86)
T ss_pred hCCCCCEEEEEEEEEC
Confidence 5789999999998864
No 46
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=33.78 E-value=47 Score=19.94 Aligned_cols=17 Identities=18% Similarity=0.231 Sum_probs=14.8
Q ss_pred eeCCCCeEEEEEceEEe
Q psy11391 44 FMDPGDKIKFRVTSELF 60 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~F 60 (112)
+|..|+.|++||.+...
T Consensus 44 ~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 44 RFKVGDEVEAKITNVDR 60 (73)
T ss_pred ccCCCCEEEEEEEEEeC
Confidence 56899999999999873
No 47
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.46 E-value=57 Score=19.71 Aligned_cols=17 Identities=24% Similarity=0.307 Sum_probs=14.8
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.|.+|+.|+.||.++.
T Consensus 46 ~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 46 KLFRVGDKVRAKVLKID 62 (77)
T ss_pred HeecCCCEEEEEEEEEe
Confidence 36799999999999877
No 48
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=31.91 E-value=58 Score=19.80 Aligned_cols=16 Identities=19% Similarity=0.146 Sum_probs=14.3
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
+|..|+.|+.||.++.
T Consensus 49 ~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 49 LVKVGRKEVVKVIRVD 64 (76)
T ss_pred eeCCCCEEEEEEEEEE
Confidence 4799999999999877
No 49
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.61 E-value=59 Score=20.54 Aligned_cols=17 Identities=18% Similarity=0.243 Sum_probs=15.3
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
=+|..|+.|+++|.++.
T Consensus 49 ~~~~~G~~v~~kVl~id 65 (74)
T cd05705 49 KYLPEGKLLTAKVLSVN 65 (74)
T ss_pred cccCCCCEEEEEEEEEE
Confidence 37899999999999987
No 50
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=29.51 E-value=1.1e+02 Score=22.72 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=12.7
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
+|..|+.|+.||.+..
T Consensus 118 ~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 118 AFKIGDIVRAKVISYT 133 (189)
T ss_pred ccCCCCEEEEEEEecC
Confidence 4688888888888775
No 51
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=29.39 E-value=45 Score=21.49 Aligned_cols=14 Identities=43% Similarity=0.861 Sum_probs=10.9
Q ss_pred eCCCCeEEEEEceE
Q psy11391 45 MDPGDKIKFRVTSE 58 (112)
Q Consensus 45 ~d~ge~IRFRV~~~ 58 (112)
|..||.|||+|...
T Consensus 3 ~~~Ge~v~~~~~~~ 16 (83)
T PF14326_consen 3 YRVGERVRFRVTSN 16 (83)
T ss_pred ccCCCEEEEEEEeC
Confidence 46788999988773
No 52
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=28.80 E-value=58 Score=19.75 Aligned_cols=18 Identities=11% Similarity=0.163 Sum_probs=15.8
Q ss_pred eeeeCCCCeEEEEEceEE
Q psy11391 42 DLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 42 ~l~~d~ge~IRFRV~~~~ 59 (112)
.-.+..|+.|++||.++.
T Consensus 46 ~~~~~~G~~v~v~v~~vd 63 (74)
T PF00575_consen 46 SEVYKIGQTVRVKVIKVD 63 (74)
T ss_dssp HGTCETTCEEEEEEEEEE
T ss_pred ccccCCCCEEEEEEEEEE
Confidence 457889999999999987
No 53
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=28.46 E-value=64 Score=19.41 Aligned_cols=16 Identities=19% Similarity=0.183 Sum_probs=14.0
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
++..|+.|+++|.+..
T Consensus 44 ~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 44 EVKVGDEVEVYVLRVE 59 (70)
T ss_pred cCCCCCEEEEEEEEEE
Confidence 4689999999998876
No 54
>KOG3400|consensus
Probab=28.33 E-value=1.3e+02 Score=22.36 Aligned_cols=57 Identities=18% Similarity=0.332 Sum_probs=42.0
Q ss_pred CcceeeeCCCCCCCCCCCCcccceEE----------EeccCCCCceeeeeCCCCeEEEEEceEEeeecCCC
Q psy11391 6 FFEDILIPPEGLQQPSRFDEKEQVWV----------WEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPI 66 (112)
Q Consensus 6 FFdDI~IP~~~L~~ps~fd~~e~~W~----------W~~~~ed~~~~l~~d~ge~IRFRV~~~~F~d~~P~ 66 (112)
-|||||--.+.-|++..||.-.++-. -.++ .+-..++.|+..|.++-+---.|-+|.
