Query 010247
Match_columns 514
No_of_seqs 274 out of 1467
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 22:46:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010247hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00358 3_prime_RNase VacB a 100.0 3.7E-81 8.1E-86 696.4 38.2 348 121-475 122-518 (654)
2 PRK11642 exoribonuclease R; Pr 100.0 7.4E-80 1.6E-84 696.1 37.2 348 121-475 188-582 (813)
3 TIGR02063 RNase_R ribonuclease 100.0 2.7E-79 5.8E-84 687.7 38.5 311 158-475 217-570 (709)
4 TIGR02062 RNase_B exoribonucle 100.0 7.8E-79 1.7E-83 674.9 38.6 344 121-475 121-508 (639)
5 COG0557 VacB Exoribonuclease R 100.0 1.3E-79 2.8E-84 689.3 32.3 290 181-475 244-569 (706)
6 PRK05054 exoribonuclease II; P 100.0 1.1E-78 2.4E-83 674.5 37.1 346 120-475 123-512 (644)
7 PF00773 RNB: RNB domain CAUTI 100.0 1.1E-74 2.3E-79 594.2 30.2 287 185-475 1-319 (325)
8 KOG2102 Exosomal 3'-5' exoribo 100.0 6.1E-63 1.3E-67 563.2 20.7 354 112-475 370-799 (941)
9 COG4776 Rnb Exoribonuclease II 100.0 4.5E-57 9.8E-62 465.8 14.7 286 184-475 189-512 (645)
10 cd05692 S1_RPS1_repeat_hs4 S1_ 57.8 15 0.00033 28.0 3.8 25 485-510 43-67 (69)
11 cd05697 S1_Rrp5_repeat_hs5 S1_ 53.1 22 0.00047 28.0 4.0 26 485-510 43-68 (69)
12 cd05690 S1_RPS1_repeat_ec5 S1_ 52.9 16 0.00034 28.5 3.1 25 485-509 44-68 (69)
13 cd04472 S1_PNPase S1_PNPase: P 51.8 20 0.00044 27.5 3.6 25 485-510 43-67 (68)
14 cd05708 S1_Rrp5_repeat_sc12 S1 50.7 23 0.00051 28.0 3.9 26 485-510 46-71 (77)
15 PF06345 Drf_DAD: DRF Autoregu 48.3 17 0.00037 20.9 1.8 12 71-82 1-12 (15)
16 cd05685 S1_Tex S1_Tex: The C-t 47.1 22 0.00048 27.1 3.1 25 485-509 43-67 (68)
17 cd04471 S1_RNase_R S1_RNase_R: 47.0 24 0.00053 28.3 3.5 26 485-510 56-81 (83)
18 cd05698 S1_Rrp5_repeat_hs6_sc5 46.4 33 0.00072 26.8 4.1 28 484-511 42-69 (70)
19 PF00575 S1: S1 RNA binding do 45.8 31 0.00067 27.2 3.9 28 483-510 45-72 (74)
20 cd05703 S1_Rrp5_repeat_hs12_sc 45.4 33 0.00072 27.7 4.0 28 484-511 44-71 (73)
21 cd05696 S1_Rrp5_repeat_hs4 S1_ 44.3 35 0.00075 27.4 3.9 28 483-510 43-70 (71)
22 cd05689 S1_RPS1_repeat_ec4 S1_ 44.3 25 0.00055 27.7 3.1 25 485-509 47-71 (72)
23 cd05688 S1_RPS1_repeat_ec3 S1_ 43.7 29 0.00062 26.6 3.3 25 485-509 43-67 (68)
24 cd04452 S1_IF2_alpha S1_IF2_al 43.7 36 0.00078 27.0 3.9 26 485-510 48-73 (76)
25 cd05691 S1_RPS1_repeat_ec6 S1_ 43.0 38 0.00083 26.5 4.0 26 485-510 43-68 (73)
26 cd05707 S1_Rrp5_repeat_sc11 S1 42.8 28 0.00061 27.2 3.1 26 484-509 42-67 (68)
27 cd05705 S1_Rrp5_repeat_hs14 S1 42.6 31 0.00067 28.0 3.4 26 484-509 48-73 (74)
28 cd05706 S1_Rrp5_repeat_sc10 S1 42.6 39 0.00085 26.7 4.0 26 485-510 46-71 (73)
29 cd05687 S1_RPS1_repeat_ec1_hs1 42.6 41 0.0009 26.3 4.1 28 484-511 42-69 (70)
30 smart00316 S1 Ribosomal protei 42.2 39 0.00085 25.5 3.8 26 485-510 45-70 (72)
31 cd00164 S1_like S1_like: Ribos 39.3 38 0.00081 25.1 3.3 25 485-509 40-64 (65)
32 cd05695 S1_Rrp5_repeat_hs3 S1_ 37.7 37 0.00081 26.8 3.1 26 484-509 40-65 (66)
33 cd04461 S1_Rrp5_repeat_hs8_sc7 37.2 50 0.0011 27.0 3.9 27 484-510 56-82 (83)
34 cd05686 S1_pNO40 S1_pNO40: pNO 36.9 46 0.001 26.6 3.6 26 484-510 46-71 (73)
35 PF04225 OapA: Opacity-associa 34.9 34 0.00073 28.9 2.5 62 228-298 4-67 (85)
36 PRK05807 hypothetical protein; 33.1 54 0.0012 30.1 3.8 25 485-510 47-71 (136)
37 PF03544 TonB_C: Gram-negative 32.8 65 0.0014 25.5 3.9 24 275-298 15-38 (79)
38 PHA02945 interferon resistance 32.3 59 0.0013 28.0 3.6 23 487-510 58-80 (88)
39 PF05800 GvpO: Gas vesicle syn 31.6 1E+02 0.0023 27.1 5.1 23 206-228 40-62 (100)
40 PF13103 TonB_2: TonB C termin 31.4 67 0.0015 26.1 3.8 24 275-298 25-48 (85)
41 PRK07252 hypothetical protein; 29.6 72 0.0016 28.7 3.9 26 485-510 46-71 (120)
42 cd05684 S1_DHX8_helicase S1_DH 29.0 76 0.0017 25.6 3.7 24 485-510 47-70 (79)
43 TIGR01352 tonB_Cterm TonB fami 28.9 92 0.002 24.3 4.1 21 277-297 11-31 (74)
44 PRK08059 general stress protei 27.7 84 0.0018 28.1 4.0 27 485-511 50-76 (123)
45 cd05694 S1_Rrp5_repeat_hs2_sc2 24.0 1.3E+02 0.0028 24.5 4.1 26 485-510 42-67 (74)
46 COG4451 RbcS Ribulose bisphosp 23.3 1.4E+02 0.003 27.3 4.4 47 73-137 63-110 (127)
47 cd04465 S1_RPS1_repeat_ec2_hs2 23.1 1.2E+02 0.0026 23.5 3.7 24 488-511 43-66 (67)
No 1
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=100.00 E-value=3.7e-81 Score=696.36 Aligned_cols=348 Identities=27% Similarity=0.388 Sum_probs=294.8
Q ss_pred cCCeeeeEEeeCCCCCccc--eEEccCCCccc----cCccceeeecCCCCCCCHHHHHHHHHH---hc-hhccCCCCCCC
Q 010247 121 DSDRVLLAVAQRPDGKKNW--MVYDQNGASCS----IKPQQVTFVVPGVEKFDHKDISNFLQK---AE-DNLLNRKDLTH 190 (514)
Q Consensus 121 ~~~rv~l~i~~~pd~~k~~--~~~~~~~~~~s----l~p~~~~~~~~~~~~f~~~~~~~~~~~---~~-~~~~~R~Dlr~ 190 (514)
.|++|.+.|..+|.....+ .++...|.... +...-..|+++. .||++.++++..- +. ...+.|+|||+
T Consensus 122 ~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~--~f~~~v~~~a~~~~~~~~~~~~~~R~Dlr~ 199 (654)
T TIGR00358 122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPF--EFPDGVEQQAAKLQFDVDEQAKKYREDLTD 199 (654)
T ss_pred CCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCC--CCCHHHHHHHHhccccCChhHhhCcccccc
Confidence 4677788888888765544 23433232211 111113456665 3888777655321 21 34567999999
Q ss_pred CeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCChhhhcccCCCC
Q 010247 191 LKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLR 270 (514)
Q Consensus 191 l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~~~~SL~ 270 (514)
+++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+||++||||||||++++||||+.||+++|||+
T Consensus 200 ~~~~TID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~ 279 (654)
T TIGR00358 200 LAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLN 279 (654)
T ss_pred CcEEEECCCCCCcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccC
Confidence 99999999999999999999999899999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeeEEEEEEEECCCCCeeeEEEEEeEEecccccCHHHHHHHHhcCcc-------chHHHHHHHHHHHHHHHHHHhCC
Q 010247 271 QGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQG 343 (514)
Q Consensus 271 pg~~r~AlSv~~~ld~~G~I~~~~i~~siIrs~~~LtY~ev~~il~~~~~-------~~~~L~~L~~la~~l~~~R~~~G 343 (514)
||++|+||||.+++|++|+|.+++|++|+|+|.++|||++|+++|+++.. ..++|..|+++|++|+++|.++|
T Consensus 280 p~~~R~a~s~~~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~lr~~R~~~G 359 (654)
T TIGR00358 280 PNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRG 359 (654)
T ss_pred CCCcceEEEEEEEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999987531 24579999999999999999999
Q ss_pred CccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCChh-hhc---
Q 010247 344 AIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA--- 419 (514)
Q Consensus 344 al~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~~-~l~--- 419 (514)
+++|+.||.+|.+++ ++.++.+.... .++|+.|||||||+||++||+|+.++++|++||+|+.|+.++. +|.
