Query 009063
Match_columns 545
No_of_seqs 366 out of 2231
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 19:57:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009063.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009063hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10334 mechanosensitive chan 100.0 5E-45 1.1E-49 371.7 36.9 251 191-461 29-280 (286)
2 PRK11465 putative mechanosensi 100.0 9.7E-43 2.1E-47 387.2 43.9 298 139-456 417-722 (741)
3 PRK11281 hypothetical protein; 100.0 6.4E-40 1.4E-44 380.1 44.1 253 190-461 836-1091(1113)
4 PRK10929 putative mechanosensi 100.0 1.5E-39 3.2E-44 375.8 37.9 251 192-461 835-1088(1109)
5 COG3264 Small-conductance mech 100.0 3.3E-36 7.1E-41 332.3 37.4 244 199-460 566-812 (835)
6 PF00924 MS_channel: Mechanose 100.0 9.9E-37 2.1E-41 296.3 22.2 203 239-449 2-206 (206)
7 COG0668 MscS Small-conductance 100.0 4.1E-34 9E-39 294.3 35.6 208 236-457 86-296 (316)
8 KOG4629 Predicted mechanosensi 99.8 5.2E-20 1.1E-24 204.3 14.9 222 232-460 478-702 (714)
9 PRK05886 yajC preprotein trans 77.6 10 0.00023 33.4 7.2 37 298-338 39-75 (109)
10 PRK05585 yajC preprotein trans 75.7 7.5 0.00016 34.1 5.8 41 298-342 53-93 (106)
11 TIGR00739 yajC preprotein tran 75.6 8.6 0.00019 32.3 5.9 37 298-338 38-74 (84)
12 PF09953 DUF2187: Uncharacteri 66.7 9.7 0.00021 29.6 3.9 28 298-329 4-31 (57)
13 COG1862 YajC Preprotein transl 66.3 26 0.00056 30.3 6.9 42 298-343 44-85 (97)
14 PRK10263 DNA translocase FtsK; 66.3 1.5E+02 0.0033 37.0 15.5 8 531-538 524-531 (1355)
15 smart00739 KOW KOW (Kyprides, 64.9 12 0.00025 23.9 3.6 24 297-321 1-26 (28)
16 COG4873 Uncharacterized protei 55.8 14 0.0003 29.5 3.1 27 298-328 24-50 (81)
17 PF12794 MscS_TM: Mechanosensi 54.5 2.9E+02 0.0062 29.2 19.2 30 234-263 193-223 (340)
18 PF12961 DUF3850: Domain of Un 53.1 31 0.00068 28.2 4.8 31 294-324 25-56 (72)
19 PRK06531 yajC preprotein trans 51.7 39 0.00083 30.1 5.6 41 298-342 37-78 (113)
20 PF14545 DBB: Dof, BCAP, and B 50.5 34 0.00074 31.7 5.3 81 290-376 15-96 (142)
21 PF14801 GCD14_N: tRNA methylt 50.0 9.1 0.0002 29.4 1.2 24 295-322 3-26 (54)
22 PF00467 KOW: KOW motif; Inte 48.6 28 0.00061 23.4 3.4 22 300-322 1-24 (32)
23 PF02699 YajC: Preprotein tran 44.4 7.4 0.00016 32.4 0.0 39 296-338 35-73 (82)
24 PRK08559 nusG transcription an 42.6 77 0.0017 29.5 6.5 47 296-343 93-145 (153)
25 COG4956 Integral membrane prot 42.2 3.1E+02 0.0067 28.9 11.1 35 100-134 34-68 (356)
26 PF00575 S1: S1 RNA binding do 41.8 1.3E+02 0.0029 23.4 7.1 39 314-353 9-47 (74)
27 PRK10334 mechanosensitive chan 39.0 4.5E+02 0.0098 27.1 14.0 25 110-134 30-54 (286)
28 PF09926 DUF2158: Uncharacteri 38.9 31 0.00067 26.4 2.6 23 298-322 1-23 (53)
29 PF13726 Na_H_antiport_2: Na+- 38.2 60 0.0013 27.6 4.5 45 246-290 5-50 (88)
30 PRK12281 rplX 50S ribosomal pr 38.1 40 0.00087 27.8 3.4 27 297-324 6-34 (76)
31 cd04466 S1_YloQ_GTPase S1_YloQ 36.3 67 0.0015 24.9 4.4 28 296-324 36-63 (68)
32 PF05552 TM_helix: Conserved T 35.9 63 0.0014 24.3 4.0 35 188-223 13-47 (53)
33 TIGR00405 L26e_arch ribosomal 35.8 86 0.0019 28.6 5.7 25 296-321 85-111 (145)
34 PF11449 DUF2899: Protein of u 35.1 5.2E+02 0.011 27.0 11.7 42 233-274 178-223 (298)
35 PF02934 GatB_N: GatB/GatE cat 34.3 2.5E+02 0.0053 29.2 9.1 143 288-443 85-234 (289)
36 PF05552 TM_helix: Conserved T 34.2 90 0.002 23.5 4.6 30 108-137 15-44 (53)
37 CHL00141 rpl24 ribosomal prote 33.4 52 0.0011 27.6 3.4 26 297-323 8-35 (83)
38 cd05705 S1_Rrp5_repeat_hs14 S1 33.3 1.4E+02 0.0031 23.9 6.0 44 298-351 1-44 (74)
39 PRK04439 S-adenosylmethionine 32.9 1.5E+02 0.0033 32.0 7.6 80 360-445 156-244 (399)
40 COG0370 FeoB Fe2+ transport sy 32.3 5.5E+02 0.012 29.8 12.2 57 234-290 498-576 (653)
41 PF01941 AdoMet_Synthase: S-ad 31.1 2E+02 0.0044 31.1 8.1 80 360-445 156-244 (396)
42 COG2139 RPL21A Ribosomal prote 30.5 88 0.0019 27.0 4.3 38 296-334 31-79 (98)
43 PF09378 HAS-barrel: HAS barre 30.5 60 0.0013 26.7 3.4 27 297-323 22-49 (91)
44 cd04461 S1_Rrp5_repeat_hs8_sc7 29.9 1.3E+02 0.0028 24.4 5.3 44 298-351 12-55 (83)
45 PRK11281 hypothetical protein; 29.7 1.2E+03 0.026 29.1 18.0 8 74-81 454-461 (1113)
46 PRK10694 acyl-CoA esterase; Pr 29.7 57 0.0012 29.6 3.3 31 291-329 61-91 (133)
47 PRK13889 conjugal transfer rel 28.9 90 0.002 37.9 5.7 47 296-343 599-651 (988)
48 PF01157 Ribosomal_L21e: Ribos 28.8 66 0.0014 28.0 3.4 28 296-323 31-69 (99)
49 PF04156 IncA: IncA protein; 28.4 2.5E+02 0.0054 26.6 7.8 39 252-296 24-63 (191)
50 PRK00004 rplX 50S ribosomal pr 28.2 69 0.0015 28.0 3.4 26 297-323 4-31 (105)
51 PRK00409 recombination and DNA 27.6 1.7E+02 0.0037 34.7 7.5 46 296-344 635-680 (782)
52 PF11282 DUF3082: Protein of u 27.2 3.8E+02 0.0082 22.5 8.4 25 199-223 13-37 (82)
53 COG3264 Small-conductance mech 27.0 1.1E+03 0.025 28.1 15.6 69 236-305 510-599 (835)
54 PF02933 CDC48_2: Cell divisio 26.9 1.3E+02 0.0029 23.3 4.6 30 293-322 14-43 (64)
55 PRK01191 rpl24p 50S ribosomal 26.2 70 0.0015 28.8 3.1 25 297-322 45-71 (120)
56 PF10929 DUF2811: Protein of u 25.6 49 0.0011 25.8 1.8 19 376-394 10-28 (57)
57 TIGR01080 rplX_A_E ribosomal p 25.3 76 0.0016 28.3 3.2 24 297-321 41-66 (114)
58 smart00333 TUDOR Tudor domain. 25.1 2.9E+02 0.0062 20.4 6.1 46 297-343 2-50 (57)
59 smart00743 Agenet Tudor-like d 25.0 2.3E+02 0.005 21.5 5.6 26 297-322 2-29 (61)
60 PF06107 DUF951: Bacterial pro 24.6 1.9E+02 0.004 22.7 4.8 44 298-343 2-48 (57)
61 PF02559 CarD_CdnL_TRCF: CarD- 24.4 2E+02 0.0043 24.2 5.6 44 297-343 1-51 (98)
62 PRK04306 50S ribosomal protein 23.9 1.2E+02 0.0026 26.4 4.0 29 296-324 33-72 (98)
63 cd03452 MaoC_C MaoC_C The C-t 23.7 2E+02 0.0043 26.0 5.9 16 291-306 82-97 (142)
64 PRK08582 hypothetical protein; 22.6 2.9E+02 0.0063 25.3 6.6 41 298-348 3-43 (139)
65 PRK10929 putative mechanosensi 22.4 1.6E+03 0.034 28.0 17.9 9 316-324 809-817 (1109)
66 TIGR01079 rplX_bact ribosomal 22.4 1E+02 0.0023 26.9 3.5 25 297-322 3-29 (104)
67 PRK12773 flhB flagellar biosyn 22.2 1.3E+03 0.027 26.8 18.9 17 432-448 587-603 (646)
68 COG1607 Acyl-CoA hydrolase [Li 22.1 80 0.0017 29.8 2.9 30 292-329 64-93 (157)
69 PRK09014 rfaH transcriptional 22.1 1E+02 0.0023 28.6 3.7 26 295-321 107-134 (162)
70 PRK13692 (3R)-hydroxyacyl-ACP 21.6 2.1E+02 0.0046 26.7 5.7 16 291-306 90-105 (159)
71 PF09871 DUF2098: Uncharacteri 21.4 1.1E+02 0.0025 26.1 3.4 23 296-320 1-23 (91)
72 CHL00084 rpl19 ribosomal prote 21.2 2.2E+02 0.0047 25.5 5.3 11 297-307 22-32 (117)
73 PRK14725 pyruvate kinase; Prov 21.1 1.4E+02 0.003 34.2 5.0 81 298-381 373-467 (608)
74 TIGR01069 mutS2 MutS2 family p 20.6 4.1E+02 0.0089 31.5 9.0 44 296-343 624-667 (771)
75 PRK05609 nusG transcription an 20.6 2.7E+02 0.0059 26.1 6.3 26 295-321 124-151 (181)
76 PF13452 MaoC_dehydrat_N: N-te 20.5 2.1E+02 0.0046 25.1 5.2 19 288-306 78-96 (132)
77 PF01545 Cation_efflux: Cation 20.5 4.5E+02 0.0098 26.2 8.3 57 380-441 210-267 (284)
78 PRK09554 feoB ferrous iron tra 20.4 1.5E+03 0.032 26.9 14.3 58 234-291 509-592 (772)
79 cd04454 S1_Rrp4_like S1_Rrp4_l 20.3 1.8E+02 0.0038 23.5 4.3 38 299-346 5-42 (82)
No 1
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=100.00 E-value=5e-45 Score=371.65 Aligned_cols=251 Identities=18% Similarity=0.252 Sum_probs=224.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHH
Q 009063 191 LNFVRSLSTVLAFAYCLSSLIQQIQKFLTEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGL 270 (545)
Q Consensus 191 ~~~i~~l~~i~~~~~~~~~li~~~~~~~~~~~~~~~~~~r~~~i~~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi 270 (545)
++++.++ ++++++|++.++++...+...++... +.+..+++.++++++++++++++++..+|++.++++|++|+
T Consensus 29 ~~i~~al-~il~~~~~~~~~i~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~i~~~~~~~~l~~lGi~~~~l~a~~G~ 102 (286)
T PRK10334 29 VNIVAAL-AIIIVGLIIARMISNAVNRLMISRKI-----DATVADFLSALVRYGIIAFTLIAALGRVGVQTASVIAVLGA 102 (286)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhcCC-----ChHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 3444444 45577888888888776555444331 22346788999999999999999999999999999999999
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEE
Q 009063 271 GTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRN 350 (545)
Q Consensus 271 ~glalgfAaqd~l~N~~aGi~I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N 350 (545)
+|+++|||+|++++|++||++|+++|||++||||++ +|.+|+|++|++++ |++|++||+.++|||+.+.++.|+|
T Consensus 103 ~glaiG~a~q~~l~N~~sGi~i~~~rpf~vGD~I~i----~~~~G~V~~I~~r~-T~i~t~d~~~v~IPNs~~~~~~i~N 177 (286)
T PRK10334 103 AGLAVGLALQGSLSNLAAGVLLVMFRPFRAGEYVDL----GGVAGTVLSVQIFS-TTMRTADGKIIVIPNGKIIAGNIIN 177 (286)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCEEEE----CCEEEEEEEEEeEE-EEEEcCCCCEEEEcchHhcCCeeEE
Confidence 999999999999999999999999999999999999 78999999999999 9999999999999999999999999
Q ss_pred cccCCceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccceEEEEEeeCCCCCeEEEEEEEEEecCChhhHHH
Q 009063 351 LSQKTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLC 429 (545)
Q Consensus 351 ~sr~~~~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ 429 (545)
||+++.+|+.+.++++| +|+++++++ ++++++++|.+.++|. |.+.+.+++ |+++++++++|+++.+ +++
T Consensus 178 ~s~~~~rr~~~~v~V~y~~d~~~~~~i---l~~~~~~~~~vl~~p~-p~v~~~~~~--dssi~~~v~~wv~~~~---~~~ 248 (286)
T PRK10334 178 FSREPVRRNEFIIGVAYDSDIDQVKQI---LTNIIQSEDRILKDRE-MTVRLNELG--ASSINFVVRVWSNSGD---LQN 248 (286)
T ss_pred cCCCCeEEEEEEEEecCCCCHHHHHHH---HHHHHHhCCceecCCC-CEEEEEeee--CceEEEEEEEEEecch---hHH
Confidence 99988899999999999 899999998 8899999999988764 789999999 8899999999999754 678
Q ss_pred HHHHHHHHHHHHHHHCCCccCCCceEEEEecC
Q 009063 430 VKEAILLDLLHVISHHRARMATPIRTVQKIYS 461 (545)
Q Consensus 430 ir~~i~~~i~~~l~~~gI~ia~P~~~l~~~~~ 461 (545)
+++++++++++.|+++||++|||+++++....