T Consensus 5 lfdDiF~V~~vDpeGkkydrVsR~~~~S~~~~m~l~LDiN----t~lyPl~~gdkf~l~iastL~eDgtpd 71 (143)
T KOG3400|consen 5 LFDDIFKVSDVDPEGKKYDRVSRIEAKSESFKMDLILDIN----TQLYPLATGDKFTLVIASTLNEDGTPD 71 (143)
T ss_pred hhhhceeeeecCcccchhhheEeEEeeCCCceEEEEEecc----cEEEeeccCCEEEEEEecccccCCCcc
Confidence 59999999999999999987666422 2222 234568888999988887776666665
No 55
>COG3319 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.84 E-value=37 Score=27.10 Aligned_cols=16 Identities=31% Similarity=0.347 Sum_probs=12.9
Q ss_pred CCCCCeEEEeccceee
Q psy11391 82 TPKIPYSYGYYSLAVL 97 (112)
Q Consensus 82 ~~~~Py~I~~~~~gs~ 97 (112)
.+.-||.+.|||+|..
T Consensus 62 QP~GPy~L~G~S~GG~ 77 (257)
T COG3319 62 QPEGPYVLLGWSLGGA 77 (257)
T ss_pred CCCCCEEEEeeccccH
Confidence 3456999999999963
No 56
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=27.82 E-value=63 Score=18.73 Aligned_cols=16 Identities=38% Similarity=0.503 Sum_probs=13.9
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
.+..|+.|+.||.++.
T Consensus 44 ~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 44 VLKEGDKVKVKVLSID 59 (69)
T ss_pred ccCCCCEEEEEEEEEC
Confidence 5789999999998875
No 57
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=27.71 E-value=9.1 Score=23.46 Aligned_cols=14 Identities=50% Similarity=0.683 Sum_probs=9.2
Q ss_pred cCcceeeeCCCCCC
Q psy11391 5 GFFEDILIPPEGLQ 18 (112)
Q Consensus 5 gFFdDI~IP~~~L~ 18 (112)
++-+|||||+..|.
T Consensus 17 ~~~~DifIp~~~l~ 30 (58)
T PF08206_consen 17 DGGEDIFIPPRNLN 30 (58)
T ss_dssp T-TEEEEE-HHHHT
T ss_pred CCCCCEEECHHHHC
Confidence 45689999988773
No 58
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=27.30 E-value=61 Score=19.48 Aligned_cols=16 Identities=25% Similarity=0.243 Sum_probs=14.0
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
.+..|+.|++||.++.
T Consensus 44 ~~~~G~~i~v~v~~~d 59 (70)
T cd05698 44 HFRVGQVVKVKVLSCD 59 (70)
T ss_pred cccCCCEEEEEEEEEc
Confidence 4678999999999876
No 59
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.55 E-value=74 Score=19.19 Aligned_cols=17 Identities=41% Similarity=0.391 Sum_probs=15.0
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.|..|+.|++||.++.
T Consensus 43 ~~~~~Gd~i~~~V~~id 59 (69)
T cd05697 43 KKFKPGLKVKCRVLSVE 59 (69)
T ss_pred HcCCCCCEEEEEEEEEE
Confidence 36889999999999886
No 60
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=25.09 E-value=83 Score=19.44 Aligned_cols=17 Identities=24% Similarity=0.345 Sum_probs=14.7
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-++..|++|+.||.+..
T Consensus 47 ~~~~~Gd~v~vkv~~vd 63 (73)
T cd05686 47 EVVDVGEKVWVKVIGRE 63 (73)
T ss_pred hEECCCCEEEEEEEEEC
Confidence 35899999999998876
No 61
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.55 E-value=83 Score=19.07 Aligned_cols=16 Identities=19% Similarity=0.021 Sum_probs=14.2
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
.|..|+.|+++|.+..