T Consensus 360 ai~~~~~e~~~~~d~---~g~~~~i~~~~-~~~a~~lIeE~MilAN~~vA~~~~~~~~p~iyR~h~~p~~~~~~~l~~~~ 435 (654)
T TIGR00358 360 LIDFEHPETKFIVDE---EGRVIDIVAEV-RRIAEKIIEEAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFL 435 (654)
T ss_pred CcccCCCceeEEECC---CCCeeEEEecc-CcHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCCCHHHHHHHHHHH
Confidence 999999999999987 24467888877 8999999999999999999999999999999999999987654 221
Q ss_pred -----cCCCC------c-----------------chHHHHHHhcccCccccCCCCcccccCCCCccccccchhhhHHHHH
Q 010247 420 -----HLPEG------P-----------------VRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLA 471 (514)
Q Consensus 420 -----~l~~g------~-----------------v~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIRRYaDLvv 471 (514)
.++.+ + +....++|+|++|.|++ .|.+|||||++.|||||||||||+||+|
T Consensus 436 ~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y~~-~~~~HfgL~~~~YthfTSPIRRY~DLiv 514 (654)
T TIGR00358 436 AELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYSP-EPLGHFGLGLEHYAHFTSPIRRYPDLTN 514 (654)
T ss_pred HHcCCCccCCCcCCCChHHHHHHHHHhhCCCHHHHHHHHHHHhhcccccCC-CCCCccccccccccccCCccccchHHHH
Confidence 11111 0 11346789999999999 9999999999999999999999999999
Q ss_pred HHHh
Q 010247 472 HYQV 475 (514)
Q Consensus 472 HrQL 475 (514)
||||
T Consensus 515 Hr~L 518 (654)
T TIGR00358 515 HRLI 518 (654)
T ss_pred HHHH
Confidence 9999
No 2
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=7.4e-80 Score=696.13 Aligned_cols=348 Identities=23% Similarity=0.334 Sum_probs=295.4
Q ss_pred cCCeeeeEEeeCCCCCccc--eEEccCCCccc----cCccceeeecCCCCCCCHHHHHHHHHH---hc-hhccCCCCCCC
Q 010247 121 DSDRVLLAVAQRPDGKKNW--MVYDQNGASCS----IKPQQVTFVVPGVEKFDHKDISNFLQK---AE-DNLLNRKDLTH 190 (514)
Q Consensus 121 ~~~rv~l~i~~~pd~~k~~--~~~~~~~~~~s----l~p~~~~~~~~~~~~f~~~~~~~~~~~---~~-~~~~~R~Dlr~ 190 (514)
.|+.|++.|..+|.....+ .++...|.... +...-..|++|.. ||++.++++..- +. ...++|+|||+
T Consensus 188 ~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~--Fp~~v~~ea~~~~~~~~~~~~~~R~DLr~ 265 (813)
T PRK11642 188 MGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYI--WPQAVEQQVAGLKEEVPEEAKAGRVDLRD 265 (813)
T ss_pred CCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCC--CCHHHHHHHHhccccCChhHhcccccccc
Confidence 4567788888888765544 34443332111 1111123566654 888877765432 22 23467999999
Q ss_pred CeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCChhhhcccCCCC
Q 010247 191 LKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLR 270 (514)
Q Consensus 191 l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~~~~SL~ 270 (514)
+++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+||++||||||||++++||||+.||+++|||+
T Consensus 266 l~~vTID~~~akD~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYlpd~viPMLP~~Lsn~lcSL~ 345 (813)
T PRK11642 266 LPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLN 345 (813)
T ss_pred CcEEEECCCCCCcccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHHHhCCeEeCCCceeeCCCHHHhcCccccC
Confidence 99999999999999999999999888999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeeEEEEEEEECCCCCeeeEEEEEeEEecccccCHHHHHHHHhcCcc-------chHHHHHHHHHHHHHHHHHHhCC
Q 010247 271 QGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQG 343 (514)
Q Consensus 271 pg~~r~AlSv~~~ld~~G~I~~~~i~~siIrs~~~LtY~ev~~il~~~~~-------~~~~L~~L~~la~~l~~~R~~~G 343 (514)
||++|+||||.++||.+|+|.+++|++|+|+|.++|||++|+++|+++.. ..+.|..|+++++.|+++|.++|
T Consensus 346 p~~dRla~s~~~~id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~Lr~~R~~~G 425 (813)
T PRK11642 346 PQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERG 425 (813)
T ss_pred CCCceeEEEEEEEECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999987532 23678999999999999999999
Q ss_pred CccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCChh-hhc---
Q 010247 344 AIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA--- 419 (514)
Q Consensus 344 al~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~~-~l~--- 419 (514)
+++|+.||.++.+++. +....+...+ +.+++.|||||||+||++||+|+.++++|++||+|+.|+.++. +|.
T Consensus 426 ai~~d~~E~~i~ld~~---g~~~~i~~~~-~~~a~~lIEE~MllAN~~vA~~l~~~~~p~lyR~H~~P~~ekl~~l~~~l 501 (813)
T PRK11642 426 GISFESEEAKFIFNAE---RRIERIEQTQ-RNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVL 501 (813)
T ss_pred CcccCCCceEEEECCC---CCEeeEEecc-cccHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCCHHHHHHHHHHH
Confidence 9999999999999872 3467888877 8999999999999999999999999999999999999997765 221
Q ss_pred ---c--CCC---------------------CcchHHHHHHhcccCccccCCCCcccccCCCCccccccchhhhHHHHHHH
Q 010247 420 ---H--LPE---------------------GPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHY 473 (514)
Q Consensus 420 ---~--l~~---------------------g~v~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIRRYaDLvvHr 473 (514)
. ++. ..+.+.+++|+|++|.|++ .|.+|||||++.|||||||||||+||+|||
T Consensus 502 ~~lG~~l~~~~~~~~~~~~~ll~~~~~~~~~~~l~~~llRsm~~A~Y~~-~~~gHfGLa~~~YtHFTSPIRRY~DLivHR 580 (813)
T PRK11642 502 AELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDP-ENRGHFGLALQSYAHFTSPIRRYPDLSLHR 580 (813)
T ss_pred HHcCCcccCCCCCCHHHHHHHHHHHhCCcHHHHHHHHHHHhccccccCC-CCCCccccccccccccCchhhhhHHHHHHH
Confidence 1 110 0112346789999999999 999999999999999999999999999999
Q ss_pred Hh
Q 010247 474 QV 475 (514)
Q Consensus 474 QL 475 (514)
||
T Consensus 581 ~L 582 (813)
T PRK11642 581 AI 582 (813)
T ss_pred HH
Confidence 88
No 3
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=100.00 E-value=2.7e-79 Score=687.72 Aligned_cols=311 Identities=29% Similarity=0.431 Sum_probs=275.0
Q ss_pred eecCCCCCCCHHHHHHHHHH---h-chhccCCCCCCCCeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCC
Q 010247 158 FVVPGVEKFDHKDISNFLQK---A-EDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEP 233 (514)
Q Consensus 158 ~~~~~~~~f~~~~~~~~~~~---~-~~~~~~R~Dlr~l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~ 233 (514)
|+++. .|+++.++++..- + ....++|+|||++++|||||++|+|+||||||++.++|+|+|||||||||+||++
