Query 009110
Match_columns 543
No_of_seqs 368 out of 2212
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 20:32:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009110.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009110hhsearch_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 3.6E-45 7.9E-50 372.4 34.7 250 189-458 29-279 (286)
2 PRK11465 putative mechanosensi 100.0 2.2E-42 4.7E-47 384.2 41.8 298 137-454 417-722 (741)
3 PRK11281 hypothetical protein; 100.0 3.4E-40 7.3E-45 382.2 41.7 253 188-459 836-1091(1113)
4 PRK10929 putative mechanosensi 100.0 1.7E-39 3.8E-44 375.0 35.3 251 190-459 835-1088(1109)
5 COG3264 Small-conductance mech 100.0 3.2E-36 6.9E-41 332.2 37.6 244 197-458 566-812 (835)
6 PF00924 MS_channel: Mechanose 100.0 1.3E-36 2.7E-41 295.4 20.0 203 237-447 2-206 (206)
7 COG0668 MscS Small-conductance 100.0 4.2E-34 9.1E-39 294.1 34.4 208 234-455 86-296 (316)
8 KOG4629 Predicted mechanosensi 99.8 6.1E-20 1.3E-24 203.6 14.9 222 230-458 478-702 (714)
9 TIGR00739 yajC preprotein tran 71.6 12 0.00026 31.4 5.8 38 296-337 38-75 (84)
10 PRK05585 yajC preprotein trans 70.8 11 0.00025 33.0 5.8 41 296-340 53-93 (106)
11 PF09953 DUF2187: Uncharacteri 61.3 14 0.00029 28.8 3.8 28 296-327 4-31 (57)
12 smart00739 KOW KOW (Kyprides, 60.7 15 0.00033 23.3 3.5 24 295-319 1-26 (28)
13 PF14545 DBB: Dof, BCAP, and B 60.3 53 0.0012 30.4 8.2 82 287-374 14-96 (142)
14 PRK05886 yajC preprotein trans 57.9 31 0.00066 30.5 6.0 37 296-336 39-75 (109)
15 PF14801 GCD14_N: tRNA methylt 54.1 8 0.00017 29.6 1.5 24 293-320 3-26 (54)
16 COG4956 Integral membrane prot 53.8 1.7E+02 0.0036 30.8 11.2 33 99-131 35-67 (356)
17 COG4873 Uncharacterized protei 49.1 20 0.00044 28.6 3.1 27 296-326 24-50 (81)
18 COG0053 MMT1 Predicted Co/Zn/C 49.0 3.3E+02 0.0071 28.3 15.5 34 354-387 244-278 (304)
19 PF09926 DUF2158: Uncharacteri 48.0 18 0.0004 27.7 2.6 23 296-320 1-23 (53)
20 PRK06531 yajC preprotein trans 48.0 50 0.0011 29.4 5.7 41 296-340 37-78 (113)
21 COG1862 YajC Preprotein transl 47.9 52 0.0011 28.4 5.7 42 296-341 44-85 (97)
22 PF12961 DUF3850: Domain of Un 47.6 43 0.00093 27.4 4.8 31 292-322 25-56 (72)
23 PF00467 KOW: KOW motif; Inte 44.3 35 0.00077 22.9 3.4 22 298-320 1-24 (32)
24 PF05552 TM_helix: Conserved T 42.5 64 0.0014 24.3 4.9 29 108-136 17-45 (53)
25 PF12794 MscS_TM: Mechanosensi 41.3 4.5E+02 0.0098 27.7 15.3 29 233-261 194-223 (340)
26 PRK13692 (3R)-hydroxyacyl-ACP 41.1 1.3E+02 0.0027 28.2 7.8 17 288-304 89-105 (159)
27 PF02934 GatB_N: GatB/GatE cat 40.1 2.5E+02 0.0054 29.1 10.3 142 286-440 85-233 (289)
28 cd03452 MaoC_C MaoC_C The C-t 39.8 91 0.002 28.2 6.5 16 289-304 82-97 (142)
29 PRK08559 nusG transcription an 38.6 95 0.0021 28.8 6.5 47 294-341 93-145 (153)
30 PF00575 S1: S1 RNA binding do 38.0 1.6E+02 0.0035 22.9 7.0 40 311-351 8-47 (74)
31 PRK12281 rplX 50S ribosomal pr 37.5 41 0.00089 27.7 3.4 27 295-322 6-34 (76)
32 PF02699 YajC: Preprotein tran 37.3 11 0.00024 31.4 -0.0 37 296-336 37-73 (82)
33 PRK10694 acyl-CoA esterase; Pr 36.2 57 0.0012 29.6 4.5 31 289-327 61-91 (133)
34 PF09378 HAS-barrel: HAS barre 36.2 43 0.00093 27.6 3.4 32 290-321 15-49 (91)
35 PF05552 TM_helix: Conserved T 35.1 75 0.0016 23.9 4.3 35 186-221 13-47 (53)
36 cd04466 S1_YloQ_GTPase S1_YloQ 34.8 71 0.0015 24.7 4.3 28 294-322 36-63 (68)
37 PRK10334 mechanosensitive chan 34.6 5.3E+02 0.011 26.5 14.0 27 108-134 30-56 (286)
38 PRK10263 DNA translocase FtsK; 33.8 6.4E+02 0.014 31.8 13.7 9 529-537 524-532 (1355)
39 COG2139 RPL21A Ribosomal prote 33.1 73 0.0016 27.5 4.2 38 294-332 31-79 (98)
40 PF01941 AdoMet_Synthase: S-ad 33.0 4.2E+02 0.009 28.7 10.8 80 358-443 156-244 (396)
41 TIGR00405 L26e_arch ribosomal 32.6 1E+02 0.0023 28.0 5.7 25 294-319 85-111 (145)
42 PF13452 MaoC_dehydrat_N: N-te 32.5 1.1E+02 0.0023 27.0 5.6 25 280-304 72-96 (132)
43 CHL00141 rpl24 ribosomal prote 32.4 55 0.0012 27.4 3.4 27 295-322 8-36 (83)
44 cd03455 SAV4209 SAV4209 is a S 30.8 1.8E+02 0.004 25.3 6.8 43 285-334 69-115 (123)
45 cd03453 SAV4209_like SAV4209_l 30.8 2.1E+02 0.0045 25.1 7.2 18 287-304 72-89 (127)
46 PRK04439 S-adenosylmethionine 30.6 1.7E+02 0.0037 31.6 7.5 80 358-443 156-244 (399)
47 PF06442 DHFR_2: R67 dihydrofo 30.6 58 0.0013 25.9 3.0 42 281-326 8-50 (78)
48 PF13726 Na_H_antiport_2: Na+- 30.3 76 0.0017 27.0 3.9 45 244-288 5-50 (88)
49 PRK13889 conjugal transfer rel 30.1 82 0.0018 38.2 5.6 47 294-341 599-651 (988)
50 PRK10929 putative mechanosensi 29.3 8.5E+02 0.018 30.2 13.9 31 107-137 834-864 (1109)