T Consensus 47 ~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 47 KFKKNDIVRACVLSVD 62 (73)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 5689999999999876
No 62
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=24.23 E-value=81 Score=18.43 Aligned_cols=16 Identities=25% Similarity=0.424 Sum_probs=14.1
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
.|..|+.|+.+|.++.
T Consensus 44 ~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 44 VLKVGDEVKVKVIEVD 59 (68)
T ss_pred ccCCCCEEEEEEEEEC
Confidence 5799999999998876
No 63
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=23.83 E-value=63 Score=20.85 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=13.3
Q ss_pred eeeeCCCCeEEEEEceEE
Q psy11391 42 DLFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 42 ~l~~d~ge~IRFRV~~~~ 59 (112)
+=-|..||+|+||+.-..
T Consensus 8 r~iYrPGetV~~~~~~~~ 25 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRD 25 (99)
T ss_dssp SSEE-TTSEEEEEEEEEE
T ss_pred ccCcCCCCEEEEEEEEec
Confidence 445789999999998444
No 64
>PRK15458 tagatose 6-phosphate aldolase subunit KbaZ; Provisional
Probab=23.72 E-value=35 Score=29.52 Aligned_cols=23 Identities=22% Similarity=0.151 Sum_probs=19.0
Q ss_pred CCCCCeEEEeccceeeeCCCCceeeeeee
Q psy11391 82 TPKIPYSYGYYSLAVLRTQLLSPVRFQHV 110 (112)
Q Consensus 82 ~~~~Py~I~~~~~gs~~~~GLGpv~W~~~ 110 (112)
..++.-+|+ +.++=|||..|||.
T Consensus 78 ~gf~~~~ii------LGGDHLGPn~Wq~l 100 (426)
T PRK15458 78 LNFPQEALI------LGGDHLGPNRWQNL 100 (426)
T ss_pred cCCChhhEE------eecCCCCCccccCC
Confidence 446666788 88999999999985
No 65
>TIGR03834 EAGR_box EAGR box. The EAGR box (Enriched in Aromatic and Glycine Residues) is found in three different proteins of the Mycoplasma genitalium terminal organelle, which acts in both cytadherence and gliding motility. The presence of this domain in a genome predicts the Mycoplasma-type terminal organelle structure, gliding motility, and cytadherence. The EAGR box may occur from one to nine times in a protein.
Probab=23.10 E-value=59 Score=17.87 Aligned_cols=11 Identities=27% Similarity=1.208 Sum_probs=7.5
Q ss_pred CCCcccceEEEe
Q psy11391 22 RFDEKEQVWVWE 33 (112)
Q Consensus 22 ~fd~~e~~W~W~ 33 (112)
+|| +.+.|+|.
T Consensus 8 ~yd-~~~~WiW~ 18 (28)
T TIGR03834 8 YYD-ENGEWIWK 18 (28)
T ss_pred cCc-CCCcEEEe
Confidence 356 45679995
No 66
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=22.85 E-value=92 Score=17.99 Aligned_cols=17 Identities=24% Similarity=0.217 Sum_probs=14.7
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.+..|+.|+.||.++.
T Consensus 43 ~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 43 DVVSVGDIVEVKVISID 59 (68)
T ss_pred HhcCCCCEEEEEEEEEE
Confidence 35799999999998887
No 67
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=22.71 E-value=1.1e+02 Score=18.06 Aligned_cols=17 Identities=12% Similarity=0.059 Sum_probs=14.8
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.|..|+.|+.+|.++.
T Consensus 44 ~~~~~G~~v~v~v~~id 60 (69)
T cd05690 44 EIYKKGQEVEAVVLNID 60 (69)
T ss_pred hEECCCCEEEEEEEEEE
Confidence 35799999999999887
No 68
>PRK15267 subtilase cytotoxin subunit B-like protein; Provisional
Probab=22.34 E-value=53 Score=24.37 Aligned_cols=24 Identities=4% Similarity=0.350 Sum_probs=21.9
Q ss_pred ceeeeeCCCCeEEEEEceEEeeec
Q psy11391 40 KHDLFMDPGDKIKFRVTSELFTET 63 (112)
Q Consensus 40 ~~~l~~d~ge~IRFRV~~~~F~d~ 63 (112)
..++||-.|+.||.-+..-.|++.