T Consensus 217 ~~i~~--~f~~~v~~~a~~~~~~~~~~~~~~R~Dl~~~~~~tID~~~a~D~DDAisie~~~~g~~~l~VhIADVs~~V~~ 294 (709)
T TIGR02063 217 HGIPY--EFPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVRE 294 (709)
T ss_pred cCcCC--CCCHHHHHHHHhCCCCCChhHhhcccccccCcEEEECCCCCcccccEEEEEEcCCCCEEEEEEEechhhEeCC
Confidence 44544 3766665544321 1 1234679999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHhcCceeecCCCcccCCChhhhcccCCCCCCCeeeEEEEEEEECCCCCeeeEEEEEeEEecccccCHHHHHH
Q 010247 234 GSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATE 313 (514)
Q Consensus 234 gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~~~~SL~pg~~r~AlSv~~~ld~~G~I~~~~i~~siIrs~~~LtY~ev~~ 313 (514)
||+||+||++||||+|||++++||||+.||+++|||+||++|+||||.+++|++|+|.+++|++|+|+|+++|||++|++
T Consensus 295 ~s~lD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~~~id~~G~i~~~~~~~svI~s~~~ltY~~v~~ 374 (709)
T TIGR02063 295 GSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVND 374 (709)
T ss_pred CChHHHHHHHhCeeEeCCCCcccCCChHHccCccccCCCCceEEEEEEEEECCCCCEEEeEEEEEEEEeCeEEcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCcc-------chHHHHHHHHHHHHHHHHHHhCCCccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHH
Q 010247 314 LLHLNLE-------EEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMI 386 (514)
Q Consensus 314 il~~~~~-------~~~~L~~L~~la~~l~~~R~~~Gal~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MI 386 (514)
+|+++.. ..++|..|+++|+.|+++|.++|+++|+.|+.+|.+++ ++.++.+...+ +++|+.|||||||
T Consensus 375 ~l~~~~~~~~~~~~~~~~L~~l~~la~~l~~~R~~~G~i~~~~~e~~~~~d~---~g~~~~i~~~~-~~~a~~lIeE~Ml 450 (709)
T TIGR02063 375 IIEGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDE---NGKPIDIVPRE-RGDAHKLIEEFMI 450 (709)
T ss_pred HHcCCccccchhhHHHHHHHHHHHHHHHHHHHHHhCCCcccCCccceeEECC---CCCeEEEEecc-chHHHHHHHHHHH
Confidence 9987532 24679999999999999999999999999999999987 24468888888 8999999999999
Q ss_pred HHHHHHHHHhhhCCCCceeecCCCCCCChh-hhc--------cCCCC-----------------------cchHHHHHHh
Q 010247 387 LCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA--------HLPEG-----------------------PVRSSAIVKI 434 (514)
Q Consensus 387 lAN~~vA~~l~~~~ip~~yR~q~~P~~~~~-~l~--------~l~~g-----------------------~v~~~~l~r~ 434 (514)
+||++||+|+.++++|++||+|+.|+.++. +|. .++.+ .+...+++|+
T Consensus 451 lAN~~vA~~l~~~~~p~iyR~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~ 530 (709)
T TIGR02063 451 AANETVAEHLEKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRS 530 (709)
T ss_pred HHHHHHHHHHHhCCCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCCCCCCHHHHHHHHHHhhCCcHHHHHHHHHHHH
Confidence 999999999999999999999999997665 221 11110 0123467899
Q ss_pred cccCccccCCCCcccccCCCCccccccchhhhHHHHHHHHh
Q 010247 435 MRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475 (514)
Q Consensus 435 m~~A~ys~~~~~~H~gLgl~~YthfTSPIRRYaDLvvHrQL 475 (514)
|++|.|++ .|.+|||||++.|||||||||||+||+|||||
T Consensus 531 m~~A~y~~-~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L 570 (709)
T TIGR02063 531 MQQAKYSP-ENIGHFGLALEYYTHFTSPIRRYPDLIVHRLI 570 (709)
T ss_pred hcCcccCC-CCCCccccccccccccCCccccchHHHHHHHH
Confidence 99999999 99999999999999999999999999999999
No 4
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=100.00 E-value=7.8e-79 Score=674.90 Aligned_cols=344 Identities=24% Similarity=0.339 Sum_probs=292.2
Q ss_pred cCCeeeeEEeeCCCCC-ccc--eEEccCCCccc----cCccceeeecCCCCCCCHHHHHHHHHHhchhccCCCCCCCCeE
Q 010247 121 DSDRVLLAVAQRPDGK-KNW--MVYDQNGASCS----IKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKV 193 (514)
Q Consensus 121 ~~~rv~l~i~~~pd~~-k~~--~~~~~~~~~~s----l~p~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~R~Dlr~l~~ 193 (514)
.++.|++.|..+|... +.+ .++...|.... +.-.-..|+++.. ||++.+++... ...+|+|||++++
T Consensus 121 ~gd~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~~--f~~~v~~ea~~----~~~~R~DLr~~~~ 194 (639)
T TIGR02062 121 EGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLERE--EPDGVADEMLL----DGLVREDLTALDF 194 (639)
T ss_pred CCCEEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCCC--CCHHHHHhhhh----ccccCcccccCCE
Confidence 5778888999999754 222 34443332211 1111124566664 88877766532 2257999999999
Q ss_pred EEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCChhhhcccCCCCCCC
Q 010247 194 YAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGE 273 (514)
Q Consensus 194 fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~~~~SL~pg~ 273 (514)
|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||+
T Consensus 195 ~TID~~~akD~DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e 274 (639)
T TIGR02062 195 VTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANE 274 (639)
T ss_pred EEECCCCCCcccceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHHHHHHhCCcEeCCCceecCCCHHHhcCccccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEEEEECCCCCeee-EEEEEeEEecccccCHHHHHHHHhcCcc-------chHHHHHHHHHHHHHHHHHHhCCCc
Q 010247 274 VCNAVTVSVVLHSDGSIAE-YSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQGAI 345 (514)
Q Consensus 274 ~r~AlSv~~~ld~~G~I~~-~~i~~siIrs~~~LtY~ev~~il~~~~~-------~~~~L~~L~~la~~l~~~R~~~Gal 345 (514)
+|+|+||.|++|++|+|++ ++|++|+|+|.++|||++|+++|+++.. ..++|..|+++|+.|+++|.++|++
T Consensus 275 ~R~als~~~~ld~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~~~~~~~~~~i~~~L~~L~~la~~l~~~R~~~G~i 354 (639)
T TIGR02062 275 VRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENTSDWQPESEEIAQQVRLLHQFCQARIEWRHTHALV 354 (639)
T ss_pred CeeEEEEEEEEcCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHhCCcc
Confidence 9999999999999999999 7999999999999999999999987532 1356899999999999999999999
Q ss_pred cCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCChh-hhc-----
Q 010247 346 DTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA----- 419 (514)
Q Consensus 346 ~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~~-~l~----- 419 (514)
.++.||.++.+++ ++.+..+.... +++++.|||||||+||++||+|+.++++|++||+|+.|+..+. +|.