51 cd03441 R_hydratase_like (R)-h 29.1 2.2E+02 0.0047 24.3 6.9 20 285-304 70-89 (127)
52 PF01157 Ribosomal_L21e: Ribos 28.2 67 0.0015 27.9 3.3 28 294-321 31-69 (99)
53 cd03454 YdeM YdeM is a Bacillu 28.1 2.1E+02 0.0046 25.4 6.9 16 289-304 82-97 (140)
54 cd05705 S1_Rrp5_repeat_hs14 S1 28.0 2E+02 0.0043 23.1 5.9 38 311-349 7-44 (74)
55 PF02559 CarD_CdnL_TRCF: CarD- 27.9 1.7E+02 0.0036 24.7 5.8 45 295-342 1-52 (98)
56 PRK00004 rplX 50S ribosomal pr 27.3 73 0.0016 27.9 3.4 26 295-321 4-31 (105)
57 PF10929 DUF2811: Protein of u 27.0 46 0.001 25.9 1.8 18 375-392 11-28 (57)
58 COG1607 Acyl-CoA hydrolase [Li 26.8 87 0.0019 29.5 4.0 30 290-327 64-93 (157)
59 PF02933 CDC48_2: Cell divisio 26.7 1.2E+02 0.0026 23.6 4.3 30 292-321 15-44 (64)
60 PRK04306 50S ribosomal protein 26.5 1E+02 0.0022 26.8 4.0 33 294-327 33-76 (98)
61 PRK11281 hypothetical protein; 26.4 1.3E+03 0.029 28.6 16.8 8 72-79 454-461 (1113)
62 cd04486 YhcR_OBF_like YhcR_OBF 26.4 81 0.0017 25.9 3.4 28 286-320 33-62 (78)
63 COG3264 Small-conductance mech 26.3 1.1E+03 0.023 28.3 13.3 23 234-256 510-532 (835)
64 TIGR02286 PaaD phenylacetic ac 26.0 2.3E+02 0.005 24.3 6.5 41 286-334 60-104 (114)
65 PRK00409 recombination and DNA 25.6 1.9E+02 0.004 34.3 7.4 46 294-342 635-680 (782)
66 PF11449 DUF2899: Protein of u 25.4 7.9E+02 0.017 25.6 11.9 42 231-272 178-223 (298)
67 PRK14725 pyruvate kinase; Prov 25.0 1.1E+02 0.0023 35.1 5.0 82 295-379 372-467 (608)
68 cd04461 S1_Rrp5_repeat_hs8_sc7 24.9 1.8E+02 0.0039 23.5 5.3 43 296-348 12-54 (83)
69 PF03061 4HBT: Thioesterase su 24.7 1.7E+02 0.0038 22.5 5.1 33 286-326 34-66 (79)
70 PHA02945 interferon resistance 24.5 2.8E+02 0.0061 23.6 6.2 43 297-348 10-54 (88)
71 PRK01191 rpl24p 50S ribosomal 24.1 80 0.0017 28.4 3.1 25 295-320 45-71 (120)
72 PF09871 DUF2098: Uncharacteri 23.6 94 0.002 26.6 3.3 23 294-318 1-23 (91)
73 TIGR01080 rplX_A_E ribosomal p 23.4 86 0.0019 27.9 3.1 24 295-319 41-66 (114)
74 PRK08187 pyruvate kinase; Vali 22.7 1.6E+02 0.0034 32.9 5.8 81 294-378 251-346 (493)
75 COG4858 Uncharacterized membra 22.1 7.5E+02 0.016 24.2 12.8 18 90-107 107-124 (226)
76 PF01545 Cation_efflux: Cation 22.0 4.1E+02 0.0089 26.5 8.4 58 377-439 209-267 (284)
77 TIGR01079 rplX_bact ribosomal 21.9 1.1E+02 0.0023 26.8 3.4 26 295-321 3-30 (104)
78 cd04465 S1_RPS1_repeat_ec2_hs2 21.7 2.2E+02 0.0047 21.9 4.9 35 311-347 4-38 (67)
79 PF14221 DUF4330: Domain of un 21.5 2.4E+02 0.0051 26.8 6.0 43 296-339 72-117 (168)
80 cd03446 MaoC_like MoaC_like 21.0 2.6E+02 0.0057 24.6 6.0 16 289-304 84-99 (140)
81 cd05698 S1_Rrp5_repeat_hs6_sc5 20.2 2.4E+02 0.0052 21.7 5.0 38 310-348 3-40 (70)
No 1
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=100.00 E-value=3.6e-45 Score=372.43 Aligned_cols=250 Identities=18% Similarity=0.259 Sum_probs=224.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHH
Q 009110 189 LNFVRSLSTVLAFAYCLSSLIQQIQKFLTEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGL 268 (543)
Q Consensus 189 ~~~i~~l~~il~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~i~~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi 268 (543)
++++.++ ++++++|++.++++...+....+.+. +.+..+++.+++++++++++++++|..+|++.++++|++|+
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 45577889999888776655444331 22346788999999999999999999999999999999999
Q ss_pred HHHHHHHhchhhhhhhhhheeeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEE
Q 009110 269 GTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRN 348 (543)
Q Consensus 269 ~glalgfAaq~~l~N~~aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N 348 (543)
+|+++|||+|++++|++||++|+++|||++||||++ +|.+|+|++|++|+ |++|++||+.++|||+.+.++.|+|
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-CCHHHHHHHHHHHHHHHHcCCCccccccccEEEEEeeCCCCCeEEEEEEEEEecCChhhHHH
Q 009110 349 LSQKTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLC 427 (543)
Q Consensus 349 ~sr~~~~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ 427 (543)
||+.+.+|+++.++++| +|+++++++ ++++++++|.+.++|. |.+.+.+++ |+++++++++|+++. ++++
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--ASSINFVVRVWSNSG---DLQN 248 (286)
T ss_pred cCCCCeEEEEEEEEecCCCCHHHHHHH---HHHHHHhCCceecCCC-CEEEEEeee--CceEEEEEEEEEecc---hhHH
Confidence 99988899999999999 799999998 8899999999988764 799999999 899999999999985 4678
Q ss_pred HHHHHHHHHHHHHHHCCCccCCCceEEEEec
Q 009110 428 VKEAILLDLLHVISHHRARMATPIRTVQKIY 458 (543)
Q Consensus 428 ir~~i~~~i~~~l~~~gI~ia~P~~~v~~~~ 458 (543)
++++++++++++|+++||++|||+++++...