T Consensus 88 qA~YyYtTG~~VRIYy~~nVWt~p 111 (141)
T PRK15267 88 TAKYYYTTGGDVRIYYKENVWRDP 111 (141)
T ss_pred hhheeeecCceEEEEEcCCcccCc
Confidence 368999999999999999999986
No 69
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.15 E-value=97 Score=18.59 Aligned_cols=17 Identities=18% Similarity=0.057 Sum_probs=14.3
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.|..|+.|++||.+..
T Consensus 43 ~~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 43 KRFKVGQLVKGKIVSID 59 (68)
T ss_pred hccCCCCEEEEEEEEEe
Confidence 34689999999998876
No 70
>TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit. Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, required both for full activity and for good stability of the aldolase. Note that members of this protein family appear in public databases annotated as putative tagatose 6-phosphate kinases, possibly in error.
Probab=22.01 E-value=43 Score=28.98 Aligned_cols=23 Identities=22% Similarity=0.109 Sum_probs=18.8
Q ss_pred CCCCCeEEEeccceeeeCCCCceeeeeee
Q psy11391 82 TPKIPYSYGYYSLAVLRTQLLSPVRFQHV 110 (112)
Q Consensus 82 ~~~~Py~I~~~~~gs~~~~GLGpv~W~~~ 110 (112)
..++.-+|+ +.++=|||..|||.
T Consensus 74 ~gf~~~~ii------LggDHlGPn~Wq~l 96 (420)
T TIGR02810 74 IGFPRDRLI------LGGDHLGPNPWQHL 96 (420)
T ss_pred cCCChhcEE------eecCCCCCccccCC
Confidence 446666788 88999999999985
No 71
>KOG3409|consensus
Probab=21.86 E-value=1.7e+02 Score=22.78 Aligned_cols=13 Identities=38% Similarity=0.629 Sum_probs=10.5
Q ss_pred eCCCCeEEEEEce
Q psy11391 45 MDPGDKIKFRVTS 57 (112)
Q Consensus 45 ~d~ge~IRFRV~~ 57 (112)
|.+|+.||=||.+
T Consensus 123 FrPgDiVlAkVis 135 (193)
T KOG3409|consen 123 FRPGDIVLAKVIS 135 (193)
T ss_pred cCCCcEEEEEEee
Confidence 5588888888877
No 72
>PF12306 PixA: Inclusion body protein; InterPro: IPR021087 This entry represents bacterial proteins that are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein []. This signature also identifies AidA.
Probab=21.63 E-value=1.3e+02 Score=22.37 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=15.5
Q ss_pred eeeeeCCCCeEEEEEceE
Q psy11391 41 HDLFMDPGDKIKFRVTSE 58 (112)
Q Consensus 41 ~~l~~d~ge~IRFRV~~~ 58 (112)
-.+-..+|+.||+|+.+.
T Consensus 58 L~i~a~~GD~Irwr~tSl 75 (172)
T PF12306_consen 58 LSIKANVGDTIRWRATSL 75 (172)
T ss_pred eEEeccCCCEEEEEEEee
Confidence 457778999999999987
No 73
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.26 E-value=86 Score=19.48 Aligned_cols=16 Identities=19% Similarity=0.322 Sum_probs=13.7
Q ss_pred eeCCCCeEEEEEceEE
Q psy11391 44 FMDPGDKIKFRVTSEL 59 (112)
Q Consensus 44 ~~d~ge~IRFRV~~~~ 59 (112)
+|..|+.||.+|.+..
T Consensus 48 ~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 48 GFKPGKIVRCCILSKK 63 (72)
T ss_pred hCCCCCEEEEEEEEec
Confidence 5689999999998874
No 74
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.03 E-value=96 Score=19.51 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=15.1
Q ss_pred eeeCCCCeEEEEEceEE
Q psy11391 43 LFMDPGDKIKFRVTSEL 59 (112)
Q Consensus 43 l~~d~ge~IRFRV~~~~ 59 (112)
-.|..|++|++||.+..
T Consensus 57 ~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 57 FGFKKGQSVTAKVTSVD 73 (83)
T ss_pred HhcCCCCEEEEEEEEEc
Confidence 56889999999999876
Done!