T Consensus 355 ~ld~pE~~~~ld~---~g~~~~i~~~~-~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyR~H~~P~~~~l~~l~~~~~~ 430 (639)
T TIGR02062 355 FKDRPDYRFILSE---KGEVLDIVAEP-RRIANRIVEEAMIIANICAARFLRDKLGFGIYNTHAGFDPANAENVVALLKT 430 (639)
T ss_pred cccCCceEEEECC---CCCEEEEEEec-CCHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEecCCCCCHHHHHHHHHHHHH
Confidence 9999999999987 24467888877 8999999999999999999999999999999999999997655 221
Q ss_pred ---cCCCCc--------------------chHHHHHHhcccCccccCCCCcccccCCCCccccccchhhhHHHHHHHHh
Q 010247 420 ---HLPEGP--------------------VRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475 (514)
Q Consensus 420 ---~l~~g~--------------------v~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIRRYaDLvvHrQL 475 (514)
.++... .....++|+|.+|.|++ .|.+|||||++.|||||||||||+||+|||||
T Consensus 431 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~r~~~~a~ys~-~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L 508 (639)
T TIGR02062 431 NGLHVDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAEIST-EPGPHFGLGLEAYATWTSPIRKYGDMINHRLL 508 (639)
T ss_pred cCCCCCcccccCHHHHHHHHHHhhcchHHHHHHHHHHHhhhcccCC-CCcCcchhccccccccCChhhhhHHHHHHHHH
Confidence 111110 11235679999999999 99999999999999999999999999999999
No 5
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=1.3e-79 Score=689.32 Aligned_cols=290 Identities=34% Similarity=0.509 Sum_probs=266.7
Q ss_pred hccCCCCCCCCeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCCh
Q 010247 181 NLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPE 260 (514)
Q Consensus 181 ~~~~R~Dlr~l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~ 260 (514)
..++|.|||++++|||||++|+|+|||+|++++.+|+|+|||||||||+||+|||+||+||++||||||||+++|||||+
T Consensus 244 ~~~~R~Dlr~l~~~TID~~~akD~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~RgtSVYlp~~vipMLPe 323 (706)
T COG0557 244 DLKGRVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPE 323 (706)
T ss_pred hhcCccccccCCEEEECCCCCccccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHHcCCeEEcCCcccCCCch
Confidence 44689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcccCCCCCCCeeeEEEEEEEECCCCCeeeEEEEEeEEecccccCHHHHHHHHhcCc-----cchHHHHHHHHHHHHH
Q 010247 261 KLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNL-----EEEAELKILSEAAALR 335 (514)
Q Consensus 261 ~Ls~~~~SL~pg~~r~AlSv~~~ld~~G~I~~~~i~~siIrs~~~LtY~ev~~il~~~~-----~~~~~L~~L~~la~~l 335 (514)
.||+++|||+||++|+|+||.|++|.+|+|.+++|++++|+|.++|||++|+++|+++. +..+.|..+..+++.+
T Consensus 324 ~Ls~~lcSL~p~~dRla~s~~m~ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~l~~~l~~~~~l~~~l 403 (706)
T COG0557 324 ALSNGLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKYAPLLDSLLELLELAKIL 403 (706)
T ss_pred hhcCCccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcchhcccchHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999853 2357788888899999
Q ss_pred HHHHHhCCCccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCCh
Q 010247 336 LQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDV 415 (514)
Q Consensus 336 ~~~R~~~Gal~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~ 415 (514)
+++|.++|+++|+.+|.++.+++ ++.++.+...+ +++++.||||||++||++||+++.++++|.+||+|+.|+.++
T Consensus 404 ~~~R~~rg~i~~~~~E~ki~~d~---~~~~~~i~~~~-r~~a~~lIee~Ml~AN~~vA~~l~~~~~~~~~R~h~~P~~ek 479 (706)
T COG0557 404 KKKRLSRGAIDFDTPEAKIVLDE---EGRPVEIEIRE-RLDAEKLIEEFMLLANETVAEHLEKHKIPLLYRTHERPSTEK 479 (706)
T ss_pred HHHHHhCCCcccCCcceeEEECC---CCCeeeEEEec-ccHHHHHHHHHHHHHHHHHHHHHHHcCCCcceeCCCCCCHHH
Confidence 99999999999999999999998 34578999998 889999999999999999999999999999999999998765
Q ss_pred h----hhc-c----CC----------------CC------cchHHHHHHhcccCccccCCCCcccccCCCCccccccchh
Q 010247 416 S----AFA-H----LP----------------EG------PVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIR 464 (514)
Q Consensus 416 ~----~l~-~----l~----------------~g------~v~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIR 464 (514)
. +++ . ++ .. .+....++|+|++|.|++ .+.+|||||++.|||||||||
T Consensus 480 ~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~lRsm~~a~Ys~-~~~~HfgL~~~~YtHFTSPIR 558 (706)
T COG0557 480 LQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPLEAVLQTLLLRSMKQAEYSP-DNVGHFGLALDYYTHFTSPIR 558 (706)
T ss_pred HHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccCChHHHHHHHHHHHhhhcCeecC-CCCCceeccccchhccCCchh
Confidence 4 111 0 00 00 133456889999999999 999999999999999999999
Q ss_pred hhHHHHHHHHh
Q 010247 465 RYMDLLAHYQV 475 (514)
Q Consensus 465 RYaDLvvHrQL 475 (514)
||+||+|||||
T Consensus 559 RY~DLivHR~L 569 (706)
T COG0557 559 RYPDLIVHRQL 569 (706)
T ss_pred hchHHHHHHHH
Confidence 99999999999
No 6
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=1.1e-78 Score=674.51 Aligned_cols=346 Identities=24% Similarity=0.325 Sum_probs=287.6
Q ss_pred ecCCeeeeEEeeCCCC-Cccc--eEEccCCCccc----cCccceeeecCCCCCCCHHHHHHHHHHhchhccCCCCCCCCe
Q 010247 120 KDSDRVLLAVAQRPDG-KKNW--MVYDQNGASCS----IKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLK 192 (514)
Q Consensus 120 ~~~~rv~l~i~~~pd~-~k~~--~~~~~~~~~~s----l~p~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~R~Dlr~l~ 192 (514)
+.++.|.+.|..+|.. .+.+ .+++.-|.... +...-..|+++.. |+++.++. ++.+.-.+|+|||+++
T Consensus 123 ~~gd~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~~--f~~~~~~~---~~~~~~~~R~Dlr~~~ 197 (644)
T PRK05054 123 KEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLERE--APAGGVAW---EMLDEGLEREDLTALD 197 (644)
T ss_pred CCCCEEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCCC--CCchhhhc---cCChhccCcccccCCc
Confidence 3466777888888864 2323 34433332111 0011123555554 66654431 2221113799999999
Q ss_pred EEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCChhhhcccCCCCCC
Q 010247 193 VYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQG 272 (514)
Q Consensus 193 ~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~~~~SL~pg 272 (514)
+|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||
T Consensus 198 ~~TID~~~akD~DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~ 277 (644)
T PRK05054 198 FVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPN 277 (644)
T ss_pred EEEECCCCCCcccceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHHHHHHhCceEeCCCCcccCCChHHhcCccccCCC
Confidence 99999999999999999999989999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeeEEEEEEEECCCCCeee-EEEEEeEEecccccCHHHHHHHHhcCcc-------chHHHHHHHHHHHHHHHHHHhCCC
Q 010247 273 EVCNAVTVSVVLHSDGSIAE-YSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQGA 344 (514)
Q Consensus 273 ~~r~AlSv~~~ld~~G~I~~-~~i~~siIrs~~~LtY~ev~~il~~~~~-------~~~~L~~L~~la~~l~~~R~~~Ga 344 (514)
++|+|+||.++||++|+|++ ++|++|+|+|.++|||++|+++|+++.. ..+.|..|+++++.++++|.++|+
T Consensus 278 ~~R~als~~~~id~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~i~~~l~~L~~l~~~l~~~R~~~G~ 357 (644)
T PRK05054 278 ERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHAL 357 (644)
T ss_pred CCceEEEEEEEEeCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCCCccccchhHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 99999999999999999998 8999999999999999999999987532 235689999999999999999999
Q ss_pred ccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCChh-hhc----
Q 010247 345 IDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA---- 419 (514)
Q Consensus 345 l~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~~-~l~---- 419 (514)
+.++.||.++.+++ ++.+..+...+ +++++.|||||||+||++||+|+.++++|++||+|+.|+..+. +|.
T Consensus 358 i~~d~~e~~i~ld~---~g~~~~i~~~~-~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyRvH~~P~~~~l~~l~~~~~ 433 (644)
T PRK05054 358 VFKDRPDYRFELGE---KGEVLDIVAEP-RRIANRIVEESMIAANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLK 433 (644)
T ss_pred ccccCCceEEEECC---CCCEEEEEEec-CcHHHHHHHHHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHH
Confidence 99999999999987 24467888888 9999999999999999999999999999999999999987664 221
Q ss_pred --c--CCCC---cc-----------------hHHHHHHhcccCccccCCCCcccccCCCCccccccchhhhHHHHHHHHh
Q 010247 420 --H--LPEG---PV-----------------RSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475 (514)
Q Consensus 420 --~--l~~g---~v-----------------~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIRRYaDLvvHrQL 475 (514)
. ++.. .. -...++|+|.+|.|++ .|.+|||||++.|||||||||||+||+|||||
T Consensus 434 ~~g~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~~llr~~~~a~ys~-~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L 512 (644)
T PRK05054 434 EHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEIST-EPGPHFGLGLEAYATWTSPIRKYGDMINHRLL 512 (644)
T ss_pred HCCCCcCCCcccChHHHHHHHHHHhcchHHHHHHHHHHHHhceecCC-CCcCccccccccccccCChhhhhHHHHHHHHH
Confidence 1 1100 00 0124679999999999 99999999999999999999999999999999
No 7
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=100.00 E-value=1.1e-74 Score=594.24 Aligned_cols=287 Identities=38% Similarity=0.565 Sum_probs=235.7
Q ss_pred CCCCCCCeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCChhhhc
Q 010247 185 RKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAM 264 (514)
Q Consensus 185 R~Dlr~l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~ 264 (514)
|+||+++++||||+++|+|+||||||+++++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++
T Consensus 1 R~Dl~~~~~~tID~~~~~d~DDAisie~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~ 80 (325)
T PF00773_consen 1 RKDLRDLPVFTIDPPGAKDIDDAISIEKLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSE 80 (325)
T ss_dssp SEECTTSEEEEEESTTSS---EEEEEEEETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHC
T ss_pred CccCCCCCEEEEcCCCCCCCCCeEEEEECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCeeeEEEEEEEECCCCCeeeEEEEEeEEecccccCHHHHHHHHhcCccc------hHHHHHHHHHHHHHHHH
Q 010247 265 EGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEE------EAELKILSEAAALRLQW 338 (514)
Q Consensus 265 ~~~SL~pg~~r~AlSv~~~ld~~G~I~~~~i~~siIrs~~~LtY~ev~~il~~~~~~------~~~L~~L~~la~~l~~~ 338 (514)
+.|||.||++|+|||+.+++|++|+|.+++|++++|+|.++|||++|+++|++.... .++|..|+++|+.++++
T Consensus 81 ~~~SL~~~~~r~a~S~~~~l~~~G~i~~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~~~~~~~~L~~l~~la~~l~~~ 160 (325)
T PF00773_consen 81 DLCSLNPGKDRLAFSVIFTLDEDGEILDYEIYPSIIRSVARLTYEEVDEILEGKSQEEPESPIEEDLKLLYELAKALRKK 160 (325)
T ss_dssp TTSSTTBTSEEEEEEEEEEE-TTS-EEEEEEEEEEEEBSEEEEHHHHHHHHHTTTS--HCSHCHHHHHHHHHHHHHHHHH
T ss_pred ccccCCCCCCceEEEEEEEEeeCCeEeeeEEEEEEEecccccCHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999986432 68999999999999999
Q ss_pred HHhCCCccC-CCcceEEEecCCCCCCCcEEEEEec--CCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCCh
Q 010247 339 RLQQGAIDT-ATLETRIKVANPEDPEPIINLYVED--QADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDV 415 (514)
Q Consensus 339 R~~~Gal~~-~~pe~~~~l~~~~d~~~~i~i~~~~--~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~ 415 (514)
|.++|++.+ +.|+..+.+++. +......... ..++++.||+||||+||++||+|+.++++|++||+|+.|+...