T Consensus 249 ~~~~~~~~I~~~f~~~gI~ip~p~~~v~~~~ 279 (286)
T PRK10334 249 VYWDVLERIKREFDAAGISFPYPQMDVNFKR 279 (286)
T ss_pred HHHHHHHHHHHHHHHCCCcCCCCCeEEEecc
Confidence 9999999999999999999999999998865
No 2
>PRK11465 putative mechanosensitive channel protein; Provisional
Probab=100.00 E-value=2.2e-42 Score=384.22 Aligned_cols=298 Identities=13% Similarity=0.152 Sum_probs=230.0
Q ss_pred cccccccccchHHHHHHhHHHHHHHHHHHHHHHhhccCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Q 009110 137 RTDGSWKRSRTHYILTSYLQPLLLWTGVTLICRELDPLVLPSETSQGVKQRVLNFVRSLSTVLAFAYCLSSLIQQ-IQKF 215 (543)
Q Consensus 137 r~~~~~~~s~~~~il~~~~~Pl~l~l~~i~i~~al~~~~l~~~~~~~v~~~l~~~i~~l~~il~~~~~l~~~i~~-~~~~ 215 (543)
|+.+.|++ .+++.++ |+.+++.+++++.++..+.++..........+...+..++++++++++.+.+.+. +.++
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 44566764 5666666 9888887777777776544432110001112222222333333333333333332 2333
Q ss_pred HHhhc--cCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhchhhhhhhhhheeeeec
Q 009110 216 LTEAN--DADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSVMIHAT 293 (543)
Q Consensus 216 ~~~~~--~~~~~~~~~~~i~~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi~glalgfAaq~~l~N~~aGi~I~~~ 293 (543)
+.++. +..++....+..+++++++++++++++++++|+.+|+++++++|++|++|+++|||+|++++|++||++|+++
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 1112234457889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccCCCceEEEEEEEecc-CCHHHHH
Q 009110 294 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-LDVHKVN 372 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~v~y-td~e~v~ 372 (543)
|||++||||++ +|++|+||+|++|+ |++|++||+.++|||+++.+ ++||||. ..+..++++|+| +|+|+++
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 557788999999 8999999
Q ss_pred HHHHHHHHHHHcCCCc----cccccccEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCccC
Q 009110 373 SIVADMRKVLAKNPQV----EQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARMA 448 (543)
Q Consensus 373 ~l~~~l~e~l~~~p~i----~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~ia 448 (543)
++++++.+.+.++|++ .+++ +.+.+.+++ |+++++++++|+++ .++|++++++++++++.|+++||++|
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 9988877777777764 3333 357889998 88999999999976 56899999999999999999999987
Q ss_pred CCceEE
Q 009110 449 TPIRTV 454 (543)
Q Consensus 449 ~P~~~v 454 (543)
+|+..+
T Consensus 717 ~~tv~v 722 (741)
T PRK11465 717 VQTYQV 722 (741)
T ss_pred CCceEe
Confidence 666554
No 3
>PRK11281 hypothetical protein; Provisional
Probab=100.00 E-value=3.4e-40 Score=382.19 Aligned_cols=253 Identities=19% Similarity=0.208 Sum_probs=223.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHH
Q 009110 188 VLNFVRSLSTVLAFAYCLSSLIQQIQKFL-TEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAG 266 (543)
Q Consensus 188 l~~~i~~l~~il~~~~~l~~~i~~~~~~~-~~~~~~~~~~~~~~~i~~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~ 266 (543)
+.+++.++ ++++++|++.+.+..+.+.+ .++.+.++ .....+.+++++++++++++++++.+|++.+++.+.+
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 34445444 45577888888888765433 33322111 1246678999999999999999999999999999999
Q ss_pred HHHHHHHHHhchhhhhhhhhheeeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeE
Q 009110 267 GLGTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVV 346 (543)
Q Consensus 267 Gi~glalgfAaq~~l~N~~aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I 346 (543)
|++|+++|||+|++++||+||++|+++|||+|||+|++ +|.+|+|++|++|+ |+++++||+.++|||+.+.++.|
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 EEccCCCc-eEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccccEEEEEeeCCCCCeEEEEEEEEEecCChhh
Q 009110 347 RNLSQKTH-WRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEE 424 (543)
Q Consensus 347 ~N~sr~~~-~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~ 424 (543)
+|||.++. +|+.++++|+| +|+++++++ +.++++++|.+.++|. |.|++.++| |+++++++++|+++. .+
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 99999874 78999999999 899999998 8899999999998875 799999999 899999999999864 57
Q ss_pred HHHHHHHHHHHHHHHHHHCCCccCCCceEEEEecC
Q 009110 425 YLCVKEAILLDLLHVISHHRARMATPIRTVQKIYS 459 (543)
Q Consensus 425 ~~~ir~~i~~~i~~~l~~~gI~ia~P~~~v~~~~~ 459 (543)
++.++++++.+|++.|+++||++|||++++++...