T Consensus 249 ~~~~~~~~I~~~f~~~gI~ip~p~~~v~~~~~ 280 (286)
T PRK10334 249 VYWDVLERIKREFDAAGISFPYPQMDVNFKRV 280 (286)
T ss_pred HHHHHHHHHHHHHHHCCCcCCCCCeEEEeccC
Confidence 99999999999999999999999999998653
No 2
>PRK11465 putative mechanosensitive channel protein; Provisional
Probab=100.00 E-value=9.7e-43 Score=387.23 Aligned_cols=298 Identities=13% Similarity=0.152 Sum_probs=231.2
Q ss_pred cccCccccchhHHHHHHhhHHHHHHHHHHHHHHhhccCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Q 009063 139 RTDGSWKRSRTHYILTSYLQPLLLWTGVTLICRELDPLVLPSETSQGVKQRVLNFVRSLSTVLAFAYCLSSLIQQ-IQKF 217 (545)
Q Consensus 139 ~~~~~~~~s~~~~il~~~~~Pl~l~l~~~~i~~al~~~~l~~~~~~~i~~~l~~~i~~l~~i~~~~~~~~~li~~-~~~~ 217 (545)
++.+.|++ .+++.++ |+.+++.+++++.++..+.++..........+.+.+..++++++++++.+.+.+. +.++
T Consensus 417 ~r~~~~~~----~~l~~lr-~l~~~~~vl~ll~a~~~l~l~~~~~~~~g~~~i~~l~~i~iil~i~~v~w~l~~~~ie~~ 491 (741)
T PRK11465 417 KRLNGWLS----AALKTAR-ILTVCVAVMLLLNAWGLFDFWNWLQNGAGEKTVDILIRIALILFFSAVGWTVLASLIENR 491 (741)
T ss_pred HHHhhhhH----HHHHHHH-HHHHHHHHHHHHHHHHhcchHhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455655 4666666 9988888888888877554433111111122333333333444334444444332 2333
Q ss_pred HHhhc--cCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc
Q 009063 218 LTEAN--DADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSVMIHAT 295 (545)
Q Consensus 218 ~~~~~--~~~~~~~r~~~i~~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi~glalgfAaqd~l~N~~aGi~I~~~ 295 (545)
+.+.. +..+....++..+++++++++++++++++++|+.+|+++++++|++|++|+++|||+|++++|+++|++|+++
T Consensus 492 l~~~~~~~~~~~~r~~Tl~~ll~~~~~~~i~~i~~l~vL~~lGi~it~LlA~aGi~GlaiGfaaQ~~l~N~isGi~Il~e 571 (741)
T PRK11465 492 LASDIHGRPLPSARTRTLLTLFRNALAVIISTITIMIVLSEIGVNIAPLLAGAGALGLAISFGSQTLVKDIITGVFIQFE 571 (741)
T ss_pred HhhhhhcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 32221 1112233457789999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEcccCCceEEEEEEEecc-CCHHHHH
Q 009063 296 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-LDVHKVN 374 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~V~y-td~~~i~ 374 (545)
|||++||||++ +|++|+||+|++|+ |++|++||+.++|||+++.+ |+||||. ..+..++++|+| +|.|+++
T Consensus 572 ~pf~vGD~I~v----~g~~GtVe~I~lRs-T~iRt~dg~~i~IPNs~i~~--v~N~Sr~-~~~~~v~v~V~Y~~Didka~ 643 (741)
T PRK11465 572 NGMNTGDLVTI----GPLTGTVERMSIRS-VGVRQDTGAYHIIPWSSITT--FANFVRG-IGSVVANYDVDRHEDADKAN 643 (741)
T ss_pred CCcCCCCEEEE----CCeEEEEEEEeeeE-EEEEcCCCCEEEEECCccee--eEEeccC-ceEEEEEEEeCCCCCHHHHH
Confidence 99999999999 78999999999999 99999999999999999974 9999986 557888999999 8999999
Q ss_pred HHHHHHHHHHHcCCCc----cccccceEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCccC
Q 009063 375 SIVADMRKVLAKNPQV----EQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARMA 450 (545)
Q Consensus 375 ~i~~~l~e~l~~~p~i----~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~ia 450 (545)
++++++.+.+.++|++ .+++ +.+.+.+++ |+++++++++|+++ .++|++++++++++++.|+++||++|
T Consensus 644 ~iL~ev~~el~~dpe~~~~il~~p--~~vgV~~lg--dSsi~lrvr~~t~p---~~qw~v~rel~~~IK~~Fde~GIeIP 716 (741)
T PRK11465 644 QALKDAVAELMENEEIRGLIIGEP--NFAGIVGLT--NTAFTLRVSFTTLP---LKQWTVRFALDSQVKKHFDLAGVRAP 716 (741)
T ss_pred HHHHHHHHHhhcCccccccccCCC--CeEEEEEec--CceEEEEEEEEECc---chHHHHHHHHHHHHHHHHHHCCCCCC
Confidence 9987777777777764 2333 357889998 88999999999976 46799999999999999999999987
Q ss_pred CCceEE
Q 009063 451 TPIRTV 456 (545)
Q Consensus 451 ~P~~~l 456 (545)
+|+..+
T Consensus 717 ~~tv~v 722 (741)
T PRK11465 717 VQTYQV 722 (741)
T ss_pred CCceEe
Confidence 665543
No 3
>PRK11281 hypothetical protein; Provisional
Probab=100.00 E-value=6.4e-40 Score=380.14 Aligned_cols=253 Identities=19% Similarity=0.206 Sum_probs=223.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHH
Q 009063 190 VLNFVRSLSTVLAFAYCLSSLIQQIQKFL-TEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAG 268 (545)
Q Consensus 190 l~~~i~~l~~i~~~~~~~~~li~~~~~~~-~~~~~~~~~~~r~~~i~~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~ 268 (545)
+.+++.++ ++++++|++.+.+..+.+.+ .++...++ .....+.++++++++++++++++..+|++.+++.+.+
T Consensus 836 l~~Ll~al-lIl~i~~~l~r~l~~ll~~~~~~rl~l~~-----~~~~~i~~li~y~I~~i~iliaL~~lGi~~t~L~~l~ 909 (1113)
T PRK11281 836 LGNLLFAL-IILVVTYVLVRNLPGLLEVLVLSRLNLRQ-----GTSYAITTLLTYIIIAVGAVTAFSTLGVSWDKLQWLV 909 (1113)
T ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhccCCc-----hHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHH
Confidence 34444444 45577888888887765433 33322112 1246678999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeE
Q 009063 269 GLGTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVV 348 (545)
Q Consensus 269 Gi~glalgfAaqd~l~N~~aGi~I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I 348 (545)
|++|+++|||+|++++||+||++|+++|||++||+|++ ++.+|+|++|++|+ |+++|+||+.++|||+.+.++.|
T Consensus 910 gaLgVgIGfglQ~ilsNfISGiiIl~eRPfrIGD~I~I----~~~~G~V~~I~lRs-T~Irt~D~~~ViIPNs~~~t~~I 984 (1113)
T PRK11281 910 AALSVGLGFGLQEIFANFVSGLIILFERPVRIGDTVTI----GTFSGTVSKIRIRA-TTITDFDRKEVIVPNKAFVTERL 984 (1113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCcCCCCEEEE----CCEEEEEEEEEeEE-EEEEcCCCCEEEEechhhhcCce
Confidence 99999999999999999999999999999999999999 78999999999999 99999999999999999999999
Q ss_pred EEcccCC-ceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccceEEEEEeeCCCCCeEEEEEEEEEecCChhh
Q 009063 349 RNLSQKT-HWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEE 426 (545)
Q Consensus 349 ~N~sr~~-~~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~ 426 (545)
+|||.++ .+|+.++++|+| +|+++++++ +.++++++|.+.++|. |.|++.+|+ ++++++++++|+++. .+
T Consensus 985 iN~S~~~~~~Rv~i~vgV~Y~sDi~~v~~i---L~eaa~~~p~Vl~~P~-P~V~~~~fg--dssi~~~lr~wv~~~--~~ 1056 (1113)
T PRK11281 985 INWSLSDTVTRVVIKVGVAYGSDLEKVREL---LLQAATENPRVMKEPE-PQVFFLNFG--ASTLDHELRLYVREL--GD 1056 (1113)
T ss_pred EeCCCCCcceEEEEEEEeCCCCCHHHHHHH---HHHHHHcCcccccCCC-CEEEEEecc--CceEEEEEEEEEcCH--hh
Confidence 9999987 478999999999 899999999 8999999999998875 799999999 899999999999864 57
Q ss_pred HHHHHHHHHHHHHHHHHHCCCccCCCceEEEEecC
Q 009063 427 YLCVKEAILLDLLHVISHHRARMATPIRTVQKIYS 461 (545)
Q Consensus 427 ~~~ir~~i~~~i~~~l~~~gI~ia~P~~~l~~~~~ 461 (545)
++.++++++.+|++.|+++||++|||++++++...
T Consensus 1057 ~~~v~s~L~~~I~~~f~e~GIeIpfPq~~V~i~~~ 1091 (1113)
T PRK11281 1057 RSPTVDELNRRIDRLFRENDINIAFNQLDVFLKNQ 1091 (1113)
T ss_pred HHHHHHHHHHHHHHHHHHCCCcCCCCCeeEEecCC
Confidence 89999999999999999999999999999998764
No 4
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=100.00 E-value=1.5e-39 Score=375.77 Aligned_cols=251 Identities=16% Similarity=0.149 Sum_probs=221.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHH
Q 009063 192 NFVRSLSTVLAFAYCLSSLIQQIQK-FLTEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGL 270 (545)
Q Consensus 192 ~~i~~l~~i~~~~~~~~~li~~~~~-~~~~~~~~~~~~~r~~~i~~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi 270 (545)
+++.++ ++++++|++.+.+..+.+ .+.++.+.++ ....++.+++++++++++++++++.+|++.+++.+.+|+
T Consensus 835 ~ll~Al-lIliv~~~l~r~l~~lle~~l~~~~~l~~-----~~~~~i~~l~~y~I~~ig~l~~L~~lGI~~t~l~al~ga 908 (1109)
T PRK10929 835 SVLIAI-LVFIITTQLVRNLPALLELALLQHLDLTP-----GTGYAITTITKYLLMLIGGLVGFSMIGIEWSKLQWLVAA 908 (1109)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHHhhhcCCCh-----hHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHH
Confidence 344444 455677777777776544 4434433222 235778899999999999999999999999999999999
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEE
Q 009063 271 GTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRN 350 (545)
Q Consensus 271 ~glalgfAaqd~l~N~~aGi~I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N 350 (545)
+|+++|||+|++++||+||++|+++|||++||+|++ +|.+|+|++|++|+ |+++|+||+.++|||+.+.++.|+|
T Consensus 909 lGVgIGfAlQ~ilsNfiSGIiIL~erPfrVGD~I~I----~~~~GtV~~I~lRs-T~Irt~Dg~~IiIPNs~~it~~IiN 983 (1109)
T PRK10929 909 LGVGLGFGLQEIFANFISGLIILFEKPIRIGDTVTI----RDLTGSVTKINTRA-TTISDWDRKEIIVPNKAFITEQFIN 983 (1109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCEEEE----CCEEEEEEEEeeeE-EEEEeCCCCEEEEEChhhhcCceEe
Confidence 999999999999999999999999999999999999 78999999999999 9999999999999999999999999
Q ss_pred cccCCc-eEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccceEEEEEeeCCCCCeEEEEEEEEEecCChhhHH
Q 009063 351 LSQKTH-WRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYL 428 (545)
Q Consensus 351 ~sr~~~-~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~ 428 (545)
||+++. +|+.+.++|+| +|+++++++ +.++++++|.+.++|. |.|++.+++ ++++++++++|++.. .+++
T Consensus 984 ~S~~d~~~Rv~i~VgV~Y~sDie~v~~i---L~eaa~~~~~VL~~P~-P~V~~~~fg--dssi~~elr~wv~~~--~~~~ 1055 (1109)
T PRK10929 984 WSLSDSVTRVVLTIPAPADANSEEVTEI---LLTAARRCSLVLDNPA-PEVFLVDLQ--QGIQIFELRIYAAEM--GHRM 1055 (1109)
T ss_pred cCCCCcceEEEEEEEeCCCCCHHHHHHH---HHHHHHhCccccCCCC-CEEEEEecC--CCceEEEEEEEEcCh--hhHH
Confidence 999875 79999999999 899999999 8899999999988775 799999998 789999999999743 5789
Q ss_pred HHHHHHHHHHHHHHHHCCCccCCCceEEEEecC
Q 009063 429 CVKEAILLDLLHVISHHRARMATPIRTVQKIYS 461 (545)
Q Consensus 429 ~ir~~i~~~i~~~l~~~gI~ia~P~~~l~~~~~ 461 (545)
.++++++.+|++.|+++||++|||++++|+...