T Consensus 161 R~~~Ga~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~~~ip~iyR~~~~p~~~~ 237 (325)
T PF00773_consen 161 RLSRGAIELFNSPELKFSLDED---GPPKEINRESSDESSPAHSLVEELMILANRAVAQFLSENGIPAIYRVQPEPDPER 237 (325)
T ss_dssp HHHTTS-----SHCEEEEEETT---TTEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHHCTTTSEEEEB-SSSCCC
T ss_pred hhhccCccccCCCceEEEEecC---CCcceEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHHcCCCceeeeCCCCCHHH
Confidence 999999999 789999999872 3334444432 3789999999999999999999999999999999999998874
Q ss_pred h-hh---ccC----------------CC---CcchHHHHHHhcccCccccCCCCcccccCCCCccccccchhhhHHHHHH
Q 010247 416 S-AF---AHL----------------PE---GPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAH 472 (514)
Q Consensus 416 ~-~l---~~l----------------~~---g~v~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIRRYaDLvvH 472 (514)
. ++ +.+ .. .......++++|++|+|++ .|.+|||||++.|||||||||||+||+||
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a~y~~-~p~~H~~L~l~~Yt~~TSPlRRY~Dl~~h 316 (325)
T PF00773_consen 238 LEELLKLLKLDLDETKSLTLQNLLQAENPPNSLALRYLLLKTLPPAEYST-EPSGHFGLGLPAYTHFTSPLRRYADLVVH 316 (325)
T ss_dssp HHHHHHHHT---STCHHHCHHCHHCCCCTTSSHHHHHHHHCCC--EEEES-SGC-BTTTTBSS-B--S-TTTBHHHHHHH
T ss_pred HHHHHHHhcCCCCCcchhhHHHHHHhcCChHHHHHHHHHHHhhccccccc-CCCcceeeeccccccccChhhhhHHHHHH
Confidence 3 21 110 11 1233457889999999999 99999999999999999999999999999
Q ss_pred HHh
Q 010247 473 YQV 475 (514)
Q Consensus 473 rQL 475 (514)
|||
T Consensus 317 rql 319 (325)
T PF00773_consen 317 RQL 319 (325)
T ss_dssp HHH
T ss_pred HHH
Confidence 998
No 8
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.1e-63 Score=563.22 Aligned_cols=354 Identities=29% Similarity=0.381 Sum_probs=296.6
Q ss_pred CccEEEEEecCCeeee-EEeeC-C----------CCCccceEEccCCCccccCccceeeecCCCCCCCHHHHHHHHHH--
Q 010247 112 KGLLLEFKKDSDRVLL-AVAQR-P----------DGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQK-- 177 (514)
Q Consensus 112 ~g~lv~f~~~~~rv~l-~i~~~-p----------d~~k~~~~~~~~~~~~sl~p~~~~~~~~~~~~f~~~~~~~~~~~-- 177 (514)
..+.+||++.|+|||+ .|..+ - .+++.|+.+ |.+|++..++..|..+-.+.+.+.++-+
T Consensus 370 ~~~~~~~~p~DkRvP~i~i~t~~~~~~~~~~~~~~~I~~W~~t-------s~~p~g~~v~~lG~i~~~~~e~~aLL~en~ 442 (941)
T KOG2102|consen 370 SALIVLFIPSDKRVPLIRILTDDQAQDLIDKRIVAAIDRWPRT-------SLYPFGHLVRELGTIGDTETETEALLLENG 442 (941)
T ss_pred ccceeeeccccCCCCeeeccccccccchhceeEEEEecccccC-------CcccCceehhhccCcCCccchhhhhhhcCC
Confidence 4556999999999988 55444 1 246677766 8899999998888776666666555432
Q ss_pred -------------hc---------hhccC-CCCCCCCeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCC
Q 010247 178 -------------AE---------DNLLN-RKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPG 234 (514)
Q Consensus 178 -------------~~---------~~~~~-R~Dlr~l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~g 234 (514)
+. ..... |.|||++.+|+|||.++.|||||+|++.++||+|+|||||||||+||+||
T Consensus 443 v~~~~f~~~~~~~lp~~~~~~~~~~~~~~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evGVHIADVt~fV~pg 522 (941)
T KOG2102|consen 443 VPHKPFSQALLDCLPRSHPWPITEEELQKLRKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVGVHIADVTHFVKPG 522 (941)
T ss_pred CcccccCHHHHhcCCccCCCCcChHHhhhhhhhhhhceEEeecCCCccchhhhhheeecCCCcEEEEEEeccchhhcCCC
Confidence 01 11244 99999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHhcCceeecCCCcccCCChhhhcccCCCCCCCeeeEEEEEEEECCCCCeeeEEEEEeEEecccccCHHHHHHH
Q 010247 235 SLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATEL 314 (514)
Q Consensus 235 S~LD~eA~~RgtSVYLp~~~ipMLP~~Ls~~~~SL~pg~~r~AlSv~~~ld~~G~I~~~~i~~siIrs~~~LtY~ev~~i 314 (514)
|+||+||++||||||||+++|||||+.|++++|||.||.+|.|||+.+++|.+|.|++.||++|+|+|+.+|+|+++|++
T Consensus 523 s~lD~eA~~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~~f~ksvI~s~~~lsye~Aq~~ 602 (941)
T KOG2102|consen 523 SALDREAARRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILKTWFGKSVIRSKAALSYEEAQDI 602 (941)
T ss_pred CccCHHHHhhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceeeceecchhcccchhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCcc---chHHHHHHHHHHHHHHHHHHhCCCccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHH
Q 010247 315 LHLNLE---EEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEA 391 (514)
Q Consensus 315 l~~~~~---~~~~L~~L~~la~~l~~~R~~~Gal~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~ 391 (514)
|+++.. -...|..|.++|+.++++|..+|++.+..++..+.+++. +..+..+...+ ...++.+|+|||++||..