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=1.7e-39 Score=374.97 Aligned_cols=251 Identities=16% Similarity=0.149 Sum_probs=222.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHH
Q 009110 190 NFVRSLSTVLAFAYCLSSLIQQIQK-FLTEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGL 268 (543)
Q Consensus 190 ~~i~~l~~il~~~~~l~~~i~~~~~-~~~~~~~~~~~~~~~~~i~~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi 268 (543)
+++.++ ++++++|++.+.+..+.+ .+.++.+.++ ....++.+++++++++++++++++.+|++.+++.+.+|+
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 455677777777777654 3434433222 235778999999999999999999999999999999999
Q ss_pred HHHHHHHhchhhhhhhhhheeeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEE
Q 009110 269 GTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRN 348 (543)
Q Consensus 269 ~glalgfAaq~~l~N~~aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N 348 (543)
+|+++|||+|++++||+||++|+++|||++||+|++ +|.+|+|++|++|+ |+++++||+.++|||+.+.++.|+|
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-CCHHHHHHHHHHHHHHHHcCCCccccccccEEEEEeeCCCCCeEEEEEEEEEecCChhhHH
Q 009110 349 LSQKTH-WRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYL 426 (543)
Q Consensus 349 ~sr~~~-~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~ 426 (543)
||+++. +|+.+.++|+| +|+++++++ +.++++++|.+.++|. |.|++.+++ ++++++++++|++.. .+++
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 789999999999753 5789
Q ss_pred HHHHHHHHHHHHHHHHCCCccCCCceEEEEecC
Q 009110 427 CVKEAILLDLLHVISHHRARMATPIRTVQKIYS 459 (543)
Q Consensus 427 ~ir~~i~~~i~~~l~~~gI~ia~P~~~v~~~~~ 459 (543)
.++++++.+|++.|+++||++|||++++|+...
T Consensus 1056 ~v~~el~~~I~~~F~~~GIeIPfPq~~v~i~~~ 1088 (1109)
T PRK10929 1056 PLRHEIHQLILAGFREHGIDMPFPPFQMRLESL 1088 (1109)
T ss_pred HHHHHHHHHHHHHHHHCCCcCCCCCeEEEeecC
Confidence 999999999999999999999999999998864
No 5
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=100.00 E-value=3.2e-36 Score=332.19 Aligned_cols=244 Identities=20% Similarity=0.221 Sum_probs=222.3
Q ss_pred HHHHHHHHHHHHHHHHH-HHHHhhccCCchhhhhchHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHH
Q 009110 197 TVLAFAYCLSSLIQQIQ-KFLTEANDADSTDARNMGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTL 275 (543)
Q Consensus 197 ~il~~~~~l~~~i~~~~-~~~~~~~~~~~~~~~~~~i~~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi~glalgf 275 (543)
+++++++++.+.+.... ..+..+.+.+.+. -..+.+++.+.+..+++++.++..|+|.+++-..+|+.|+++||
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 44566777777777764 4677776644433 35688899999999999999999999999999999999999999
Q ss_pred hchhhhhhhhhheeeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccCCC-c
Q 009110 276 AGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKT-H 354 (543)
Q Consensus 276 Aaq~~l~N~~aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr~~-~ 354 (543)
+.|++++||+||++|+++|||||||||++ |+.+|+|.+|+.|+ |.|+++||+-++|||+.|.++.|.|||.++ .
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 88999999999999 999999999999999999999999999987 6
Q ss_pred eEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccccEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHH
Q 009110 355 WRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAIL 433 (543)
Q Consensus 355 ~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~ 433 (543)
.|+++.++++| +|+++++++ +-|+.++||.+.++|. |.|++.+|+ ++++++++++|+..... ...++++++
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 9999999999999986 799999999 89999999999998753 445999999
Q ss_pred HHHHHHHHHCCCccCCCceEEEEec
Q 009110 434 LDLLHVISHHRARMATPIRTVQKIY 458 (543)
Q Consensus 434 ~~i~~~l~~~gI~ia~P~~~v~~~~ 458 (543)
..|.+.|+||||++|||++++++..
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=1.3e-36 Score=295.43 Aligned_cols=203 Identities=24% Similarity=0.419 Sum_probs=170.0
Q ss_pred HHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhchhhhhhhhhheeeeecCCccCCcEEEEeecCcceEEEEE
Q 009110 237 KAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGYEVSGTVE 316 (543)
Q Consensus 237 ~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi~glalgfAaq~~l~N~~aGi~I~~~rpfrVGD~I~i~i~g~~~~G~Ve 316 (543)
+++.+++++++++.++..+|.+.+++++++|++|+++|||+|++++|++||++|++++||++||||++ ++..|+|+
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 57889999999999999999999999999999999999999999999999999999999999999999 78999999
Q ss_pred EEcceeEEEEEeCCCcEEEEeCcccccCeEEEccC-CCceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCCccccccc
Q 009110 317 HVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQ-KTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQQRLH 394 (543)
Q Consensus 317 eIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr-~~~~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~i~~~~~~ 394 (543)
+|+|++ |++|++||+.++|||+++.+++|.|+|+ ++.++..+.+.++| +|.++++++.+++.+.++++|.+...+ .