T Consensus 1056 ~v~~el~~~I~~~F~~~GIeIPfPq~~v~i~~~ 1088 (1109)
T PRK10929 1056 PLRHEIHQLILAGFREHGIDMPFPPFQMRLESL 1088 (1109)
T ss_pred HHHHHHHHHHHHHHHHCCCcCCCCCeEEEeecC
Confidence 999999999999999999999999999999863
No 5
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=100.00 E-value=3.3e-36 Score=332.34 Aligned_cols=244 Identities=20% Similarity=0.221 Sum_probs=221.5
Q ss_pred HHHHHHHHHHHHHHHHH-HHHHhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHH
Q 009063 199 TVLAFAYCLSSLIQQIQ-KFLTEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTL 277 (545)
Q Consensus 199 ~i~~~~~~~~~li~~~~-~~~~~~~~~~~~~~r~~~i~~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi~glalgf 277 (545)
+++++++++.+.+.... ..+..+.+.+.+. -..+.+++.+.+..++.++.++.+|+|.+++--.+|+.|+++||
T Consensus 566 l~~~~~~~l~r~~~~~L~~~vl~r~~~~~G~-----r~~I~t~~~Y~~~~i~~l~~lS~~Gi~lssL~~~~gALsvGiGF 640 (835)
T COG3264 566 LLFLITYVLTRNLPGWLEVRVLQRLDLDAGT-----RYSITTLLGYLLIAIGGLVGLSTLGIDLSSLQWLAGALSVGLGF 640 (835)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCcch-----HHHHHHHHHHHHHHHHHHHHHHHcCcChHHHHHHHHHhhhhhch
Confidence 44566677777776654 4667766644433 25588999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEcccCC-c
Q 009063 278 AGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKT-H 356 (545)
Q Consensus 278 Aaqd~l~N~~aGi~I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr~~-~ 356 (545)
+.|++++||+||++|+++|||||||||++ |+.+|+|.+|+.|+ |.|+|+|++-++|||+.|.++.|.|||.++ .
T Consensus 641 GLQ~I~~NFVSGlIiL~ErpvkvGD~It~----g~~~G~V~~I~vRA-T~I~~fd~~~vIVPNs~fI~~qV~NWs~~~~~ 715 (835)
T COG3264 641 GLQEIVSNFVSGLIILFERPVKVGDTVTI----GTVSGTVRKISVRA-TTIRTFDRKEVIVPNSAFITEQVINWSLRDTT 715 (835)
T ss_pred hHHHHHHHhhhhhhhheecCcccCCEEEE----CCceEEEEEEEeeE-EEEEeCCCCeEEeccHHHHhhheeeeeccCce
Confidence 99999999999999999999999999999 78999999999999 999999999999999999999999999987 7
Q ss_pred eEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccceEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHH
Q 009063 357 WRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAIL 435 (545)
Q Consensus 357 ~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~ 435 (545)
.|+.+.++++| +|+++++++ +-+..++||.+.++|. |.|++.+|+ ++++++++++|+..... ...++++++
T Consensus 716 ~R~~i~v~vay~sD~~~V~~~---Ll~~A~~~p~Vl~~P~-P~v~f~~fg--~s~L~fELr~~v~~~~~--~~~~~~~l~ 787 (835)
T COG3264 716 TRLVIPVGVAYGSDPELVREL---LLEAAREHPRVLKDPA-PEVFFTAFG--ASSLDFELRVYVAELGD--RMPVRSELN 787 (835)
T ss_pred EEEEEEecccCCCCHHHHHHH---HHHHHHhCCCccCCCC-CeeEeeccc--ccceeEEEEEEeecccc--ccchHHHHH
Confidence 89999999999 899999999 9999999999999886 799999999 88999999999998753 344999999
Q ss_pred HHHHHHHHHCCCccCCCceEEEEec
Q 009063 436 LDLLHVISHHRARMATPIRTVQKIY 460 (545)
Q Consensus 436 ~~i~~~l~~~gI~ia~P~~~l~~~~ 460 (545)
..|.+.|+||||++|||++++++.+
T Consensus 788 ~~I~~~fre~gI~ipfpq~~v~l~~ 812 (835)
T COG3264 788 RAILDRFRENGIEIPFPQREVRLKN 812 (835)
T ss_pred HHHHHHHHHcCCCCCCchHheEecC
Confidence 9999999999999999999999987
No 6
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=100.00 E-value=9.9e-37 Score=296.34 Aligned_cols=203 Identities=24% Similarity=0.419 Sum_probs=170.1
Q ss_pred HHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCccCCcEEEEeecCCCeEEEEE
Q 009063 239 KAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVE 318 (545)
Q Consensus 239 ~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi~glalgfAaqd~l~N~~aGi~I~~~rpf~VGD~I~i~i~g~~~~G~Ve 318 (545)
+++.+++++++++.++..+|.+.+++++++|++|+++|||+|++++|++||++|++++||++||||++ ++..|+|+
T Consensus 2 ~i~~~~~~~~~~~~~l~~~g~~~~~l~~~~g~~~~~i~f~~~~~~~n~~~gi~i~~~~pf~vGD~I~i----~~~~G~V~ 77 (206)
T PF00924_consen 2 KIIRIVIIIVGILIILSILGIDVSSLLASLGVLGLAIGFAFQDIISNFISGIIILFERPFKVGDRIEI----GGVEGRVE 77 (206)
T ss_dssp -HHHHHHHHHHHHHHHHCCT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCC-SS-TT-EEES----SS-EEEEE
T ss_pred hHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccCCCEEEE----EEeehHHH
Confidence 57888999999999999999999999999999999999999999999999999999999999999998 78999999
Q ss_pred EEcceeEEEEEeCCCcEEEEeCcccccCeEEEccc-CCceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccc
Q 009063 319 HVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQ-KTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLH 396 (545)
Q Consensus 319 eIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr-~~~~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~i~~~~~~ 396 (545)
+|+|++ |++|++||+.++|||+.+.+++|.|+|+ ++.++..+.+.++| +|.++++++.+++.+.++++|.+...+ .
T Consensus 78 ~I~l~~-t~l~~~~g~~v~IPNs~l~~~~i~N~s~~~~~~~~~v~~~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~-~ 155 (206)
T PF00924_consen 78 EIGLRS-TRLRTWDGEIVIIPNSKLISSPIVNYSRSSPYRRVVVEIPVDYDTDPEKIEELREKIEEALRSNPYIFKEP-E 155 (206)
T ss_dssp EE-SSE-EEEEETTS-EEEEEHHHHHCS-EEETTT-SSEEEEEEEEEE-TTS----HHHHHHHHHHHHHH-TTC-TTS--
T ss_pred hcCcce-eeeecCCCCEEEEEchheeeEEEEEeeccCCceeeeeeeeEecCCCchHHHHHHHHHHHHHhcCchhhcCC-C
Confidence 999999 9999999999999999999999999999 77899999999999 788999999999999999999888755 3
Q ss_pred eEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCcc
Q 009063 397 RRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARM 449 (545)
Q Consensus 397 p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~i 449 (545)
|.+.+..++ ++++.++++||++..++.+++++|++++.++++.+++|||+|
T Consensus 156 ~~~~~~~~~--~~~~~~~i~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~gI~~ 206 (206)
T PF00924_consen 156 PRVVVDEIG--DSSLEFRIRVYVKNQDPEKYWEIRSEIRKRILEILEEHGIEI 206 (206)
T ss_dssp EEEEEEEE---SSSEEEEEEEEEEC---CCHHHHHHHHHHHHHHHHHHHT---
T ss_pred CeEEEcccc--CCceEEEEEEEEEeCchhhHHHHHHHHHHHHHHHHHHccCCC
Confidence 688899988 789999999999997788999999999999999999999985
No 7
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=100.00 E-value=4.1e-34 Score=294.32 Aligned_cols=208 Identities=23% Similarity=0.392 Sum_probs=193.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCccCCcEEEEeecCC-CeE
Q 009063 236 FAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGY-EVS 314 (545)
Q Consensus 236 ~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi~glalgfAaqd~l~N~~aGi~I~~~rpf~VGD~I~i~i~g~-~~~ 314 (545)
++.++.++++++++++.++..+|++.+++++++|++|+++|||+|++++|+++|+++++++||++||||++ + +.+
T Consensus 86 ~~~~~~~~~~~~~~~~~~l~~~g~~~~~lla~~G~~glaigla~q~~~~n~~~Gi~il~~~~f~vGD~I~i----~~~~~ 161 (316)
T COG0668 86 FLSNLLRILILVVALLIVLSVLGVQVTSLLAGLGALGLAIGLALQDLLSNLIAGIFLLLERPFKVGDWIEI----GSGVE 161 (316)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhHhheecCcCcCCEEEE----CCCce
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999 7 699
Q ss_pred EEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEcccCCceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccc-
Q 009063 315 GTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQ- 392 (545)
Q Consensus 315 G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~i~~- 392 (545)
|+|++|++++ |++|++||+.+++|||.+.++.|+|+|++..+++.++++++| +|.++++++ +++.+++.+....
T Consensus 162 G~V~~i~~~~-T~ir~~dg~~v~iPNs~i~~~~i~N~s~~~~~~~~~~v~v~~~~~~~~~~~i---~~~~~~~~~~~~~~ 237 (316)
T COG0668 162 GTVEDIGLRS-TTIRTLDGRIVTIPNSKLFTANVVNYSREPGRRVEVKVGVAYDSDLEKALKI---LKEVLEELPEVLKI 237 (316)
T ss_pred EEEEEEEEEE-EEEEcCCCCEEEccchhhccCceEeCCCCCcEEEEEEEeeccCCCHHHHHHH---HHHHHHhccccccc
Confidence 9999999999 999999999999999999999999999998889999999999 899999999 5666666555542
Q ss_pred cccceEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCccCCCceEEE
Q 009063 393 QRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARMATPIRTVQ 457 (545)
Q Consensus 393 ~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~ia~P~~~l~ 457 (545)
++ +|.+.+.+++ ++++++++++|+++.+ ++..+++++..+++.++++||++|+|++.+.
T Consensus 238 ~~-~~~v~~~~~~--~~~~~i~v~~~t~~~~---~~~~~~~~~~~i~~~~~~~gi~i~~p~~~~~ 296 (316)
T COG0668 238 EP-EPVIGVSELG--DSGINIRVRFWTNPED---LWSVQRELNLRIKEALEEAGIEIPYPQQSVL 296 (316)
T ss_pred CC-CcEEEEeecc--CCceEEEEEEEecchh---HHHHHHHHHHHHHHHHHHcCCCCCCCCeeEE
Confidence 44 3689999998 8899999999999854 8999999999999999999999999999998
No 8
>KOG4629 consensus Predicted mechanosensitive ion channel [Cell wall/membrane/envelope biogenesis]
Probab=99.82 E-value=5.2e-20 Score=204.32 Aligned_cols=222 Identities=16% Similarity=0.190 Sum_probs=192.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhhhHHHHHHHHHH-HHHhcCCccCCcEEEEeecC
Q 009063 232 MGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSV-MIHATQPFVINEWIQTKIQG 310 (545)
Q Consensus 232 ~~i~~l~~i~~~vv~vi~~i~~L~~lGv~~~~lla~~Gi~glalgfAaqd~l~N~~aGi-~I~~~rpf~VGD~I~i~i~g 310 (545)
+.++-+.+++.+++.++++++.+-.+|++.+.+++..+..-+++.|.+.+++++++.++ +++..+||+|||+|.+
T Consensus 478 taV~kL~~il~~Iv~vv~~~i~lil~~i~~~~~l~~~~sq~v~l~fif~~~~k~~~esiIFlfv~HPyDvGDRv~V---- 553 (714)
T KOG4629|consen 478 TAVNKLDRILNFIVAVVLLVIWLILLGINTSKLLLVISSQLVGLAFIFGNIVKELLESIIFLFVMHPYDVGDRVVV---- 553 (714)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcccceeeeeeecccceeeeeehhhHHHHHHHHHhheeecCCCCCCCeEEE----
Confidence 55888889999999999999999999999999999888888999999999999999985 5667799999999998
Q ss_pred CCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEcccCCceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCC
Q 009063 311 YEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQ 389 (545)
Q Consensus 311 ~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~V~y-td~~~i~~i~~~l~e~l~~~p~ 389 (545)
+|+.-.|||+++.+ |....+||+.+++||+.+.+++|.|+.|++.+...+++.++. |+.+|++.+.+.+.++++++|+
T Consensus 554 Dg~~~vVeemnLls-TvF~~~dg~kI~~PNS~L~~k~I~N~rRS~~~~~~v~f~i~~~T~~~Ki~~Lk~rI~~ylks~~~ 632 (714)
T KOG4629|consen 554 DGVNLVVEEMNLLS-TVFLRVDGRKIFIPNSVLWTKAISNYRRSPDMGDEVEFLISSSTPFEKIERLKERIAEYLKSSPD 632 (714)
T ss_pred eceEEEEEEeccce-EEEEEECCeEEEeecHHHHhhhhhhhhcCccccccEEEEecCCCCHHHHHHHHHHHHHHHhcCcc
Confidence 66999999999999 999999999999999999999999999999999999999999 8999999999999999999998
Q ss_pred ccccccceEEEEEeeCCC-CCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCccCCCceEEEEec
Q 009063 390 VEQQRLHRRVFLENINPE-SQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARMATPIRTVQKIY 460 (545)
Q Consensus 390 i~~~~~~p~v~v~~~~~~-~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~ia~P~~~l~~~~ 460 (545)
..... +.+.+.++.+. +-.+.+.+..+.+.+|..+++..|.++...+.+.+++.||+.-++++++...+
T Consensus 633 ~~~p~--~~~~i~~~e~~n~v~i~v~~~h~~n~Qd~~~~~~Rr~~~~~~l~~~~~eLdI~y~l~p~~in~~~ 702 (714)
T KOG4629|consen 633 DYYPD--LMVVIEEIEDLNSVKICVVVQHKINFQDMKERWSRRTEFVSALTKIMRELDIEYTLYPLDINLKN 702 (714)
T ss_pred ccccc--hhhHHHhhhhcCcceEEEEEEeecchhhHHHHHhhHHHHHHHHHHHHHHcCcceeecCcchhhhc
Confidence 77322 35667666532 23445556666667788899999999999999999999999877776665544
No 9
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=77.60 E-value=10 Score=33.45 Aligned_cols=37 Identities=5% Similarity=-0.093 Sum_probs=29.1
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEE
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHI 338 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~I 338 (545)
.++||.|.. .+|..|+|.+|+=-+ ..++..+|..+.+
T Consensus 39 Lk~GD~VvT---~gGi~G~V~~I~d~~-v~leia~gv~i~~ 75 (109)
T PRK05886 39 LQPGDRVHT---TSGLQATIVGITDDT-VDLEIAPGVVTTW 75 (109)
T ss_pred cCCCCEEEE---CCCeEEEEEEEeCCE-EEEEECCCeEEEE
Confidence 799999997 267999999998655 7777766655554
No 10
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=75.73 E-value=7.5 Score=34.12 Aligned_cols=41 Identities=20% Similarity=0.169 Sum_probs=32.2
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcc
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHK 342 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~ 342 (545)
.++||+|... +|..|+|.+|+=-+ ..++..+|..+.+=-+.