T Consensus 603 id~~~~~~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~--~~~p~~~e~~~-~~~~n~lveEfmllaN~~ 679 (941)
T KOG2102|consen 603 LDTPNSSDPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEE--KPNPQDVEVKE-LTETNFLVEEFMLLANIS 679 (941)
T ss_pred hcCCcccchhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccC--CCCccccceee-eehhhhHHHHHHHHHhHH
Confidence 998642 245699999999999999999999999999999999873 22345666655 677888999999999999
Q ss_pred HHHHhhhC-CCCceeecCCCCCCChh----hhc---cC----------C------CCcch-------HHHHHHhcccCcc
Q 010247 392 IATYGSFN-NLALPYRGQPQSNIDVS----AFA---HL----------P------EGPVR-------SSAIVKIMRAAAI 440 (514)
Q Consensus 392 vA~~l~~~-~ip~~yR~q~~P~~~~~----~l~---~l----------~------~g~v~-------~~~l~r~m~~A~y 440 (514)
+|+++.+. .-..++|.|+.|..... ++. .+ . .++.+ ..+..++|.+|.|
T Consensus 680 vA~~I~~~f~~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~~p~~~~~l~~l~~r~m~~A~y 759 (941)
T KOG2102|consen 680 VAEKILASFPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDDKPYLNTLLRILATRSMTRAVY 759 (941)
T ss_pred HHHHHHHhCCchhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCchHHHHHHHHHHHhhhhhceeE
Confidence 99999877 66778999998875443 111 11 0 01111 2345689999987
Q ss_pred ccC-----CCCcccccCCCCccccccchhhhHHHHHHHHh
Q 010247 441 DFR-----KPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475 (514)
Q Consensus 441 s~~-----~~~~H~gLgl~~YthfTSPIRRYaDLvvHrQL 475 (514)
... ....||||+++.|||||||||||+|++|||||
T Consensus 760 f~sg~~~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL 799 (941)
T KOG2102|consen 760 FCSGSSDTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQL 799 (941)
T ss_pred EeecccCcchhhchhhcccchhhccCcccccchHHHHHHH
Confidence 651 34779999999999999999999999999999
No 9
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=4.5e-57 Score=465.79 Aligned_cols=286 Identities=29% Similarity=0.411 Sum_probs=254.8
Q ss_pred CCCCCCCCeEEEEeCCCCCCccceEEEEEecCCeEEEEEEecCcccccCCCCHHHHHHHhcCceeecCCCcccCCChhhh
Q 010247 184 NRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLA 263 (514)
Q Consensus 184 ~R~Dlr~l~~fTID~~~a~DiDDAlSie~l~dG~~~vgVHIADVa~~V~~gS~LD~eA~~RgtSVYLp~~~ipMLP~~Ls 263 (514)
.|+||+.+.++|||+++|+|+|||+.++++.+|.|.+-|+|||||.||.+||.||++|++|+.|.|||+..|||||..||
T Consensus 189 ~RedLTaL~FvTID~~sT~DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~s~ld~~A~~R~FTnYLPGfNIPMLPreLs 268 (645)
T COG4776 189 VREDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSKLDKEAKIRAFTNYLPGFNIPMLPRELS 268 (645)
T ss_pred hhccccccceEEecCccccccchhhhccccCCCcEEEEEEecCCccccCCcchhhHHHHHHHHhhcCCCCCCCCCChhhh
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCeeeEEEEEEEECCCCCee-eEEEEEeEEecccccCHHHHHHHHhcCcc-------chHHHHHHHHHHHHH
Q 010247 264 MEGMSLRQGEVCNAVTVSVVLHSDGSIA-EYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALR 335 (514)
Q Consensus 264 ~~~~SL~pg~~r~AlSv~~~ld~~G~I~-~~~i~~siIrs~~~LtY~ev~~il~~~~~-------~~~~L~~L~~la~~l 335 (514)
.++|||.||+.||++.|+++++.+|.|. +.+|..++|+|+++|.|+.|.++|++... ..+++.+|+++++++
T Consensus 269 d~lCSL~~ne~RPaL~C~it~~~~G~I~~~i~F~aA~i~SkakL~YdhVSDwlE~~~~WqPe~~~iAqqi~~L~~~~~aR 348 (645)
T COG4776 269 DDLCSLRANEVRPALACRITIDKDGNITDKIRFFAATIESKAKLVYDHVSDWLENTGDWQPESEAIAQQIRLLHQFCQAR 348 (645)
T ss_pred hhhhhccccccCceEEEEEEEecCCccccchhhHHHhhhhhhhhhhhhHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999998 48999999999999999999999997531 246899999999999
Q ss_pred HHHHHhCCCccCCCcceEEEecCCCCCCCcEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhCCCCceeecCCCCCCCh
Q 010247 336 LQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDV 415 (514)
Q Consensus 336 ~~~R~~~Gal~~~~pe~~~~l~~~~d~~~~i~i~~~~~~~~a~~LVeE~MIlAN~~vA~~l~~~~ip~~yR~q~~P~~~~ 415 (514)
-+||....-+--++|+|+|.+.+. +..+.|.... +..+++||||.||+||.++|++|.++---++|-+|..-+...
T Consensus 349 ~~WRk~hal~FkdrpdYrF~l~e~---g~V~~I~ae~-RRiAnriVEE~MI~ANIcAa~~L~~~~gfGI~N~HsGFd~~~ 424 (645)
T COG4776 349 IEWRKTHALVFKDRPDYRFILGEK---GEVLDIVAEP-RRIANRIVEESMIAANICAARVLREKLGFGIYNVHSGFDPAN 424 (645)
T ss_pred HHHHhhceeeccCCCceEEEecCC---CceEeeehhH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCcceeeccccCCHHH
Confidence 999998776666899999999883 3467777766 889999999999999999999999986667899998655433
Q ss_pred h----hhc-------------cC-------------CCCcchHHHHHHhcccCccccCCCCcccccCCCCccccccchhh
Q 010247 416 S----AFA-------------HL-------------PEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRR 465 (514)
Q Consensus 416 ~----~l~-------------~l-------------~~g~v~~~~l~r~m~~A~ys~~~~~~H~gLgl~~YthfTSPIRR 465 (514)
. +|+ ++ +.+ .-...++|+++-|++++ .|.||||||++.|+.||||||+
T Consensus 425 ~e~a~~~l~~~~~~~~~e~l~Tl~Gfc~lRr~l~~~~t~-yld~RiRrfqsfae~~t-~p~PHFglGl~~YATWTSPIRK 502 (645)
T COG4776 425 AEAAAALLKTNGLNVDAEELLTLEGFCKLRRELDAQPTG-YLDSRIRRFQSFAEIST-EPGPHFGLGLEAYATWTSPIRK 502 (645)
T ss_pred HHHHHHHHHhcCcCCCHHHHhhhHHHHHHHHHhhccccc-hHHHHHHHHHhHHhhcc-CcCccccccchheeeccchhhh
Confidence 2 121 11 111 11235788999999999 9999999999999999999999
Q ss_pred hHHHHHHHHh
Q 010247 466 YMDLLAHYQV 475 (514)
Q Consensus 466 YaDLvvHrQL 475 (514)
|.|+||||.|
T Consensus 503 Y~DMiNHRLl 512 (645)
T COG4776 503 YGDMINHRLL 512 (645)
T ss_pred hhhHHHHHHH
Confidence 9999999999
No 10
>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=57.84 E-value=15 Score=28.02 Aligned_cols=25 Identities=32% Similarity=0.260 Sum_probs=21.7
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.+.+++..+|+ .+.+.|+
T Consensus 43 ~~~~~Gd~v~v~v~~~~~-~~~i~ls 67 (69)
T cd05692 43 DVLKEGDKVKVKVLSIDA-RGRISLS 67 (69)
T ss_pred HccCCCCEEEEEEEEECC-CCcEEEE
Confidence 447999999999999999 8888775
No 11
>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=53.12 E-value=22 Score=27.98 Aligned_cols=26 Identities=19% Similarity=0.230 Sum_probs=23.3
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.+.+++.++|+.+..+.|.
T Consensus 43 ~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 43 KKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred HcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 45799999999999999999998875
No 12
>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=52.93 E-value=16 Score=28.49 Aligned_cols=25 Identities=28% Similarity=0.177 Sum_probs=22.3
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
..+++||+|.|++..+|+..+.|+|
T Consensus 44 ~~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 44 EIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred hEECCCCEEEEEEEEEECCcCEEeC
Confidence 3479999999999999999998876
No 13
>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=51.81 E-value=20 Score=27.51 Aligned_cols=25 Identities=40% Similarity=0.415 Sum_probs=21.8
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.+.|++..+|+ ...+.|.
T Consensus 43 ~~~~~Gd~v~v~v~~~d~-~~~i~ls 67 (68)
T cd04472 43 DVLKVGDEVKVKVIEVDD-RGRISLS 67 (68)
T ss_pred HccCCCCEEEEEEEEECC-CCcEEee
Confidence 447999999999999999 8888775
No 14
>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=50.69 E-value=23 Score=27.95 Aligned_cols=26 Identities=27% Similarity=0.277 Sum_probs=23.1
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.|.+++..+|+..+.+.|.
T Consensus 46 ~~~~~Gd~v~v~i~~vd~~~~~i~ls 71 (77)
T cd05708 46 KLFRVGDKVRAKVLKIDAEKKRISLG 71 (77)
T ss_pred HeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 44699999999999999999888876
No 15
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=48.32 E-value=17 Score=20.91 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=9.4
Q ss_pred hhHHHHHHHHHH
Q 010247 71 SLVDSVMQELVA 82 (514)
Q Consensus 71 ~~~~~~~~~l~~ 82 (514)
|.||+|.+||..
T Consensus 1 gvmdsllealqt 12 (15)
T PF06345_consen 1 GVMDSLLEALQT 12 (15)
T ss_dssp -HHHHHHHHHHH
T ss_pred CcHHHHHHHHHc
Confidence 579999999874
No 16
>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=47.09 E-value=22 Score=27.06 Aligned_cols=25 Identities=36% Similarity=0.312 Sum_probs=21.8
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
.-+++||.+.+++..+|+....+.|
T Consensus 43 ~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05685 43 DVVSVGDIVEVKVISIDEERGRISL 67 (68)
T ss_pred HhcCCCCEEEEEEEEEECCCCEEec
Confidence 4479999999999999998888776
No 17
>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=47.01 E-value=24 Score=28.33 Aligned_cols=26 Identities=23% Similarity=0.280 Sum_probs=23.6
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
..+++||.|.|++..+|+.++.+.|.