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 798999999999999999999887754 3
Q ss_pred cEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCcc
Q 009110 395 RRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARM 447 (543)
Q Consensus 395 p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~i 447 (543)
|.+.+..++ ++++.++++|+++..++.+++++|++++.++++.+++|||+|
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 789999999999997888999999999999999999999985
No 7
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=100.00 E-value=4.2e-34 Score=294.12 Aligned_cols=208 Identities=23% Similarity=0.392 Sum_probs=193.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhchhhhhhhhhheeeeecCCccCCcEEEEeecCc-ceE
Q 009110 234 FAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSVMIHATQPFVINEWIQTKIQGY-EVS 312 (543)
Q Consensus 234 ~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi~glalgfAaq~~l~N~~aGi~I~~~rpfrVGD~I~i~i~g~-~~~ 312 (543)
++.++.++++++++++.++..+|++.+++++++|++|+++|||+|++++|+++|+++++++||++||||++ + +.+
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 009110 313 GTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQVEQ- 390 (543)
Q Consensus 313 G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~i~~- 390 (543)
|+|++|++++ |++|++||+.+++|||.+.++.|+|+|++..+++.+.++++| +|.++++++ +++.++..+....
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 999999999999999999999999999998888999999999 899999999 5555555555542
Q ss_pred cccccEEEEEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCccCCCceEEE
Q 009110 391 QRLHRRVFLENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARMATPIRTVQ 455 (543)
Q Consensus 391 ~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~ia~P~~~v~ 455 (543)
++ +|.+++.+++ ++++++.+++|+++.+ ++..+++++..+++.++++||++|+|++.++
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 3689999999 8899999999999854 8999999999999999999999999999997
No 8
>KOG4629 consensus Predicted mechanosensitive ion channel [Cell wall/membrane/envelope biogenesis]
Probab=99.82 E-value=6.1e-20 Score=203.62 Aligned_cols=222 Identities=16% Similarity=0.190 Sum_probs=192.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHhchhhhhhhhhhe-eeeecCCccCCcEEEEeecC
Q 009110 230 MGFNFAGKAVYTAVWVAAVSLFMELLGFSTQRWLTAGGLGTVLLTLAGREIFTNFLSSV-MIHATQPFVINEWIQTKIQG 308 (543)
Q Consensus 230 ~~i~~l~~i~~~iv~vi~~~~~L~~lgi~~~~lla~~Gi~glalgfAaq~~l~N~~aGi-~I~~~rpfrVGD~I~i~i~g 308 (543)
+.++-+.+++.+++.++++++.+-.+|++.+.+++..+..-+++.|.+.+++++++.++ +++..+||++||+|.+
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 56888899999999999999999999999999999988888999999999999999875 5777899999999999
Q ss_pred cceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccCCCceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCC
Q 009110 309 YEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQ 387 (543)
Q Consensus 309 ~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~ 387 (543)
+|+.-.|||+++.+ |....+||+.+++||+.+.+++|.|+.|++.+...+++.++. |+.+|++.+.+.+.++++++|+
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 67999999999999 999999999999999999999999999999999999999999 8999999999999999999998
Q ss_pred ccccccccEEEEEeeCCC-CCeEEEEEEEEEecCChhhHHHHHHHHHHHHHHHHHHCCCccCCCceEEEEec
Q 009110 388 VEQQRLHRRVFLENINPE-SQSLNILVSCFVKTSRFEEYLCVKEAILLDLLHVISHHRARMATPIRTVQKIY 458 (543)
Q Consensus 388 i~~~~~~p~v~v~~~~~~-~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~~l~~~gI~ia~P~~~v~~~~ 458 (543)
..... +.+.+.++.+. +-.+.+.+..+.+.+|..++|..|.++...+.+.+++.||+.-++++++.+.+
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 66322 35667666532 23445555666667788899999999999999999999999866666554443
No 9
>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=71.56 E-value=12 Score=31.40 Aligned_cols=38 Identities=16% Similarity=0.158 Sum_probs=29.9
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEe
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIP 337 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IP 337 (543)
.++||+|.. .+|..|+|.+++=-+ ..++..+|..+.+-
T Consensus 38 L~~Gd~VvT---~gGi~G~V~~i~d~~-v~vei~~g~~i~~~ 75 (84)
T TIGR00739 38 LKKGDKVLT---IGGIIGTVTKIAENT-IVIELNDNTEITFS 75 (84)
T ss_pred CCCCCEEEE---CCCeEEEEEEEeCCE-EEEEECCCeEEEEE
Confidence 789999997 267999999998766 77777777665543
No 10
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=70.78 E-value=11 Score=32.97 Aligned_cols=41 Identities=20% Similarity=0.166 Sum_probs=32.0
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcc
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHK 340 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~ 340 (543)
.++||+|.. .+|..|+|.+|+=-+ ..++..+|..+.+=-+.
T Consensus 53 Lk~Gd~VvT---~gGi~G~Vv~i~~~~-v~lei~~g~~i~~~r~a 93 (106)
T PRK05585 53 LAKGDEVVT---NGGIIGKVTKVSEDF-VIIELNDDTEIKIQKSA 93 (106)
T ss_pred cCCCCEEEE---CCCeEEEEEEEeCCE-EEEEECCCeEEEEEhHH
Confidence 799999987 267999999998765 88888888666654433
No 11
>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=61.26 E-value=14 Score=28.79 Aligned_cols=28 Identities=29% Similarity=0.230 Sum_probs=22.0
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEE
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR 327 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir 327 (543)
-++||+|+++ ++..|+|+.+.=.| +.+.
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 56999999998766 5554
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=60.66 E-value=15 Score=23.28 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=16.9
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEc
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVG 319 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIg 319 (543)
+|++||.|.| ++| .+..|.|.++.