T Consensus 53 Lk~Gd~VvT~---gGi~G~Vv~i~~~~-v~lei~~g~~i~~~r~a 93 (106)
T PRK05585 53 LAKGDEVVTN---GGIIGKVTKVSEDF-VIIELNDDTEIKIQKSA 93 (106)
T ss_pred cCCCCEEEEC---CCeEEEEEEEeCCE-EEEEECCCeEEEEEhHH
Confidence 7999999872 67999999998765 88888888666654333
No 11
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=75.57 E-value=8.6 Score=32.30 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=29.8
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEE
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHI 338 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~I 338 (545)
.++||+|... +|..|+|.+|+=-+ ..++..+|..+.+
T Consensus 38 L~~Gd~VvT~---gGi~G~V~~i~d~~-v~vei~~g~~i~~ 74 (84)
T TIGR00739 38 LKKGDKVLTI---GGIIGTVTKIAENT-IVIELNDNTEITF 74 (84)
T ss_pred CCCCCEEEEC---CCeEEEEEEEeCCE-EEEEECCCeEEEE
Confidence 8999999972 67999999998766 7788777765554
No 12
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=66.66 E-value=9.7 Score=29.61 Aligned_cols=28 Identities=29% Similarity=0.230 Sum_probs=22.4
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEE
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR 329 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~ir 329 (545)
-++||+|+++ ++.+|+|+.+.=.| +.+.
T Consensus 4 a~vGdiIefk---~g~~G~V~kv~eNS-VIVd 31 (57)
T PF09953_consen 4 AKVGDIIEFK---DGFTGIVEKVYENS-VIVD 31 (57)
T ss_pred cccCcEEEEc---CCcEEEEEEEecCc-EEEE
Confidence 4799999984 46999999998766 6554
No 13
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=66.30 E-value=26 Score=30.33 Aligned_cols=42 Identities=19% Similarity=0.118 Sum_probs=32.1
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCccc
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKF 343 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l 343 (545)
.+.||.|.. .||..|+|.+|+=.+ ..+...|+..+.+--+.+
T Consensus 44 L~kGD~VvT---~gGi~G~V~~v~d~~-v~I~l~~~~~i~~~k~aI 85 (97)
T COG1862 44 LKKGDEVVT---IGGIVGTVTKVGDDT-VEIELGDGTKIKFEKEAI 85 (97)
T ss_pred ccCCCEEEE---cCCeEEEEEEEecCc-EEEEECCCeEEEEEHHHH
Confidence 789999987 257999999999876 777776777766644443
No 14
>PRK10263 DNA translocase FtsK; Provisional
Probab=66.28 E-value=1.5e+02 Score=36.95 Aligned_cols=8 Identities=38% Similarity=0.991 Sum_probs=4.8
Q ss_pred hhhHHHhh
Q 009063 531 LDWYQLLT 538 (545)
Q Consensus 531 ~~~~~~~~ 538 (545)
-+|||-..
T Consensus 524 ~~~~~~~~ 531 (1355)
T PRK10263 524 AAWYQPIP 531 (1355)
T ss_pred cccccCCC
Confidence 36777544
No 15
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=64.90 E-value=12 Score=23.87 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=17.0
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEc
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVG 321 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIg 321 (545)
+|++||.|++ ++| .+..|.|.++.
T Consensus 1 ~~~~G~~V~I-~~G~~~g~~g~i~~i~ 26 (28)
T smart00739 1 KFEVGDTVRV-IAGPFKGKVGKVLEVD 26 (28)
T ss_pred CCCCCCEEEE-eECCCCCcEEEEEEEc
Confidence 5789999998 443 24567777764
No 16
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.84 E-value=14 Score=29.52 Aligned_cols=27 Identities=30% Similarity=0.303 Sum_probs=22.0
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEE
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTII 328 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~i 328 (545)
-.|||.|+++ +|..|.||+++=-| +.+
T Consensus 24 a~vgniief~---dgl~g~vek~nens-viv 50 (81)
T COG4873 24 AKVGNIIEFK---DGLTGVVEKVNENS-VIV 50 (81)
T ss_pred eeccceEEEc---ccceeeeeeecCCc-EEE
Confidence 5799999984 56999999998877 544
No 17
>PF12794 MscS_TM: Mechanosensitive ion channel inner membrane domain 1
Probab=54.47 E-value=2.9e+02 Score=29.22 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHH-HHHHHHhCCchHH
Q 009063 234 FNFAGKAVYTAVWVAAV-SLFMELLGFSTQR 263 (545)
Q Consensus 234 i~~l~~i~~~vv~vi~~-i~~L~~lGv~~~~ 263 (545)
.+.++++...++.++-+ ++++..+|+--++
T Consensus 193 ~~~~~~l~~~~li~~Pl~li~la~~GY~yTA 223 (340)
T PF12794_consen 193 IHRLRYLWWPLLILAPLALIVLALLGYYYTA 223 (340)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 34556665555544433 3445566775443
No 18
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=53.09 E-value=31 Score=28.17 Aligned_cols=31 Identities=10% Similarity=0.077 Sum_probs=22.2
Q ss_pred hcCCccCCcEEEEe-ecCCCeEEEEEEEccee
Q 009063 294 ATQPFVINEWIQTK-IQGYEVSGTVEHVGWWS 324 (545)
Q Consensus 294 ~~rpf~VGD~I~i~-i~g~~~~G~VeeIgl~s 324 (545)
-+|.|+|||.+... .++++.+|+....-.++
T Consensus 25 NDRdf~VGD~L~L~E~~~~~YTGr~~~~~Ity 56 (72)
T PF12961_consen 25 NDRDFQVGDILVLREWDNGEYTGREIEAEITY 56 (72)
T ss_pred cCCCCCCCCEEEEEEecCCCccccEEEEEEEE
Confidence 36899999999875 44456677776666655
No 19
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=51.67 E-value=39 Score=30.10 Aligned_cols=41 Identities=15% Similarity=0.015 Sum_probs=27.9
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcce-eEEEEEeCCCcEEEEeCcc
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWW-SPTIIRGDDREAVHIPNHK 342 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~-sTT~irt~d~~~v~IPNs~ 342 (545)
.++||.|.. .||..|+|.+|+-- -+..++. +|..+.+=-+.
T Consensus 37 Lk~GD~VvT---~GGi~G~V~~I~~~~~~v~le~-~gv~i~v~r~A 78 (113)
T PRK06531 37 IQKGDEVVT---IGGLYGTVDEVDTEAKTIVLDV-DGVYLTFELAA 78 (113)
T ss_pred cCCCCEEEE---CCCcEEEEEEEecCCCEEEEEE-CCEEEEEEhhH
Confidence 789999997 26799999999752 1255665 66555544333
No 20
>PF14545 DBB: Dof, BCAP, and BANK (DBB) motif,
Probab=50.50 E-value=34 Score=31.66 Aligned_cols=81 Identities=9% Similarity=0.029 Sum_probs=48.3
Q ss_pred HHHHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEcccCCceEEEEEEEecc-C
Q 009063 290 VMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-L 368 (545)
Q Consensus 290 i~I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~V~y-t 368 (545)
++|++..|+.-||++++.+..++..-......|+. .---.+.+|+--+.-.-..|.+-.....+.-.-.+.| |
T Consensus 15 vfIiL~~~l~~~~~~eVef~~~n~~~~~~~~~~~N------~yt~~~~aPd~~~~pag~V~v~v~~~g~~~~~~~ikyys 88 (142)
T PF14545_consen 15 VFIILRDPLDEEDTVEVEFESNNKPIRRVPAKWEN------PYTLQFKAPDFCLEPAGSVNVRVYCDGVSLGTRQIKYYS 88 (142)
T ss_pred EEEEEeCCCCCCCeEEEEEEeCCCeeEeccceEEC------CEEEEEECchhcCCCCceEEEEEEECCEEEEEEeEEEEe
Confidence 45778889999999999766544332233334432 1112255666644445555554443344445566777 8
Q ss_pred CHHHHHHH
Q 009063 369 DVHKVNSI 376 (545)
Q Consensus 369 d~~~i~~i 376 (545)
+.++++++
T Consensus 89 ~~~el~~l 96 (142)
T PF14545_consen 89 RMRELEQL 96 (142)
T ss_pred cHHHHHHH
Confidence 98888887
No 21
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=50.00 E-value=9.1 Score=29.37 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=11.3
Q ss_pred cCCccCCcEEEEeecCCCeEEEEEEEcc
Q 009063 295 TQPFVINEWIQTKIQGYEVSGTVEHVGW 322 (545)
Q Consensus 295 ~rpf~VGD~I~i~i~g~~~~G~VeeIgl 322 (545)
..||+.||+|++ -+..|+---|.|
T Consensus 3 ~Gpf~~GdrVQl----TD~Kgr~~Ti~L 26 (54)
T PF14801_consen 3 RGPFRAGDRVQL----TDPKGRKHTITL 26 (54)
T ss_dssp --S--TT-EEEE----EETT--EEEEE-
T ss_pred cCCCCCCCEEEE----ccCCCCeeeEEE
Confidence 359999999998 456676544443
No 22
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=48.64 E-value=28 Score=23.43 Aligned_cols=22 Identities=14% Similarity=0.329 Sum_probs=17.1
Q ss_pred CCcEEEEeecC--CCeEEEEEEEcc
Q 009063 300 INEWIQTKIQG--YEVSGTVEHVGW 322 (545)
Q Consensus 300 VGD~I~i~i~g--~~~~G~VeeIgl 322 (545)
+||+|.+ +.| .|..|.|.+|.-
T Consensus 1 ~Gd~V~V-~~G~~~G~~G~I~~i~~ 24 (32)
T PF00467_consen 1 VGDTVKV-ISGPFKGKIGKIVEIDR 24 (32)
T ss_dssp TTSEEEE-SSSTTTTEEEEEEEEET
T ss_pred CCCEEEE-eEcCCCCceEEEEEEEC
Confidence 6999998 554 368899998865
No 23
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=44.41 E-value=7.4 Score=32.44 Aligned_cols=39 Identities=10% Similarity=0.039 Sum_probs=0.4
Q ss_pred CCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEE
Q 009063 296 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHI 338 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~I 338 (545)
+..++||+|... +|..|+|.+++=-+ ..++..+|..+.+
T Consensus 35 ~~Lk~Gd~VvT~---gGi~G~V~~i~~~~-v~lei~~g~~i~v 73 (82)
T PF02699_consen 35 ASLKPGDEVVTI---GGIYGTVVEIDDDT-VVLEIAPGVEITV 73 (82)
T ss_dssp G------------------------------------------
T ss_pred HcCCCCCEEEEC---CcEEEEEEEEeCCE-EEEEECCCeEEEE
Confidence 348999999972 57999999998776 8888888765554
No 24
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=42.57 E-value=77 Score=29.47 Aligned_cols=47 Identities=11% Similarity=0.058 Sum_probs=30.2
Q ss_pred CCccCCcEEEEeecC--CCeEEEEEEEccee-EEEEEeCC-CcE--EEEeCccc
Q 009063 296 QPFVINEWIQTKIQG--YEVSGTVEHVGWWS-PTIIRGDD-REA--VHIPNHKF 343 (545)
Q Consensus 296 rpf~VGD~I~i~i~g--~~~~G~VeeIgl~s-TT~irt~d-~~~--v~IPNs~l 343 (545)
.+|++||+|++ .+| .|..|.|++++-.. ...+...+ ... +++|++.+
T Consensus 93 ~~~~~G~~V~I-~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~ 145 (153)
T PRK08559 93 EGIKEGDIVEL-IAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQV 145 (153)
T ss_pred cCCCCCCEEEE-eccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEE
Confidence 46999999999 454 36789999985322 13333322 333 77887776
No 25
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=42.20 E-value=3.1e+02 Score=28.87 Aligned_cols=35 Identities=14% Similarity=0.102 Sum_probs=25.4
Q ss_pred hhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009063 100 DTLRGNPVILRLIPAAALVAFAAWGLVPLVRLGRT 134 (545)
Q Consensus 100 ~~~~~~~~~~~~l~al~i~~~~~~~~~~l~~~~~~ 134 (545)
..+.+|+.+..++.|+..++...|+...+..|.++
T Consensus 34 ~~~~~n~~v~~ligai~~~li~~~~~~~~~~~~~~ 68 (356)
T COG4956 34 TAFLNNEYVDALIGAIIFFLISFWFGKYVLNWLKR 68 (356)
T ss_pred chhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677888777777777777777777777776653
No 26
>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=41.75 E-value=1.3e+02 Score=23.44 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=31.9
Q ss_pred EEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccc
Q 009063 314 SGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQ 353 (545)
Q Consensus 314 ~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr 353 (545)
.|+|.++.=.. ..++-.++..-.+|.+.+......+.+.