T Consensus 56 ~~~~~gd~v~v~v~~vd~~~~~i~~~ 81 (83)
T cd04471 56 KVFRLGDKVKVRVVRVDLDRRKIDFE 81 (83)
T ss_pred CEEcCCCEEEEEEEEeccccCEEEEE
Confidence 55799999999999999988999886
No 18
>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=46.37 E-value=33 Score=26.80 Aligned_cols=28 Identities=25% Similarity=0.347 Sum_probs=24.0
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYLKE 511 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~~~ 511 (514)
...+++||.+.+++.++|+....+.|..
T Consensus 42 ~~~~~~G~~i~v~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 42 EEHFRVGQVVKVKVLSCDPEQQRLLLSC 69 (70)
T ss_pred HHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 3558999999999999999888888753
No 19
>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=45.82 E-value=31 Score=27.24 Aligned_cols=28 Identities=32% Similarity=0.275 Sum_probs=24.4
Q ss_pred cccccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 483 VSVGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 483 ~~~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
....+.+||++.+++.++|+.+..+.|.
T Consensus 45 ~~~~~~~G~~v~v~v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 45 PSEVYKIGQTVRVKVIKVDKEKGRIRLS 72 (74)
T ss_dssp SHGTCETTCEEEEEEEEEETTTTEEEEE
T ss_pred cccccCCCCEEEEEEEEEECCCCeEEEE
Confidence 3455789999999999999999999885
No 20
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.40 E-value=33 Score=27.70 Aligned_cols=28 Identities=18% Similarity=0.270 Sum_probs=24.4
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYLKE 511 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~~~ 511 (514)
...+++||.|.+++..+|+.+..|.|..
T Consensus 44 ~~~~~vG~~v~~kV~~id~~~~~i~Ls~ 71 (73)
T cd05703 44 EKKFPIGQALKAKVVGVDKEHKLLRLSA 71 (73)
T ss_pred HHhCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 3458999999999999999999998863
No 21
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=44.34 E-value=35 Score=27.36 Aligned_cols=28 Identities=14% Similarity=0.198 Sum_probs=24.4
Q ss_pred cccccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 483 VSVGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 483 ~~~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
...-+++||++.+++...||.+..+.+.
T Consensus 43 ~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 43 DTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred cccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 3455899999999999999999998874
No 22
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: 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 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=44.26 E-value=25 Score=27.70 Aligned_cols=25 Identities=36% Similarity=0.373 Sum_probs=22.1
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
.-+++||++.|++.++|+-.+.++|
T Consensus 47 ~~~~~Gd~v~v~v~~id~~~~~i~~ 71 (72)
T cd05689 47 KVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred cEeCCCCEEEEEEEEeeCCcCEEeC
Confidence 4479999999999999999888876
No 23
>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=43.69 E-value=29 Score=26.57 Aligned_cols=25 Identities=40% Similarity=0.432 Sum_probs=22.0
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
.-+++||.+.+++..+|+-...+.|
T Consensus 43 ~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05688 43 EVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred HEECCCCEEEEEEEEEECCCCEEec
Confidence 3479999999999999998888876
No 24
>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=43.66 E-value=36 Score=26.96 Aligned_cols=26 Identities=23% Similarity=0.201 Sum_probs=22.8
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.|.+++...|+-.+.+.|.
T Consensus 48 ~~~~~Gd~v~vkv~~~d~~~~~i~ls 73 (76)
T cd04452 48 KLVKVGRKEVVKVIRVDKEKGYIDLS 73 (76)
T ss_pred HeeCCCCEEEEEEEEEECCCCEEEEE
Confidence 34699999999999999988888875
No 25
>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=43.04 E-value=38 Score=26.46 Aligned_cols=26 Identities=31% Similarity=0.473 Sum_probs=22.2
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
..+++||.+.+++..+|+.+..+.|.
T Consensus 43 ~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (73)
T cd05691 43 ERFKVGDEVEAKITNVDRKNRKISLS 68 (73)
T ss_pred HccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 44799999999999999988877765
No 26
>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=42.75 E-value=28 Score=27.21 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=22.5
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
...+++||.+.+++..+||....+.|
T Consensus 42 ~~~~~~Gd~v~~~v~~~d~~~~~i~l 67 (68)
T cd05707 42 KKRFKVGQLVKGKIVSIDPDNGRIEM 67 (68)
T ss_pred hhccCCCCEEEEEEEEEeCCCCEEec
Confidence 34579999999999999998888765
No 27
>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=42.65 E-value=31 Score=28.04 Aligned_cols=26 Identities=15% Similarity=0.171 Sum_probs=23.0
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
.+-+++||.+.++|..+|+.+..|.+
T Consensus 48 ~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 48 NKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred hcccCCCCEEEEEEEEEECCCCEEec
Confidence 45679999999999999999988876
No 28
>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=42.63 E-value=39 Score=26.68 Aligned_cols=26 Identities=19% Similarity=0.047 Sum_probs=23.0
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.+.+++..+|+....+.|.
T Consensus 46 ~~~~~Gd~v~~~V~~~d~~~~~i~ls 71 (73)
T cd05706 46 YKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred cccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 44799999999999999998888876
No 29
>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=42.60 E-value=41 Score=26.30 Aligned_cols=28 Identities=29% Similarity=0.393 Sum_probs=23.9
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYLKE 511 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~~~ 511 (514)
..-+++||.+.+++...|+....+.|..
T Consensus 42 ~~~~~~Gd~i~~~i~~~~~~~~~i~lS~ 69 (70)
T cd05687 42 EDEVKVGDEVEVYVLRVEDEEGNVVLSK 69 (70)
T ss_pred hHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence 3447999999999999999988888764
No 30
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=42.18 E-value=39 Score=25.49 Aligned_cols=26 Identities=35% Similarity=0.400 Sum_probs=22.8
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.+.+++..+|+.+..+.|.
T Consensus 45 ~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 45 EVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred HeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 34799999999999999998888875
No 31
>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=39.33 E-value=38 Score=25.08 Aligned_cols=25 Identities=48% Similarity=0.569 Sum_probs=21.4
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
.-+++||.|.+++..+|+.+..+.+
T Consensus 40 ~~~~~G~~v~~~v~~~d~~~~~i~l 64 (65)
T cd00164 40 EVFKVGDEVEVKVLEVDPEKGRISL 64 (65)
T ss_pred hEeCCCCEEEEEEEEEcCCcCEEec
Confidence 3479999999999999998877765
No 32
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: 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 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.65 E-value=37 Score=26.78 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=22.8
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYL 509 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~ 509 (514)
..-+++||++.+++..+||.+..+.|
T Consensus 40 ~~~~~~G~~i~~kVi~id~~~~~i~L 65 (66)
T cd05695 40 KSTYKEGQKVRARILYVDPSTKVVGL 65 (66)
T ss_pred ccCcCCCCEEEEEEEEEeCCCCEEec
Confidence 45589999999999999998888765
No 33
>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=37.21 E-value=50 Score=26.96 Aligned_cols=27 Identities=26% Similarity=0.351 Sum_probs=23.5
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
...+++||++.|++.++|+....+.|.
T Consensus 56 ~~~~~~Gd~v~vkV~~id~~~~~i~ls 82 (83)
T cd04461 56 SFGFKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred HHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence 455799999999999999998888774
No 34
>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=36.87 E-value=46 Score=26.61 Aligned_cols=26 Identities=31% Similarity=0.314 Sum_probs=21.6
Q ss_pred ccccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 484 SVGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 484 ~~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
..-+++||++.|++..+|+.. .++|.
T Consensus 46 ~~~~~~Gd~v~vkv~~vd~~~-ki~ls 71 (73)
T cd05686 46 SEVVDVGEKVWVKVIGREMKD-KMKLS 71 (73)
T ss_pred hhEECCCCEEEEEEEEECCCC-cEEEE
Confidence 344799999999999999976 77775
No 35
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=34.91 E-value=34 Score=28.95 Aligned_cols=62 Identities=19% Similarity=0.284 Sum_probs=32.8
Q ss_pred ccccCCCCHHHHHHHhcCceeecCCC-cccCCChh-hhcccCCCCCCCeeeEEEEEEEECCCCCeeeEEEEEe
Q 010247 228 TKYIEPGSLSDKDAMKRGTSVFLPTA-TYPMFPEK-LAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNS 298 (514)
Q Consensus 228 a~~V~~gS~LD~eA~~RgtSVYLp~~-~ipMLP~~-Ls~~~~SL~pg~~r~AlSv~~~ld~~G~I~~~~i~~s 298 (514)
.+-|++|..|.....+.|-+ .. ...|+-.. -...+-.|+||+ ++.|.+|++|++....+..+
T Consensus 4 ~~~V~~GDtLs~iF~~~gls----~~dl~~v~~~~~~~k~L~~L~pGq-----~l~f~~d~~g~L~~L~~~~~ 67 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFRRAGLS----ASDLYAVLEADGEAKPLTRLKPGQ-----TLEFQLDEDGQLTALRYERS 67 (85)
T ss_dssp EEE--TT--HHHHHHHTT------HHHHHHHHHHGGGT--GGG--TT------EEEEEE-TTS-EEEEEEEEE
T ss_pred EEEECCCCcHHHHHHHcCCC----HHHHHHHHhccCccchHhhCCCCC-----EEEEEECCCCCEEEEEEEcC
Confidence 35689999999999988833 22 22222211 112455799999 89999999999987776554
No 36
>PRK05807 hypothetical protein; Provisional
Probab=33.14 E-value=54 Score=30.11 Aligned_cols=25 Identities=28% Similarity=0.223 Sum_probs=21.0
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.|.|+|..+|+ .+.|+|.