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 332 34567777764
No 13
>PF14545 DBB: Dof, BCAP, and BANK (DBB) motif,
Probab=60.31 E-value=53 Score=30.39 Aligned_cols=82 Identities=10% Similarity=0.065 Sum_probs=47.6
Q ss_pred heeeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccCCCceEEEEEEEecc-
Q 009110 287 SVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAISH- 365 (543)
Q Consensus 287 Gi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~v~y- 365 (543)
-++|++.+|+.-||++++.+..++..-......|+...+ -.+..|+--+.-.-..|.+-.....+.-.-.+.|
T Consensus 14 ~vfIiL~~~l~~~~~~eVef~~~n~~~~~~~~~~~N~yt------~~~~aPd~~~~pag~V~v~v~~~g~~~~~~~ikyy 87 (142)
T PF14545_consen 14 EVFIILRDPLDEEDTVEVEFESNNKPIRRVPAKWENPYT------LQFKAPDFCLEPAGSVNVRVYCDGVSLGTRQIKYY 87 (142)
T ss_pred EEEEEEeCCCCCCCeEEEEEEeCCCeeEeccceEECCEE------EEEECchhcCCCCceEEEEEEECCEEEEEEeEEEE
Confidence 378899999999999999665443332233334432111 1245666644444444444333333344556677
Q ss_pred CCHHHHHHH
Q 009110 366 LDVHKVNSI 374 (543)
Q Consensus 366 td~e~v~~l 374 (543)
++.++++++
T Consensus 88 s~~~el~~l 96 (142)
T PF14545_consen 88 SRMRELEQL 96 (142)
T ss_pred ecHHHHHHH
Confidence 888888876
No 14
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=57.88 E-value=31 Score=30.51 Aligned_cols=37 Identities=5% Similarity=-0.093 Sum_probs=28.8
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEE
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHI 336 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~I 336 (543)
.++||.|.. .+|..|+|.+|+=-+ ..++..+|..+.+
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 799999987 267999999998655 7777766665554
No 15
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=54.08 E-value=8 Score=29.64 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=11.5
Q ss_pred cCCccCCcEEEEeecCcceEEEEEEEcc
Q 009110 293 TQPFVINEWIQTKIQGYEVSGTVEHVGW 320 (543)
Q Consensus 293 ~rpfrVGD~I~i~i~g~~~~G~VeeIgl 320 (543)
..||+.||+|++ -+..|+---|.|
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 359999999999 556676544433
No 16
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=53.80 E-value=1.7e+02 Score=30.75 Aligned_cols=33 Identities=15% Similarity=0.110 Sum_probs=24.1
Q ss_pred HhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009110 99 TLRGNPVILRLIPAAALVAFAAWGLVPLVRLGR 131 (543)
Q Consensus 99 ~~~~~~~~~~ll~al~i~~~a~~~~~~l~~~~~ 131 (543)
.+.+++.+..++.|+.+++++.|+.+.+..+.+
T Consensus 35 ~~~~n~~v~~ligai~~~li~~~~~~~~~~~~~ 67 (356)
T COG4956 35 AFLNNEYVDALIGAIIFFLISFWFGKYVLNWLK 67 (356)
T ss_pred hhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466677777788888887887787777666653
No 17
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.13 E-value=20 Score=28.61 Aligned_cols=27 Identities=30% Similarity=0.303 Sum_probs=21.9
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEE
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTII 326 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~i 326 (543)
-.|||.|+++ +|..|.||+++=.| +.+
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 57999999998877 443
No 18
>COG0053 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=49.02 E-value=3.3e+02 Score=28.30 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=27.7
Q ss_pred ceEEEEEEEecc-CCHHHHHHHHHHHHHHHHcCCC
Q 009110 354 HWRIKTYLAISH-LDVHKVNSIVADMRKVLAKNPQ 387 (543)
Q Consensus 354 ~~ri~~~l~v~y-td~e~v~~l~~~l~e~l~~~p~ 387 (543)
...+++.+.++. -+.++..++.+++++.+++...
T Consensus 244 ~~~id~~i~v~~~ls~~eah~I~~~ie~~i~~~~~ 278 (304)
T COG0053 244 RIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEFP 278 (304)
T ss_pred eEEEEEEEEECCCCChHHHHHHHHHHHHHHHHhcC
Confidence 345678888988 6999999999999998887654
No 19
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=48.02 E-value=18 Score=27.67 Aligned_cols=23 Identities=35% Similarity=0.274 Sum_probs=18.3
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcc
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGW 320 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl 320 (543)
|++||.|+.| .||...+|++++=
T Consensus 1 f~~GDvV~LK--SGGp~MTV~~v~~ 23 (53)
T PF09926_consen 1 FKIGDVVQLK--SGGPRMTVTEVGP 23 (53)
T ss_pred CCCCCEEEEc--cCCCCeEEEEccc
Confidence 7899999984 3468899998754
No 20
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=47.96 E-value=50 Score=29.37 Aligned_cols=41 Identities=15% Similarity=0.015 Sum_probs=28.0
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcce-eEEEEEeCCCcEEEEeCcc
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWW-SPTIIRGDDREAVHIPNHK 340 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~-sTT~ir~~d~~~v~IPNs~ 340 (543)
.++||.|.. .||..|+|.+|+-- .+..++. +|..+.+--+.