T Consensus 9 ~g~V~~v~~~g-~~V~l~~~~~g~ip~~~l~~~~~~~~~~ 47 (74)
T PF00575_consen 9 EGKVTSVEDFG-VFVDLGNGIEGFIPISELSDDRIDDPSE 47 (74)
T ss_dssp EEEEEEEETTE-EEEEESTSSEEEEEGGGSSSSEESSSHG
T ss_pred EEEEEEEECCE-EEEEECCcEEEEEEeehhcCcccccccc
Confidence 48999999877 8888888999999999999875555444
No 27
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=39.04 E-value=4.5e+02 Score=27.05 Aligned_cols=25 Identities=8% Similarity=0.008 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 009063 110 RLIPAAALVAFAAWGLVPLVRLGRT 134 (545)
Q Consensus 110 ~~l~al~i~~~~~~~~~~l~~~~~~ 134 (545)
+++.+++++++++++.+.+.+++.+
T Consensus 30 ~i~~al~il~~~~~~~~~i~~~~~~ 54 (286)
T PRK10334 30 NIVAALAIIIVGLIIARMISNAVNR 54 (286)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666655555555444444
No 28
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=38.89 E-value=31 Score=26.44 Aligned_cols=23 Identities=35% Similarity=0.271 Sum_probs=18.0
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcc
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGW 322 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl 322 (545)
|++||.|+.| . ||..-+|++++=
T Consensus 1 f~~GDvV~LK-S-GGp~MTV~~v~~ 23 (53)
T PF09926_consen 1 FKIGDVVQLK-S-GGPRMTVTEVGP 23 (53)
T ss_pred CCCCCEEEEc-c-CCCCeEEEEccc
Confidence 7899999984 3 468889988753
No 29
>PF13726 Na_H_antiport_2: Na+-H+ antiporter family
Probab=38.21 E-value=60 Score=27.58 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhCCch-HHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 009063 246 WVAAVSLFMELLGFST-QRWLTAGGLGTVLLTLAGREIFTNFLSSV 290 (545)
Q Consensus 246 ~vi~~i~~L~~lGv~~-~~lla~~Gi~glalgfAaqd~l~N~~aGi 290 (545)
+-+.++.+|..+-+|+ -+++.++-++|++-|+...++++-|.+|+
T Consensus 5 iaV~vm~~L~LlR~nVvlalliaalvgGl~~Gl~l~~t~~~~~~Gm 50 (88)
T PF13726_consen 5 IAVLVMIVLSLLRVNVVLALLIAALVGGLVGGLGLGETMSAFIDGM 50 (88)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHh
Confidence 3344455666666765 57778888889999999999999988875
No 30
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=38.14 E-value=40 Score=27.77 Aligned_cols=27 Identities=19% Similarity=0.086 Sum_probs=20.6
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEccee
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVGWWS 324 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIgl~s 324 (545)
+++.||.|++ +.| .|..|.|.+|.-..
T Consensus 6 ~I~kGD~V~V-i~G~dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 6 KVKKGDMVKV-IAGDDKGKTGKVLAVLPKK 34 (76)
T ss_pred cccCCCEEEE-eEcCCCCcEEEEEEEEcCC
Confidence 7999999998 554 35688998886543
No 31
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=36.35 E-value=67 Score=24.89 Aligned_cols=28 Identities=11% Similarity=0.213 Sum_probs=19.4
Q ss_pred CCccCCcEEEEeecCCCeEEEEEEEccee
Q 009063 296 QPFVINEWIQTKIQGYEVSGTVEHVGWWS 324 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~~~~G~VeeIgl~s 324 (545)
...-+||||.+..++ +..|.|+++-=|.
T Consensus 36 ~~~~VGD~V~~~~~~-~~~~~I~~vl~R~ 63 (68)
T cd04466 36 NPPAVGDRVEFEPED-DGEGVIEEILPRK 63 (68)
T ss_pred CCCCCCcEEEEEECC-CCcEEEEEEeccc
Confidence 456899999874332 3457888876665
No 32
>PF05552 TM_helix: Conserved TM helix; InterPro: IPR008910 This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with a Mechanosensitive (MS) channel IPR006685 from INTERPRO.; PDB: 2VV5_F 2OAU_E.
Probab=35.91 E-value=63 Score=24.35 Aligned_cols=35 Identities=14% Similarity=0.339 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 009063 188 QRVLNFVRSLSTVLAFAYCLSSLIQQIQKFLTEAND 223 (545)
Q Consensus 188 ~~l~~~i~~l~~i~~~~~~~~~li~~~~~~~~~~~~ 223 (545)
+.+++++.++ +++.++|++.++++.+.+...++.+
T Consensus 13 ~~lP~iv~Ai-lIl~vG~~va~~v~~~~~~~l~~~~ 47 (53)
T PF05552_consen 13 AYLPNIVGAI-LILIVGWWVAKFVRKLVRRLLEKRG 47 (53)
T ss_dssp GGHCHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 4455555444 5668889999998888776666655
No 33
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=35.84 E-value=86 Score=28.61 Aligned_cols=25 Identities=16% Similarity=0.215 Sum_probs=19.8
Q ss_pred CCccCCcEEEEeecC--CCeEEEEEEEc
Q 009063 296 QPFVINEWIQTKIQG--YEVSGTVEHVG 321 (545)
Q Consensus 296 rpf~VGD~I~i~i~g--~~~~G~VeeIg 321 (545)
..|++||+|++ ++| .|.+|.|++++
T Consensus 85 ~~~~~Gd~V~I-~~GPf~G~~g~v~~~d 111 (145)
T TIGR00405 85 ESIKKGDIVEI-ISGPFKGERAKVIRVD 111 (145)
T ss_pred cccCCCCEEEE-eecCCCCCeEEEEEEc
Confidence 35999999999 454 36789999885
No 34
>PF11449 DUF2899: Protein of unknown function (DUF2899); InterPro: IPR021552 This is a bacterial family of uncharacterised proteins.
Probab=35.13 E-value=5.2e+02 Score=26.98 Aligned_cols=42 Identities=21% Similarity=0.299 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH----HhCCchHHHHHHHHHHHHH
Q 009063 233 GFNFAGKAVYTAVWVAAVSLFME----LLGFSTQRWLTAGGLGTVL 274 (545)
Q Consensus 233 ~i~~l~~i~~~vv~vi~~i~~L~----~lGv~~~~lla~~Gi~gla 274 (545)
..+.+....++.+|++.+.++++ ..|.+...++...|..+-.
T Consensus 178 ~~~a~~hT~~I~~~v~~~~l~~~~~i~~~G~dl~~~l~~~~~~~pl 223 (298)
T PF11449_consen 178 LQKALQHTLFIFVWVFVAFLALELVIEFIGEDLAALLSGNGILQPL 223 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHhCchHHHH
Confidence 46667777888888888877665 4488887777666554433
No 35
>PF02934 GatB_N: GatB/GatE catalytic domain; InterPro: IPR006075 Glutamyl-tRNA(Gln) amidotransferase subunit B (6.3.5 from EC) [] is a microbial enzyme that furnishes a means for formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria. ; GO: 0016874 ligase activity; PDB: 3H0M_H 3H0R_K 3H0L_K 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B 2G5H_B 2DQN_B ....
Probab=34.31 E-value=2.5e+02 Score=29.23 Aligned_cols=143 Identities=11% Similarity=0.071 Sum_probs=82.1
Q ss_pred HHHHHH-hcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEcccCCceEEEEEEEec
Q 009063 288 SSVMIH-ATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAIS 366 (545)
Q Consensus 288 aGi~I~-~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~V~ 366 (545)
.|.+|. .+.|+-.|=+|.+ ....|.-..|++.. ..++-+.|+.+.-.+ =.+.....+.|.+.--+.+.=.=+
T Consensus 85 kgYQITQ~~~Pi~~~G~i~i----~~~~~~~k~I~I~~-ihlEEDagK~~h~~~--~~~~s~vD~NRaG~PLiEIVTePd 157 (289)
T PF02934_consen 85 KGYQITQYDNPIAENGYIEI----EFEDGREKRIRIER-IHLEEDAGKSIHDGG--GEDYSLVDYNRAGVPLIEIVTEPD 157 (289)
T ss_dssp TSEEEEESSS-SEEEEEEEE----TECTSSTEEEEEEE-EEEEE---EEEEETT---TTEEEEETTSTT-EEEEEEE-TT
T ss_pred cCccccCCccceecCCEEEE----EecCCceEEEEEEE-EEehhhhhhhccccc--cceeeEEcccCCCccceEEeeCCC
Confidence 344443 4568888888887 32334457889988 999999999998865 112345678898776666655556
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCcccccc--ceEE----EEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHH
Q 009063 367 HLDVHKVNSIVADMRKVLAKNPQVEQQRL--HRRV----FLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLH 440 (545)
Q Consensus 367 ytd~~~i~~i~~~l~e~l~~~p~i~~~~~--~p~v----~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~ 440 (545)
..+.+++.+.+++|++.++...-.+.+.. .-+| .+..-+....+ -++-+++- ..+..++..+..++.+
T Consensus 158 ~~s~~EA~~~~~~L~~il~~lgvs~~~me~GslR~DvNVSv~~~g~~~~g----~rvEIKNl--nS~~~i~~AI~~Ei~R 231 (289)
T PF02934_consen 158 IRSPEEAAAFLKKLRRILRYLGVSDGNMEEGSLRCDVNVSVRPKGEEKFG----TRVEIKNL--NSFRFIEKAIEYEIER 231 (289)
T ss_dssp B-SHHHHHHHHHHHHHHHHHHTSB--SGGGTSEEEEEEEEECETTSSSTS-----EEEEEEE---SHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHhcCcccCccccCcEEeeceeeecCCCCCCCc----ceEEEecc--cCHHHHHHHHHHHHHH
Confidence 67899999999999999886654443321 1122 22222211122 23444443 3466677777777766
Q ss_pred HHH
Q 009063 441 VIS 443 (545)
Q Consensus 441 ~l~ 443 (545)
..+
T Consensus 232 Q~~ 234 (289)
T PF02934_consen 232 QIE 234 (289)
T ss_dssp HHH
T ss_pred HHH
Confidence 443
No 36
>PF05552 TM_helix: Conserved TM helix; InterPro: IPR008910 This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with a Mechanosensitive (MS) channel IPR006685 from INTERPRO.; PDB: 2VV5_F 2OAU_E.
Probab=34.18 E-value=90 Score=23.48 Aligned_cols=30 Identities=13% Similarity=0.226 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009063 108 ILRLIPAAALVAFAAWGLVPLVRLGRTIFL 137 (545)
Q Consensus 108 ~~~~l~al~i~~~~~~~~~~l~~~~~~~~~ 137 (545)
..+++.|+++++++++..+.+.+++.+.+.
T Consensus 15 lP~iv~AilIl~vG~~va~~v~~~~~~~l~ 44 (53)
T PF05552_consen 15 LPNIVGAILILIVGWWVAKFVRKLVRRLLE 44 (53)
T ss_dssp HCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346788888888888887777666655443
No 37
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=33.42 E-value=52 Score=27.57 Aligned_cols=26 Identities=19% Similarity=0.113 Sum_probs=20.2
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEcce
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVGWW 323 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIgl~ 323 (545)
+++.||.|++ +.| .|..|.|.+|.-.