T Consensus 47 ~~~kvGd~V~VkV~~id~-~gkI~LS 71 (136)
T PRK05807 47 EHLKEQDKVKVKVISIDD-NGKISLS 71 (136)
T ss_pred ccCCCCCEEEEEEEEECC-CCcEEEE
Confidence 347999999999999999 6777664
No 37
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=32.76 E-value=65 Score=25.52 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=19.7
Q ss_pred eeEEEEEEEECCCCCeeeEEEEEe
Q 010247 275 CNAVTVSVVLHSDGSIAEYSVDNS 298 (514)
Q Consensus 275 r~AlSv~~~ld~~G~I~~~~i~~s 298 (514)
.-.+.+.+.+|++|+|.+.++..+
T Consensus 15 ~G~v~v~~~I~~~G~v~~~~v~~s 38 (79)
T PF03544_consen 15 EGTVVVEFTIDPDGRVSDVRVIQS 38 (79)
T ss_dssp EEEEEEEEEEETTTEEEEEEEEEE
T ss_pred eEEEEEEEEEeCCCCEEEEEEEEc
Confidence 346889999999999999876555
No 38
>PHA02945 interferon resistance protein; Provisional
Probab=32.29 E-value=59 Score=28.01 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=21.1
Q ss_pred cCCCcEEEEEEeeecCCCCeEEEE
Q 010247 487 AQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 487 ~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
+ .|+++.++|.++||....|++.
T Consensus 58 l-~GqkvV~KVirVd~~kg~IDlS 80 (88)
T PHA02945 58 L-VGKTVKVKVIRVDYTKGYIDVN 80 (88)
T ss_pred e-cCCEEEEEEEEECCCCCEEEeE
Confidence 5 9999999999999999999873
No 39
>PF05800 GvpO: Gas vesicle synthesis protein GvpO; InterPro: IPR008634 This family consists of archaeal GvpO proteins which are required for gas vesicle synthesis []. The family also contain related sequences from bacteria.; GO: 0031412 gas vesicle organization
Probab=31.61 E-value=1e+02 Score=27.11 Aligned_cols=23 Identities=26% Similarity=0.375 Sum_probs=17.9
Q ss_pred ceEEEEEecCCeEEEEEEecCcc
Q 010247 206 DALSAMRLQDGRIKVYIHVADPT 228 (514)
Q Consensus 206 DAlSie~l~dG~~~vgVHIADVa 228 (514)
-..++++.+||+|++.|-|-...
T Consensus 40 ~V~~~~~~edgGW~v~VEVvE~~ 62 (100)
T PF05800_consen 40 GVSSVERTEDGGWRVVVEVVEDR 62 (100)
T ss_pred eEEEEeecCCCCeEEEEEEeeec
Confidence 34788898997899999876543
No 40
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=31.43 E-value=67 Score=26.11 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=16.6
Q ss_pred eeEEEEEEEECCCCCeeeEEEEEe
Q 010247 275 CNAVTVSVVLHSDGSIAEYSVDNS 298 (514)
Q Consensus 275 r~AlSv~~~ld~~G~I~~~~i~~s 298 (514)
.....|.+.||++|+|.++++.++
T Consensus 25 ~~~~~V~i~i~~dG~v~~~~i~~s 48 (85)
T PF13103_consen 25 GLSVTVRITIDPDGRVISVRIVKS 48 (85)
T ss_dssp T--EEEEEEE-TTSBEEEEEEEE-
T ss_pred CcEEEEEEEECCCCCEEEEEEecC
Confidence 456789999999999987776553
No 41
>PRK07252 hypothetical protein; Provisional
Probab=29.64 E-value=72 Score=28.68 Aligned_cols=26 Identities=23% Similarity=0.198 Sum_probs=22.2
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||.|.|+|..+|+....+.|.
T Consensus 46 ~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 46 QLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred hccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 44799999999999999977777764
No 42
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=29.04 E-value=76 Score=25.56 Aligned_cols=24 Identities=29% Similarity=0.288 Sum_probs=19.6
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
.-+++||+|.|++..+| ...+.|.
T Consensus 47 ~~~~~Gd~v~v~v~~vd--~~~i~~s 70 (79)
T cd05684 47 DVVKRGQKVKVKVISIQ--NGKISLS 70 (79)
T ss_pred heeCCCCEEEEEEEEEe--CCEEEEE
Confidence 34799999999999999 6666654
No 43
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=28.87 E-value=92 Score=24.28 Aligned_cols=21 Identities=29% Similarity=0.428 Sum_probs=18.0
Q ss_pred EEEEEEEECCCCCeeeEEEEE
Q 010247 277 AVTVSVVLHSDGSIAEYSVDN 297 (514)
Q Consensus 277 AlSv~~~ld~~G~I~~~~i~~ 297 (514)
.+.+.+.++++|+|.+.++..
T Consensus 11 ~v~v~~~i~~~G~v~~~~i~~ 31 (74)
T TIGR01352 11 TVVVRFTVDADGRVTSVSVLK 31 (74)
T ss_pred EEEEEEEECCCCCEEEEEEEE
Confidence 478899999999999988754
No 44
>PRK08059 general stress protein 13; Validated
Probab=27.65 E-value=84 Score=28.12 Aligned_cols=27 Identities=33% Similarity=0.289 Sum_probs=22.8
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLKE 511 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~~ 511 (514)
.-+++||.|.|+|..+|+..+.+.|+-
T Consensus 50 ~~~~vGD~I~vkI~~id~~~~~i~lsl 76 (123)
T PRK08059 50 DFLSVGDEVKVKVLSVDEEKGKISLSI 76 (123)
T ss_pred HcCCCCCEEEEEEEEEECCCCeEEEEE
Confidence 346899999999999999888887753
No 45
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: 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 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.01 E-value=1.3e+02 Score=24.49 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=23.1
Q ss_pred cccCCCcEEEEEEeeecCCCCeEEEE
Q 010247 485 VGAQIGDEVEVKVEEAHPRDDIIYLK 510 (514)
Q Consensus 485 ~~~~~gd~~~v~~~~~dp~~~~~~~~ 510 (514)
..+++||.+.+++.++|+.+..+.+.
T Consensus 42 ~~~~~Gq~v~~~V~~vd~~~~~v~ls 67 (74)
T cd05694 42 SKLKVGQLLLCVVEKVKDDGRVVSLS 67 (74)
T ss_pred cccCCCCEEEEEEEEEECCCCEEEEE
Confidence 66899999999999999999887764
No 46
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=23.27 E-value=1.4e+02 Score=27.27 Aligned_cols=47 Identities=15% Similarity=0.188 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHhHHHHHHhhhcccccchhhhhhhhccCccEEEEEecCCeeee-EEeeCCCCCc
Q 010247 73 VDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLL-AVAQRPDGKK 137 (514)
Q Consensus 73 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lv~f~~~~~rv~l-~i~~~pd~~k 137 (514)
.++..++||.+|.=+ + .+ ..+-=+|+-|.+.++++++ -|+++|+++.
T Consensus 63 ~~~~~evlaele~Cr--~----dh------------p~eYIRliGfDp~gkrrv~sfIVhRPng~~ 110 (127)
T COG4451 63 AKTAGEVLAELEACR--A----DH------------PGEYIRLIGFDPKGKRRVVSFIVHRPNGNP 110 (127)
T ss_pred ccchHHHHHHHHHHH--H----hC------------CCCeEEEEEecCCCceEEEEEEEECCCCCC
Confidence 467788999888764 1 11 2233467899999999988 7899998765
No 47
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=23.08 E-value=1.2e+02 Score=23.53 Aligned_cols=24 Identities=25% Similarity=0.390 Sum_probs=21.0
Q ss_pred CCCcEEEEEEeeecCCCCeEEEEE
Q 010247 488 QIGDEVEVKVEEAHPRDDIIYLKE 511 (514)
Q Consensus 488 ~~gd~~~v~~~~~dp~~~~~~~~~ 511 (514)
.+||.+.+++.++|+....|.+..
T Consensus 43 ~vG~~i~~~i~~vd~~~~~i~lS~ 66 (67)
T cd04465 43 YVGKELKFKIIEIDRERNNIVLSR 66 (67)
T ss_pred hCCCEEEEEEEEEeCCCCEEEEEc
Confidence 489999999999999888887763
Done!