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 689999987 26799999999752 1255665 66555554433
No 21
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=47.89 E-value=52 Score=28.44 Aligned_cols=42 Identities=19% Similarity=0.118 Sum_probs=31.8
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCccc
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKF 341 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l 341 (543)
.+.||.|.. .+|..|+|.+|+=.. ..+...|+..+.+--+.+
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 689999987 257999999999876 677766777766644443
No 22
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=47.55 E-value=43 Score=27.37 Aligned_cols=31 Identities=10% Similarity=0.077 Sum_probs=22.0
Q ss_pred ecCCccCCcEEEEe-ecCcceEEEEEEEccee
Q 009110 292 ATQPFVINEWIQTK-IQGYEVSGTVEHVGWWS 322 (543)
Q Consensus 292 ~~rpfrVGD~I~i~-i~g~~~~G~VeeIgl~s 322 (543)
-+|.|+|||.+... .++++..|+......++
T Consensus 25 NDRdf~VGD~L~L~E~~~~~YTGr~~~~~Ity 56 (72)
T PF12961_consen 25 NDRDFQVGDILVLREWDNGEYTGREIEAEITY 56 (72)
T ss_pred cCCCCCCCCEEEEEEecCCCccccEEEEEEEE
Confidence 46799999999883 34456677766666555
No 23
>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=44.31 E-value=35 Score=22.91 Aligned_cols=22 Identities=14% Similarity=0.329 Sum_probs=16.9
Q ss_pred CCcEEEEeecC--cceEEEEEEEcc
Q 009110 298 INEWIQTKIQG--YEVSGTVEHVGW 320 (543)
Q Consensus 298 VGD~I~i~i~g--~~~~G~VeeIgl 320 (543)
+||+|.+ ++| .|..|.|.+|.-
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 5999998 443 468899998864
No 24
>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=42.48 E-value=64 Score=24.29 Aligned_cols=29 Identities=14% Similarity=0.237 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 009110 108 RLIPAAALVAFAAWGLVPLVRLGRTIFLN 136 (543)
Q Consensus 108 ~ll~al~i~~~a~~~~~~l~~~~~~~~~~ 136 (543)
+++.|++++++++++.+++.+.+.|.+.+
T Consensus 17 ~iv~AilIl~vG~~va~~v~~~~~~~l~~ 45 (53)
T PF05552_consen 17 NIVGAILILIVGWWVAKFVRKLVRRLLEK 45 (53)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57888888888888877777777665543
No 25
>PF12794 MscS_TM: Mechanosensitive ion channel inner membrane domain 1
Probab=41.25 E-value=4.5e+02 Score=27.70 Aligned_cols=29 Identities=14% Similarity=0.210 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHhCCchHH
Q 009110 233 NFAGKAVYTAVWVAAV-SLFMELLGFSTQR 261 (543)
Q Consensus 233 ~~l~~i~~~iv~vi~~-~~~L~~lgi~~~~ 261 (543)
+.++++...++.++-+ ++++..+|+--++
T Consensus 194 ~~~~~l~~~~li~~Pl~li~la~~GY~yTA 223 (340)
T PF12794_consen 194 HRLRYLWWPLLILAPLALIVLALLGYYYTA 223 (340)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 4455555544444333 3445566775443
No 26
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=41.09 E-value=1.3e+02 Score=28.16 Aligned_cols=17 Identities=12% Similarity=0.276 Sum_probs=14.6
Q ss_pred eeeeecCCccCCcEEEE
Q 009110 288 VMIHATQPFVINEWIQT 304 (543)
Q Consensus 288 i~I~~~rpfrVGD~I~i 304 (543)
--+-+.+|.++||.+.+
T Consensus 89 q~~~f~~PV~~GDtL~~ 105 (159)
T PRK13692 89 QVLKFEKPIVAGDKLYC 105 (159)
T ss_pred eEEEEeCCccCCCEEEE
Confidence 45778899999999986
No 27
>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=40.11 E-value=2.5e+02 Score=29.14 Aligned_cols=142 Identities=11% Similarity=0.065 Sum_probs=83.5
Q ss_pred hheeee-ecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccCCCceEEEEEEEec
Q 009110 286 SSVMIH-ATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQKTHWRIKTYLAIS 364 (543)
Q Consensus 286 aGi~I~-~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr~~~~ri~~~l~v~ 364 (543)
.|.+|- ...|+-.|=+|.+ +...|.-.+|++.. ..++-+.|+.+.-.+ =.+.....+.|.+.--+++.=.=+
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 778876 5679999999998 33345557899988 999999999998865 112345678888766665544455
Q ss_pred cCCHHHHHHHHHHHHHHHHcCCCcccccc--ccEEE----EEeeCCCCCeEEEEEEEEEecCChhhHHHHHHHHHHHHHH
Q 009110 365 HLDVHKVNSIVADMRKVLAKNPQVEQQRL--HRRVF----LENINPESQSLNILVSCFVKTSRFEEYLCVKEAILLDLLH 438 (543)
Q Consensus 365 ytd~e~v~~l~~~l~e~l~~~p~i~~~~~--~p~v~----v~~~~~~~~~l~i~V~~~v~~~~~~~~~~ir~~i~~~i~~ 438 (543)
..+.+++.+.+++++..++...-.+.... .-|+- +..-+... ..-++-+++- ..+..++..+..++.+
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 IRSPEEAAAFLKKLRRILRYLGVSDGNMEEGSLRCDVNVSVRPKGEEK----FGTRVEIKNL--NSFRFIEKAIEYEIER 231 (289)
T ss_dssp B-SHHHHHHHHHHHHHHHHHHTSB--SGGGTSEEEEEEEEECETTSSS----TS-EEEEEEE---SHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHhcCcccCccccCcEEeeceeeecCCCCCC----CcceEEEecc--cCHHHHHHHHHHHHHH
Confidence 67999999999999999886544333321 11222 22222111 2233444543 3466666777666665
Q ss_pred HH
Q 009110 439 VI 440 (543)
Q Consensus 439 ~l 440 (543)
..
T Consensus 232 Q~ 233 (289)
T PF02934_consen 232 QI 233 (289)
T ss_dssp HH
T ss_pred HH
Confidence 44
No 28
>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=39.78 E-value=91 Score=28.21 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=14.2
Q ss_pred eeeecCCccCCcEEEE
Q 009110 289 MIHATQPFVINEWIQT 304 (543)
Q Consensus 289 ~I~~~rpfrVGD~I~i 304 (543)
-+-+.+|..+||.|.+
T Consensus 82 ~~rf~~PV~~GDtl~~ 97 (142)
T cd03452 82 NLRFLEPVYPGDTIQV 97 (142)
T ss_pred eEEECCCCCCCCEEEE
Confidence 5678999999999986
No 29
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=38.62 E-value=95 Score=28.82 Aligned_cols=47 Identities=11% Similarity=0.058 Sum_probs=30.0
Q ss_pred CCccCCcEEEEeecC--cceEEEEEEEccee-EEEEEeCC-CcE--EEEeCccc
Q 009110 294 QPFVINEWIQTKIQG--YEVSGTVEHVGWWS-PTIIRGDD-REA--VHIPNHKF 341 (543)
Q Consensus 294 rpfrVGD~I~i~i~g--~~~~G~VeeIgl~s-TT~ir~~d-~~~--v~IPNs~l 341 (543)
.+|++||+|++ .+| .|..|.|++++-.. ...+...+ ... +++|++.+
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 443 35789999985322 13333332 323 77887776
No 30
>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=38.03 E-value=1.6e+02 Score=22.93 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=32.2
Q ss_pred eEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEccC
Q 009110 311 VSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNLSQ 351 (543)
Q Consensus 311 ~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~sr 351 (543)
..|+|.++.=.. ..+.-.++..-.+|.+.+......+.+.