T Consensus 8 ~I~~GD~V~V-i~G~dKGK~G~V~~V~~~ 35 (83)
T CHL00141 8 HVKIGDTVKI-ISGSDKGKIGEVLKIIKK 35 (83)
T ss_pred cccCCCEEEE-eEcCCCCcEEEEEEEEcC
Confidence 6899999998 554 3578899888654
No 38
>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=33.34 E-value=1.4e+02 Score=23.92 Aligned_cols=44 Identities=14% Similarity=0.056 Sum_probs=32.3
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEc
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNL 351 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~ 351 (545)
+++||.|+ |+|.+|.=.. ..+....+-.=.||-+.++...+.|.
T Consensus 1 ~k~G~~V~---------g~V~~i~~~G-~fV~l~~~v~G~v~~~~ls~~~~~~~ 44 (74)
T cd05705 1 IKEGQLLR---------GYVSSVTKQG-VFFRLSSSIVGRVLFQNVTKYFVSDP 44 (74)
T ss_pred CCCCCEEE---------EEEEEEeCCc-EEEEeCCCCEEEEEHHHccCccccCh
Confidence 35676654 7899887655 66666678888889888888776664
No 39
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=32.87 E-value=1.5e+02 Score=32.00 Aligned_cols=80 Identities=13% Similarity=0.271 Sum_probs=56.4
Q ss_pred EEEEEeccCCHHHHHHHHHHHHHHHH------cCCCccccccceEEEEEeeCCCCCeEEEEEEEEEec---CChhhHHHH
Q 009063 360 KTYLAISHLDVHKVNSIVADMRKVLA------KNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKT---SRFEEYLCV 430 (545)
Q Consensus 360 ~~~l~V~ytd~~~i~~i~~~l~e~l~------~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~---~~~~~~~~i 430 (545)
+..+++.|.|....++++-++++++. ++|.+=.| +-+..+-. +..+.+.|-+-.-+ .+-++|.+.
T Consensus 156 DTS~gVGyAPlS~~E~~Vl~~E~~lns~~~k~~~P~~GeD-----iKVMG~R~-g~~i~lTVa~a~v~r~v~~~~~Y~~~ 229 (399)
T PRK04439 156 DTSFGVGYAPLSETERLVLETERYLNSEEFKKRFPEVGED-----IKVMGLRN-GDEITLTIAMALVDRYVNDVDEYFEV 229 (399)
T ss_pred cccceeecCCCCHHHHHHHHHHHHhcCcchhhcCCCcCCC-----eEEEEEEc-CCEEEEEEEhHHhhhhcCCHHHHHHH
Confidence 47889999999999999989999995 44444332 33444422 44566666543332 256899999
Q ss_pred HHHHHHHHHHHHHHC
Q 009063 431 KEAILLDLLHVISHH 445 (545)
Q Consensus 431 r~~i~~~i~~~l~~~ 445 (545)
++++.+.+.+...+.
T Consensus 230 k~~v~~~v~~~a~~~ 244 (399)
T PRK04439 230 KEEVKEKVEDLAQKY 244 (399)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999988664
No 40
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=32.25 E-value=5.5e+02 Score=29.80 Aligned_cols=57 Identities=12% Similarity=0.185 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhC------C----------chHHHHHHHHH------HHHHHHHhhhHHHHHHHHHH
Q 009063 234 FNFAGKAVYTAVWVAAVSLFMELLG------F----------STQRWLTAGGL------GTVLLTLAGREIFTNFLSSV 290 (545)
Q Consensus 234 i~~l~~i~~~vv~vi~~i~~L~~lG------v----------~~~~lla~~Gi------~glalgfAaqd~l~N~~aGi 290 (545)
-.++.++..+++....++.+++.+| + -.+++...+|. .++.-||++|+..-..++-+
T Consensus 498 k~Fl~kAgtiI~~~svlIW~Ls~~pp~g~~~~~~S~l~~ig~~l~Plf~plG~~~Wqa~v~Li~G~~AKEvvv~tl~~l 576 (653)
T COG0370 498 KEFLKKAGTIILAGSVLIWFLSSFPPGGVDNIKDSILAVIGKALEPLFSPLGFGDWQATVALIFGFIAKEVVVGTLGVL 576 (653)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHhCCCcccCchhhhHHHHHHHHHHHhhhhhcCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667777777777777777788776 1 12345555555 47778999999876666554
No 41
>PF01941 AdoMet_Synthase: S-adenosylmethionine synthetase (AdoMet synthetase); InterPro: IPR002795 A highly diverged class of S-adenosylmethionine synthetases have been identified in the archaea. S-adenosylmethionine is the primary alkylating agent in all known organisms. ATP:L-methionine S-adenosyltransferase (MAT) catalyses the only known biosynthetic route to this central metabolite. Although the amino acid sequence of MAT is strongly conserved among bacteria and eukarya (see IPR002133 from INTERPRO) no homologues had been recognised in the completed genome sequences of any archaea. The identification of a second major class of MAT emphasises the long evolutionary history of the archaeal lineage and the structural diversity found even in crucial metabolic enzymes []. Three bacterial genomes encode both the archaeal and eukaryotic/bacterial types of MAT [].; GO: 0004478 methionine adenosyltransferase activity, 0005524 ATP binding, 0006730 one-carbon metabolic process
Probab=31.09 E-value=2e+02 Score=31.07 Aligned_cols=80 Identities=13% Similarity=0.220 Sum_probs=57.3
Q ss_pred EEEEEeccCCHHHHHHHHHHHHHHHHcCC------CccccccceEEEEEeeCCCCCeEEEEEEEEEec---CChhhHHHH
Q 009063 360 KTYLAISHLDVHKVNSIVADMRKVLAKNP------QVEQQRLHRRVFLENINPESQSLNILVSCFVKT---SRFEEYLCV 430 (545)
Q Consensus 360 ~~~l~V~ytd~~~i~~i~~~l~e~l~~~p------~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~---~~~~~~~~i 430 (545)
+..++|.|.|....++++-++++.+.+.. .+=. .+-+..+-. +..+++.|-|-.-+ .+-++|.+.
T Consensus 156 DTS~gVGyAPlS~~E~~Vl~~Er~lns~~fk~~~p~~Ge-----DiKVMG~R~-g~~i~LTvA~a~v~r~v~~~~~Y~~~ 229 (396)
T PF01941_consen 156 DTSFGVGYAPLSETEKLVLETERYLNSPEFKKKFPEVGE-----DIKVMGLRE-GDKITLTVAMAFVDRYVSSLDEYFER 229 (396)
T ss_pred CccceeccCCccHHHHHHHHHHHHhccccccccCCCcCC-----CeEEEEEEe-CCEEEEEEEhhhhhhhcCCHHHHHHH
Confidence 47899999999999999989999998753 2222 133444422 44667776654432 266899999
Q ss_pred HHHHHHHHHHHHHHC
Q 009063 431 KEAILLDLLHVISHH 445 (545)
Q Consensus 431 r~~i~~~i~~~l~~~ 445 (545)
++++.+.+.+...+.
T Consensus 230 k~~v~~~v~~~a~~~ 244 (396)
T PF01941_consen 230 KEEVKEEVEDYAAKY 244 (396)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999988775
No 42
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=30.50 E-value=88 Score=27.02 Aligned_cols=38 Identities=18% Similarity=0.160 Sum_probs=27.5
Q ss_pred CCccCCcEEEEeecCC-----------CeEEEEEEEcceeEEEEEeCCCc
Q 009063 296 QPFVINEWIQTKIQGY-----------EVSGTVEHVGWWSPTIIRGDDRE 334 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~-----------~~~G~VeeIgl~sTT~irt~d~~ 334 (545)
+-|++||.|.|+||.. |-+|+|+...=++ -.+...||.
T Consensus 31 ~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~a-y~V~v~~G~ 79 (98)
T COG2139 31 QEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRA-YKVEVYDGN 79 (98)
T ss_pred hhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCE-EEEEEecCC
Confidence 4599999999987752 4578888887776 666555554
No 43
>PF09378 HAS-barrel: HAS barrel domain; InterPro: IPR018538 The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family []. ; PDB: 3OAA_I.
Probab=30.46 E-value=60 Score=26.71 Aligned_cols=27 Identities=19% Similarity=0.303 Sum_probs=19.4
Q ss_pred CccCCcEEEEeec-CCCeEEEEEEEcce
Q 009063 297 PFVINEWIQTKIQ-GYEVSGTVEHVGWW 323 (545)
Q Consensus 297 pf~VGD~I~i~i~-g~~~~G~VeeIgl~ 323 (545)
+.++||+|.++.+ +..+-|.|++|...
T Consensus 22 ~v~~GeyV~i~~~~~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 22 DVRVGEYVVIEYDDGEKVLGMVTSISRG 49 (91)
T ss_dssp T-BTTEEEEES----TTEEEEEEEEES-
T ss_pred CCCcCeEEEEEEechhhhhhhhheeEEc
Confidence 8999999999655 56789999988773
No 44
>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=29.93 E-value=1.3e+02 Score=24.38 Aligned_cols=44 Identities=9% Similarity=0.040 Sum_probs=34.0
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEc
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNL 351 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I~N~ 351 (545)
+++||.+. |.|.++.=.. ..+...++..-.+|.+.+....+.+.
T Consensus 12 ~~~G~i~~---------g~V~~v~~~G-~fv~l~~~~~g~v~~~el~~~~~~~~ 55 (83)
T cd04461 12 LKPGMVVH---------GYVRNITPYG-VFVEFLGGLTGLAPKSYISDEFVTDP 55 (83)
T ss_pred CCCCCEEE---------EEEEEEeece-EEEEcCCCCEEEEEHHHCCcccccCH
Confidence 77887664 7888888777 77787788889999999987665443
No 45
>PRK11281 hypothetical protein; Provisional
Probab=29.73 E-value=1.2e+03 Score=29.08 Aligned_cols=8 Identities=0% Similarity=-0.035 Sum_probs=5.0
Q ss_pred EEEEeCCC
Q 009063 74 RSVLAPGG 81 (545)
Q Consensus 74 ~~~~~~~~ 81 (545)
|++-+|++
T Consensus 454 ~lfWv~s~ 461 (1113)
T PRK11281 454 QIFWVNSN 461 (1113)
T ss_pred hhhccCCC
Confidence 45666666
No 46
>PRK10694 acyl-CoA esterase; Provisional
Probab=29.67 E-value=57 Score=29.63 Aligned_cols=31 Identities=13% Similarity=0.099 Sum_probs=24.7
Q ss_pred HHHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEE
Q 009063 291 MIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR 329 (545)
Q Consensus 291 ~I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~ir 329 (545)
-+-|-+|.++||.|++ .++|+++|=.| ..++
T Consensus 61 ~i~F~~Pv~~Gd~l~~-------~a~V~~~g~sS-~~v~ 91 (133)
T PRK10694 61 GMTFLRPVAVGDVVCC-------YARCVKTGTTS-ISIN 91 (133)
T ss_pred ceEECCCcccCcEEEE-------EEEEEEccCce-EEEE
Confidence 3578899999999985 58899888877 5544
No 47
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=28.90 E-value=90 Score=37.91 Aligned_cols=47 Identities=21% Similarity=0.242 Sum_probs=35.9
Q ss_pred CCccCCcEEEEeecC------CCeEEEEEEEcceeEEEEEeCCCcEEEEeCccc
Q 009063 296 QPFVINEWIQTKIQG------YEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKF 343 (545)
Q Consensus 296 rpf~VGD~I~i~i~g------~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l 343 (545)
+.|++||+|.+.-++ +|..|+|++|.=.. ..++..||+.+.+|...+
T Consensus 599 r~~~vGDrVm~~rNd~~lgV~NGd~GtV~~I~~~~-i~V~~d~gr~V~~~~~~~ 651 (988)
T PRK13889 599 RSFASGDRVMFLQNERGLGVKNGTLGTIEQVSAQS-MSVRLDDGRSVAFDLKDY 651 (988)
T ss_pred ccccCCCEEEEeecCCcCCEeCCCeEEEEEecCCe-EEEEECCCeEEEecHHHc
Confidence 579999999974221 35689999998766 778888888888876544
No 48
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=28.77 E-value=66 Score=27.95 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=14.2
Q ss_pred CCccCCcEEEEeecCC-----------CeEEEEEEEcce
Q 009063 296 QPFVINEWIQTKIQGY-----------EVSGTVEHVGWW 323 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~-----------~~~G~VeeIgl~ 323 (545)
+.|++||.|.|++|+. |-.|+|..++=.
T Consensus 31 ~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~ 69 (99)
T PF01157_consen 31 QEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKG 69 (99)
T ss_dssp ----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SS
T ss_pred HHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCC
Confidence 5699999999976653 457888876553
No 49
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=28.44 E-value=2.5e+02 Score=26.63 Aligned_cols=39 Identities=8% Similarity=-0.067 Sum_probs=19.0
Q ss_pred HHHHHhCCchH-HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcC
Q 009063 252 LFMELLGFSTQ-RWLTAGGLGTVLLTLAGREIFTNFLSSVMIHATQ 296 (545)
Q Consensus 252 ~~L~~lGv~~~-~lla~~Gi~glalgfAaqd~l~N~~aGi~I~~~r 296 (545)
.++..++.+.+ .+.+.+|++.+|+|.+. +.+|+.....+
T Consensus 24 ~~Lv~~~~~l~~~~s~~lg~~~lAlg~vL------~~~g~~~~~~~ 63 (191)
T PF04156_consen 24 AALVLFISGLGALISFILGIALLALGVVL------LSLGLLCLLSK 63 (191)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHc
Confidence 33444444433 33345566666666544 44555444443
No 50
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=28.18 E-value=69 Score=28.03 Aligned_cols=26 Identities=19% Similarity=0.021 Sum_probs=20.3
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEcce
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVGWW 323 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIgl~ 323 (545)
+++.||.|++ +.| .|..|.|.+|.-.
T Consensus 4 ~i~kGD~V~V-i~G~dKGk~G~V~~V~~~ 31 (105)
T PRK00004 4 KIKKGDTVIV-IAGKDKGKRGKVLKVLPK 31 (105)
T ss_pred cccCCCEEEE-eEcCCCCcEEEEEEEEcC
Confidence 7999999998 554 3578899888643
No 51
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=27.57 E-value=1.7e+02 Score=34.71 Aligned_cols=46 Identities=9% Similarity=0.123 Sum_probs=32.5
Q ss_pred CCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccc
Q 009063 296 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFT 344 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~ 344 (545)
++|++||+|.+ .+.+..|+|.+|.=-....+. .++-.+.||-+.+.
T Consensus 635 ~~~~~Gd~V~v--~~~~~~g~v~~i~~~~~~~V~-~g~~k~~v~~~~l~ 680 (782)
T PRK00409 635 EELKVGDEVKY--LSLGQKGEVLSIPDDKEAIVQ-AGIMKMKVPLSDLE 680 (782)
T ss_pred cCCCCCCEEEE--ccCCceEEEEEEcCCCeEEEE-ECCEEEEEeHHHce
Confidence 56999999998 445689999999421113333 46777888888874
No 52
>PF11282 DUF3082: Protein of unknown function (DUF3082); InterPro: IPR021434 This family of proteins has no known function.
Probab=27.21 E-value=3.8e+02 Score=22.53 Aligned_cols=25 Identities=20% Similarity=0.095 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc
Q 009063 199 TVLAFAYCLSSLIQQIQKFLTEAND 223 (545)
Q Consensus 199 ~i~~~~~~~~~li~~~~~~~~~~~~ 223 (545)
+-..++|.++.+...+..++..+.-
T Consensus 13 ~ag~la~~ly~lt~~i~~~fa~~p~ 37 (82)
T PF11282_consen 13 IAGGLAYGLYFLTTSIAASFASKPI 37 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCC
Confidence 4456778888888888888766654
No 53
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=27.02 E-value=1.1e+03 Score=28.07 Aligned_cols=69 Identities=9% Similarity=0.030 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCC---chH------------------HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Q 009063 236 FAGKAVYTAVWVAAVSLFMELLGF---STQ------------------RWLTAGGLGTVLLTLAGREIFTNFLSSVMIHA 294 (545)
Q Consensus 236 ~l~~i~~~vv~vi~~i~~L~~lGv---~~~------------------~lla~~Gi~glalgfAaqd~l~N~~aGi~I~~ 294 (545)
...++.+.+++.+++..++..+|+ ++. -.--..|+.-+++++.+--.+++++.+..+.-
T Consensus 510 ~~~~~~rl~~~~~~i~l~l~~wg~~~~~i~l~~~~~~~~~~~g~~~isl~~ll~avl~~~~~~~l~r~~~~~L~~~vl~r 589 (835)
T COG3264 510 QLLRLIRLLLLLIAIPLVLYVWGSYLEDITLWAYLGTTGGVLGVESITLGALLQAVLLFLITYVLTRNLPGWLEVRVLQR 589 (835)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHhhhcccchhhhhhcchhhhcceeEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566777777777777777772 111 01112333444455566666666666654443
Q ss_pred cCCccCCcEEE
Q 009063 295 TQPFVINEWIQ 305 (545)
Q Consensus 295 ~rpf~VGD~I~ 305 (545)
.+ ++.|=+..
T Consensus 590 ~~-~~~G~r~~ 599 (835)
T COG3264 590 LD-LDAGTRYS 599 (835)
T ss_pred cc-cCcchHHH
Confidence 33 66665443
No 54
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=26.86 E-value=1.3e+02 Score=23.31 Aligned_cols=30 Identities=13% Similarity=-0.005 Sum_probs=19.5
Q ss_pred HhcCCccCCcEEEEeecCCCeEEEEEEEcc
Q 009063 293 HATQPFVINEWIQTKIQGYEVSGTVEHVGW 322 (545)
Q Consensus 293 ~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl 322 (545)
+.++|+..||.|.+.+.|+...-.|.++.-
T Consensus 14 l~~~pv~~Gd~i~~~~~~~~~~~~V~~~~P 43 (64)
T PF02933_consen 14 LEGRPVTKGDTIVFPFFGQALPFKVVSTEP 43 (64)
T ss_dssp HTTEEEETT-EEEEEETTEEEEEEEEEECS
T ss_pred HcCCCccCCCEEEEEeCCcEEEEEEEEEEc
Confidence 456899999999986555444445555443
No 55
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=26.24 E-value=70 Score=28.80 Aligned_cols=25 Identities=20% Similarity=0.338 Sum_probs=19.4
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEcc
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVGW 322 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIgl 322 (545)
+++.||.|+| +.| .|..|.|.+|.-
T Consensus 45 ~IkkGD~V~V-isG~~KGk~GkV~~V~~ 71 (120)
T PRK01191 45 PVRKGDTVKV-MRGDFKGEEGKVVEVDL 71 (120)
T ss_pred eEeCCCEEEE-eecCCCCceEEEEEEEc
Confidence 7999999998 554 356788888744
No 56
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=25.60 E-value=49 Score=25.77 Aligned_cols=19 Identities=21% Similarity=0.459 Sum_probs=15.7
Q ss_pred HHHHHHHHHHcCCCccccc
Q 009063 376 IVADMRKVLAKNPQVEQQR 394 (545)
Q Consensus 376 i~~~l~e~l~~~p~i~~~~ 394 (545)
+-+.|+++++.||+|++++
T Consensus 10 L~~~m~~fie~hP~WDQ~R 28 (57)
T PF10929_consen 10 LHQAMKDFIETHPNWDQYR 28 (57)
T ss_pred HHHHHHHHHHcCCCchHHH
Confidence 3445999999999999875
No 57
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=25.34 E-value=76 Score=28.30 Aligned_cols=24 Identities=21% Similarity=0.383 Sum_probs=19.4
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEc
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVG 321 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIg 321 (545)
+++.||.|.| +.| .|.+|.|.+|.
T Consensus 41 ~IkkGD~V~V-i~Gk~KGk~GkV~~V~ 66 (114)
T TIGR01080 41 PVRKGDKVRI-MRGDFKGHEGKVSKVD 66 (114)
T ss_pred eeecCCEEEE-ecCCCCCCEEEEEEEE
Confidence 7999999998 554 35788998885
No 58
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=25.06 E-value=2.9e+02 Score=20.40 Aligned_cols=46 Identities=11% Similarity=0.052 Sum_probs=30.8
Q ss_pred CccCCcEEEEee-cCCCeEEEEEEEcc-eeEEEEEeCC-CcEEEEeCccc
Q 009063 297 PFVINEWIQTKI-QGYEVSGTVEHVGW-WSPTIIRGDD-REAVHIPNHKF 343 (545)
Q Consensus 297 pf~VGD~I~i~i-~g~~~~G~VeeIgl-~sTT~irt~d-~~~v~IPNs~l 343 (545)
++++|+.+..+. +|.-..|+|+++.= .. ..++=.| |....+|-+.+
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~-~~V~f~D~G~~~~v~~~~l 50 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQL-YEVFFIDYGNEEVVPPSDL 50 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCE-EEEEEECCCccEEEeHHHe
Confidence 689999999876 55556788888874 22 3444444 66666665443
No 59
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=25.05 E-value=2.3e+02 Score=21.46 Aligned_cols=26 Identities=12% Similarity=-0.045 Sum_probs=19.3
Q ss_pred CccCCcEEEEee--cCCCeEEEEEEEcc
Q 009063 297 PFVINEWIQTKI--QGYEVSGTVEHVGW 322 (545)
Q Consensus 297 pf~VGD~I~i~i--~g~~~~G~VeeIgl 322 (545)
-|++||.|++.. ++.-..|+|.++.=
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC
Confidence 489999999966 55455688877754
No 60
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=24.62 E-value=1.9e+02 Score=22.66 Aligned_cols=44 Identities=14% Similarity=0.151 Sum_probs=32.4
Q ss_pred ccCCcEEEEe--ecCCCeEEEEEEEcceeEEEEE-eCCCcEEEEeCccc
Q 009063 298 FVINEWIQTK--IQGYEVSGTVEHVGWWSPTIIR-GDDREAVHIPNHKF 343 (545)
Q Consensus 298 f~VGD~I~i~--i~g~~~~G~VeeIgl~sTT~ir-t~d~~~v~IPNs~l 343 (545)
|.+||.|+.+ -+-|+..-.|..+|.-. +++ +--|+.+.+|-+.|
T Consensus 2 ~~vgDiV~mKK~HPCG~~~Wei~R~GaDi--kikC~gCg~~imlpR~~f 48 (57)
T PF06107_consen 2 YEVGDIVEMKKPHPCGSNEWEIIRIGADI--KIKCLGCGRQIMLPRSKF 48 (57)
T ss_pred ccCCCEEEEcCCCCCCCCEEEEEEccCcE--EEEECCCCCEEEEeHHHH
Confidence 7899999986 33356778999998864 444 44588888887766
No 61
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=24.40 E-value=2e+02 Score=24.24 Aligned_cols=44 Identities=14% Similarity=0.244 Sum_probs=25.8
Q ss_pred CccCCcEEEEeecCCCeEEEEEEEcceeE-------EEEEeCCCcEEEEeCccc
Q 009063 297 PFVINEWIQTKIQGYEVSGTVEHVGWWSP-------TIIRGDDREAVHIPNHKF 343 (545)
Q Consensus 297 pf~VGD~I~i~i~g~~~~G~VeeIgl~sT-------T~irt~d~~~v~IPNs~l 343 (545)
.|++||+|.- ++.| -|+|++|.-... -.++-.++..++||-...
T Consensus 1 mf~~GD~VVh--~~~G-v~~i~~i~~~~~~~~~~~yy~L~~~~~~~i~vPv~~~ 51 (98)
T PF02559_consen 1 MFKIGDYVVH--PNHG-VGRIEGIEEIEFGGEKQEYYVLEYADDDTIYVPVDNA 51 (98)
T ss_dssp T--TTSEEEE--TTTE-EEEEEEEEEEECTTEEEEEEEEEECCCEEEEEECCCG
T ss_pred CCCCCCEEEE--CCCc-eEEEEEEEEEeeCCeeEEEEEEEECCCCEEEEEcCCh
Confidence 4899999985 3333 377777654330 345555555777777664
No 62
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=23.87 E-value=1.2e+02 Score=26.36 Aligned_cols=29 Identities=21% Similarity=0.101 Sum_probs=20.6
Q ss_pred CCccCCcEEEEeecCC-----------CeEEEEEEEccee
Q 009063 296 QPFVINEWIQTKIQGY-----------EVSGTVEHVGWWS 324 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~-----------~~~G~VeeIgl~s 324 (545)
+.|++||.|.|++|+. |-.|+|..++=+.
T Consensus 33 ~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A 72 (98)
T PRK04306 33 QEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRA 72 (98)
T ss_pred HhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeE
Confidence 3499999999977653 2256777766655
No 63
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=23.71 E-value=2e+02 Score=25.96 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=13.9
Q ss_pred HHHhcCCccCCcEEEE
Q 009063 291 MIHATQPFVINEWIQT 306 (545)
Q Consensus 291 ~I~~~rpf~VGD~I~i 306 (545)
-+-|.+|..+||.|.+
T Consensus 82 ~~rf~~PV~~GDtl~~ 97 (142)
T cd03452 82 NLRFLEPVYPGDTIQV 97 (142)
T ss_pred eEEECCCCCCCCEEEE
Confidence 4578899999999986
No 64
>PRK08582 hypothetical protein; Provisional
Probab=22.60 E-value=2.9e+02 Score=25.29 Aligned_cols=41 Identities=12% Similarity=0.150 Sum_probs=29.4
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeE
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVV 348 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~~I 348 (545)
+++||.++ |+|.+|.=.- ..+...++..=.||.+.+....+
T Consensus 3 ~kvG~iv~---------G~V~~I~~fG-~fV~L~~~~~GlVhiSels~~~v 43 (139)
T PRK08582 3 IEVGSKLQ---------GKVTGITNFG-AFVELPEGKTGLVHISEVADNYV 43 (139)
T ss_pred CcCCCEEE---------EEEEEEECCe-EEEEECCCCEEEEEeeccCcccc
Confidence 56776554 7888887776 77777777777888887765443
No 65
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=22.44 E-value=1.6e+03 Score=28.04 Aligned_cols=9 Identities=22% Similarity=0.811 Sum_probs=6.4
Q ss_pred EEEEEccee
Q 009063 316 TVEHVGWWS 324 (545)
Q Consensus 316 ~VeeIgl~s 324 (545)
.-++|+++.
T Consensus 809 ~Ld~i~LW~ 817 (1109)
T PRK10929 809 FLENISLWD 817 (1109)
T ss_pred HhcceeEEe
Confidence 456888876
No 66
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=22.35 E-value=1e+02 Score=26.89 Aligned_cols=25 Identities=20% Similarity=0.118 Sum_probs=19.6
Q ss_pred CccCCcEEEEeecC--CCeEEEEEEEcc
Q 009063 297 PFVINEWIQTKIQG--YEVSGTVEHVGW 322 (545)
Q Consensus 297 pf~VGD~I~i~i~g--~~~~G~VeeIgl 322 (545)
+++.||.|++ +.| .|..|.|.+|.-
T Consensus 3 ~ikkGD~V~V-i~G~dKGK~G~V~~V~~ 29 (104)
T TIGR01079 3 KIKKGDTVKV-ISGKDKGKRGKVLKVLP 29 (104)
T ss_pred cccCCCEEEE-eEcCCCCcEEEEEEEEc
Confidence 6899999998 554 356889988854
No 67
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=22.24 E-value=1.3e+03 Score=26.84 Aligned_cols=17 Identities=6% Similarity=0.204 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHCCCc
Q 009063 432 EAILLDLLHVISHHRAR 448 (545)
Q Consensus 432 ~~i~~~i~~~l~~~gI~ 448 (545)
.++-.+|.+.-++|||+
T Consensus 587 D~lAlrIReiAeE~gVP 603 (646)
T PRK12773 587 DDFALLIIRIARENGVP 603 (646)
T ss_pred cHHHHHHHHHHHHcCCc
Confidence 46778888888999975
No 68
>COG1607 Acyl-CoA hydrolase [Lipid metabolism]
Probab=22.13 E-value=80 Score=29.78 Aligned_cols=30 Identities=13% Similarity=0.141 Sum_probs=24.3
Q ss_pred HHhcCCccCCcEEEEeecCCCeEEEEEEEcceeEEEEE
Q 009063 292 IHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR 329 (545)
Q Consensus 292 I~~~rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~ir 329 (545)
+.|.+|+++||.|++ .+.|..+|=+| ..+.
T Consensus 64 v~F~~Pv~vGd~v~~-------~a~v~~~GrTS-m~V~ 93 (157)
T COG1607 64 VDFKKPVRVGDIVCL-------YARVVYTGRTS-MEVG 93 (157)
T ss_pred EEEccccccCcEEEE-------EEEEeecCccc-EEEE
Confidence 578899999999996 58999998877 4443
No 69
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=22.13 E-value=1e+02 Score=28.55 Aligned_cols=26 Identities=4% Similarity=-0.028 Sum_probs=20.4
Q ss_pred cCCccCCcEEEEeecC--CCeEEEEEEEc
Q 009063 295 TQPFVINEWIQTKIQG--YEVSGTVEHVG 321 (545)
Q Consensus 295 ~rpf~VGD~I~i~i~g--~~~~G~VeeIg 321 (545)
..+|+.||.|.| .+| .|.+|.|+++.
T Consensus 107 ~~~~~~G~~V~I-~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 107 PETPKPGDKVII-TEGAFEGLQAIYTEPD 134 (162)
T ss_pred ccCCCCCCEEEE-ecCCCCCcEEEEEEeC
Confidence 356999999998 454 46889999886
No 70
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=21.62 E-value=2.1e+02 Score=26.67 Aligned_cols=16 Identities=13% Similarity=0.324 Sum_probs=13.5
Q ss_pred HHHhcCCccCCcEEEE
Q 009063 291 MIHATQPFVINEWIQT 306 (545)
Q Consensus 291 ~I~~~rpf~VGD~I~i 306 (545)
-+-+-+|.++||.+.+
T Consensus 90 ~~~f~~PV~~GDtL~~ 105 (159)
T PRK13692 90 VLKFEKPIVAGDKLYC 105 (159)
T ss_pred EEEEeCCccCCCEEEE
Confidence 3567799999999986
No 71
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=21.37 E-value=1.1e+02 Score=26.07 Aligned_cols=23 Identities=17% Similarity=0.459 Sum_probs=18.9
Q ss_pred CCccCCcEEEEeecCCCeEEEEEEE
Q 009063 296 QPFVINEWIQTKIQGYEVSGTVEHV 320 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~~~~G~VeeI 320 (545)
+|+.+|+.|+- ++ -|..|.|.+|
T Consensus 1 k~I~vGs~VRY-~~-TGT~G~V~di 23 (91)
T PF09871_consen 1 KPIKVGSYVRY-IN-TGTVGKVVDI 23 (91)
T ss_pred CcceeCCEEEE-CC-CCeEEEEEEE
Confidence 58999999997 44 4788999887
No 72
>CHL00084 rpl19 ribosomal protein L19
Probab=21.23 E-value=2.2e+02 Score=25.55 Aligned_cols=11 Identities=0% Similarity=0.142 Sum_probs=9.6
Q ss_pred CccCCcEEEEe
Q 009063 297 PFVINEWIQTK 307 (545)
Q Consensus 297 pf~VGD~I~i~ 307 (545)
.|++||.|.+.
T Consensus 22 ~f~~GDtV~V~ 32 (117)
T CHL00084 22 KIRVGDTVKVG 32 (117)
T ss_pred ccCCCCEEEEE
Confidence 59999999974
No 73
>PRK14725 pyruvate kinase; Provisional
Probab=21.11 E-value=1.4e+02 Score=34.17 Aligned_cols=81 Identities=10% Similarity=0.124 Sum_probs=48.5
Q ss_pred ccCCcEEEEeecCCCeEEEEEEEccee-EEEEEe--------CCCcEEEEeCcccccCeEEEcccCC----ceEEEEEEE
Q 009063 298 FVINEWIQTKIQGYEVSGTVEHVGWWS-PTIIRG--------DDREAVHIPNHKFTVNVVRNLSQKT----HWRIKTYLA 364 (545)
Q Consensus 298 f~VGD~I~i~i~g~~~~G~VeeIgl~s-TT~irt--------~d~~~v~IPNs~l~~~~I~N~sr~~----~~ri~~~l~ 364 (545)
+++||.|-+ |+|...++|++++=.. .+++.+ .+++=+.+|++.+.-..++---+.+ ... .-.+.
T Consensus 373 v~~G~~Vli--dDG~I~l~V~~~~~~~v~~~V~~a~~~gg~L~s~KGiNlP~~~l~lp~LTekD~~dl~f~~~~-vD~Va 449 (608)
T PRK14725 373 ARVGERVWF--DDGKIGAVVVKVEADEVELRITHARPGGSKLKAGKGINLPDSHLPLPALTDKDLEDLAFVAKH-ADIVA 449 (608)
T ss_pred cCCCCEEEE--eCCeEEEEEEEEECCEEEEEEEEecCCCCEecCCCceecCCCCCCCCCCCHHHHHHHHHHHHh-CCEEE
Confidence 899999997 6678999999886222 122222 3445567888876544332211111 011 23578
Q ss_pred ecc-CCHHHHHHHHHHHH
Q 009063 365 ISH-LDVHKVNSIVADMR 381 (545)
Q Consensus 365 V~y-td~~~i~~i~~~l~ 381 (545)
++| .+.++++.+.+.+.
T Consensus 450 lSFVrs~~DV~~lr~~L~ 467 (608)
T PRK14725 450 LSFVRSPEDVRLLLDALE 467 (608)
T ss_pred ECCCCCHHHHHHHHHHHH
Confidence 888 78888888644443
No 74
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=20.63 E-value=4.1e+02 Score=31.48 Aligned_cols=44 Identities=5% Similarity=0.028 Sum_probs=30.0
Q ss_pred CCccCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCccc
Q 009063 296 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKF 343 (545)
Q Consensus 296 rpf~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l 343 (545)
.+ ++||.|.| .+.+..|+|.++.=-....+. .++-.+.||-+.+
T Consensus 624 ~~-~~Gd~V~v--~~~~~~g~v~~i~~~~~~~V~-~g~~k~~v~~~~l 667 (771)
T TIGR01069 624 AD-KIGDKVRI--RYFGQKGKIVQILGGNKWNVT-VGGMRMKVHGSEL 667 (771)
T ss_pred cC-CCCCEEEE--ccCCceEEEEEEcCCCeEEEE-ECCEEEEEeHHHc
Confidence 44 99999997 446789999999411213333 3566677887777
No 75
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=20.63 E-value=2.7e+02 Score=26.10 Aligned_cols=26 Identities=35% Similarity=0.599 Sum_probs=20.3
Q ss_pred cCCccCCcEEEEeecC--CCeEEEEEEEc
Q 009063 295 TQPFVINEWIQTKIQG--YEVSGTVEHVG 321 (545)
Q Consensus 295 ~rpf~VGD~I~i~i~g--~~~~G~VeeIg 321 (545)
..+|++||.|+| .+| .|.+|.|+++.
T Consensus 124 ~~~~~~Gd~VrI-~~GPf~G~~g~v~~i~ 151 (181)
T PRK05609 124 KVDFEVGEMVRV-IDGPFADFNGTVEEVD 151 (181)
T ss_pred ccCCCCCCEEEE-eccCCCCCEEEEEEEe
Confidence 356999999998 454 36789999885
No 76
>PF13452 MaoC_dehydrat_N: N-terminal half of MaoC dehydratase; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1S9C_K 3OML_A 3KHP_A.
Probab=20.55 E-value=2.1e+02 Score=25.08 Aligned_cols=19 Identities=11% Similarity=0.132 Sum_probs=13.3
Q ss_pred HHHHHHhcCCccCCcEEEE
Q 009063 288 SSVMIHATQPFVINEWIQT 306 (545)
Q Consensus 288 aGi~I~~~rpf~VGD~I~i 306 (545)
++--+-+-+|.++||.+.+
T Consensus 78 ~~~~~~~h~Pl~~Gd~l~~ 96 (132)
T PF13452_consen 78 GEQDIEFHRPLRPGDTLTA 96 (132)
T ss_dssp EEEEEEESS--BSSEEEEE
T ss_pred cCcEEEEeCCCCCCCEEEE
Confidence 4445667899999999996
No 77
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=20.51 E-value=4.5e+02 Score=26.23 Aligned_cols=57 Identities=16% Similarity=0.193 Sum_probs=33.7
Q ss_pred HHHHHHcCCCccccccceEEEEEeeCCCCCeEEEEEEEEEecC-ChhhHHHHHHHHHHHHHHH
Q 009063 380 MRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTS-RFEEYLCVKEAILLDLLHV 441 (545)
Q Consensus 380 l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~-~~~~~~~ir~~i~~~i~~~ 441 (545)
+++.+++.|++..-. .+.+.+.+. ....+++.+-+++. +-.+..++++++.+.+.+.
T Consensus 210 i~~~i~~~~~v~~v~---~~~~~~~g~--~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~ 267 (284)
T PF01545_consen 210 IRRIIESVPGVIEVH---DLRVWQVGR--NKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREK 267 (284)
T ss_dssp HHHHHHHTSS-SEEE---EEEEEEETT---EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhccCCceEecc---ceEEEEecC--CcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHh
Confidence 566676677776532 577888873 35666666666654 3345555555555555555
No 78
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=20.37 E-value=1.5e+03 Score=26.94 Aligned_cols=58 Identities=14% Similarity=0.111 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCc------------------hHHHHHHHHH--------HHHHHHHhhhHHHHHHH
Q 009063 234 FNFAGKAVYTAVWVAAVSLFMELLGFS------------------TQRWLTAGGL--------GTVLLTLAGREIFTNFL 287 (545)
Q Consensus 234 i~~l~~i~~~vv~vi~~i~~L~~lGv~------------------~~~lla~~Gi--------~glalgfAaqd~l~N~~ 287 (545)
-.++.+...+++.+..++.+|+.+|.+ ++++++-+|+ .++..||.+|+.+-.-+
T Consensus 509 ~~Fl~~Ag~iI~~~~iviw~l~~~~~~g~~~~~~~~S~l~~ig~~i~Pi~~plG~~~~nW~~~vali~G~~AKE~vv~tl 588 (772)
T PRK09554 509 KGFVLRAGKVIIIVSIFIGALNSFSLSGKIVDNINDSALASVSRVITPVLKPIGVHEDNWQATVGLFTGAMAKEVVVGTL 588 (772)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCccccccchhhhHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHHHHH
Confidence 567777777777777777788887632 1233333333 56778999999887777
Q ss_pred HHHH
Q 009063 288 SSVM 291 (545)
Q Consensus 288 aGi~ 291 (545)
+.+.
T Consensus 589 ~~ly 592 (772)
T PRK09554 589 NTLY 592 (772)
T ss_pred HHHH
Confidence 7664
No 79
>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=20.30 E-value=1.8e+02 Score=23.53 Aligned_cols=38 Identities=13% Similarity=0.059 Sum_probs=26.6
Q ss_pred cCCcEEEEeecCCCeEEEEEEEcceeEEEEEeCCCcEEEEeCcccccC
Q 009063 299 VINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVN 346 (545)
Q Consensus 299 ~VGD~I~i~i~g~~~~G~VeeIgl~sTT~irt~d~~~v~IPNs~l~~~ 346 (545)
++||.|. |+|.++.-.. ..+.-..+..-++|.+.+...
T Consensus 5 ~~GdiV~---------G~V~~v~~~~-~~V~i~~~~~g~l~~~~~~~~ 42 (82)
T cd04454 5 DVGDIVI---------GIVTEVNSRF-WKVDILSRGTARLEDSSATEK 42 (82)
T ss_pred CCCCEEE---------EEEEEEcCCE-EEEEeCCCceEEeechhccCc
Confidence 6788775 7888887776 666666666666777766543
Done!