T Consensus 8 v~g~V~~v~~~g-~~V~l~~~~~g~ip~~~l~~~~~~~~~~ 47 (74)
T PF00575_consen 8 VEGKVTSVEDFG-VFVDLGNGIEGFIPISELSDDRIDDPSE 47 (74)
T ss_dssp EEEEEEEEETTE-EEEEESTSSEEEEEGGGSSSSEESSSHG
T ss_pred EEEEEEEEECCE-EEEEECCcEEEEEEeehhcCcccccccc
Confidence 358999999877 8888878999999999999875555444
No 31
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=37.50 E-value=41 Score=27.67 Aligned_cols=27 Identities=19% Similarity=0.086 Sum_probs=20.6
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEccee
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVGWWS 322 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIgl~s 322 (543)
+++.||.|.+ +.| .|..|+|.+|.-..
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 543 46789999886543
No 32
>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=37.27 E-value=11 Score=31.39 Aligned_cols=37 Identities=11% Similarity=0.040 Sum_probs=0.0
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEE
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHI 336 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~I 336 (543)
.++||+|.. . +|..|+|.+++=-+ ..++..+|..+.+
T Consensus 37 Lk~Gd~VvT--~-gGi~G~V~~i~~~~-v~lei~~g~~i~v 73 (82)
T PF02699_consen 37 LKPGDEVVT--I-GGIYGTVVEIDDDT-VVLEIAPGVEITV 73 (82)
T ss_dssp -----------------------------------------
T ss_pred CCCCCEEEE--C-CcEEEEEEEEeCCE-EEEEECCCeEEEE
Confidence 789999987 2 57999999998776 8888887765554
No 33
>PRK10694 acyl-CoA esterase; Provisional
Probab=36.16 E-value=57 Score=29.60 Aligned_cols=31 Identities=13% Similarity=0.099 Sum_probs=24.8
Q ss_pred eeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEE
Q 009110 289 MIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR 327 (543)
Q Consensus 289 ~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir 327 (543)
-+-|-+|.++||.|++ .++|+.+|=.| ..++
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 4678899999999986 58888888877 5544
No 34
>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=36.16 E-value=43 Score=27.58 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=21.5
Q ss_pred eeecC--CccCCcEEEEeec-CcceEEEEEEEcce
Q 009110 290 IHATQ--PFVINEWIQTKIQ-GYEVSGTVEHVGWW 321 (543)
Q Consensus 290 I~~~r--pfrVGD~I~i~i~-g~~~~G~VeeIgl~ 321 (543)
+..+. +.++||+|.++.+ +..+-|.|++|...
T Consensus 15 f~~~~~~~v~~GeyV~i~~~~~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 15 FIVEPSKDVRVGEYVVIEYDDGEKVLGMVTSISRG 49 (91)
T ss_dssp EEEEE-TT-BTTEEEEES----TTEEEEEEEEES-
T ss_pred EEEeCCCCCCcCeEEEEEEechhhhhhhhheeEEc
Confidence 34444 8999999999655 56788999988773
No 35
>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=35.10 E-value=75 Score=23.89 Aligned_cols=35 Identities=14% Similarity=0.339 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 009110 186 QRVLNFVRSLSTVLAFAYCLSSLIQQIQKFLTEAND 221 (543)
Q Consensus 186 ~~l~~~i~~l~~il~~~~~l~~~i~~~~~~~~~~~~ 221 (543)
+++++++.++ ++++++|++.++++...+...++.+
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 4455555455 4668899999999888777766665
No 36
>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=34.83 E-value=71 Score=24.72 Aligned_cols=28 Identities=11% Similarity=0.213 Sum_probs=19.2
Q ss_pred CCccCCcEEEEeecCcceEEEEEEEccee
Q 009110 294 QPFVINEWIQTKIQGYEVSGTVEHVGWWS 322 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~~~~G~VeeIgl~s 322 (543)
...-+||||.+..++ +..|.|+++-=|.
T Consensus 36 ~~~~VGD~V~~~~~~-~~~~~I~~vl~R~ 63 (68)
T cd04466 36 NPPAVGDRVEFEPED-DGEGVIEEILPRK 63 (68)
T ss_pred CCCCCCcEEEEEECC-CCcEEEEEEeccc
Confidence 346899999874332 3457888876665
No 37
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=34.58 E-value=5.3e+02 Score=26.53 Aligned_cols=27 Identities=7% Similarity=0.062 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009110 108 RLIPAAALVAFAAWGLVPLVRLGRTIF 134 (543)
Q Consensus 108 ~ll~al~i~~~a~~~~~~l~~~~~~~~ 134 (543)
+++.+++++++++++.+++.+.+.+.+
T Consensus 30 ~i~~al~il~~~~~~~~~i~~~~~~~~ 56 (286)
T PRK10334 30 NIVAALAIIIVGLIIARMISNAVNRLM 56 (286)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355555555555555555544444433
No 38
>PRK10263 DNA translocase FtsK; Provisional
Probab=33.81 E-value=6.4e+02 Score=31.79 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=5.4
Q ss_pred hhhHHHhhh
Q 009110 529 LDWYQLLTT 537 (543)
Q Consensus 529 ~~~~~~~~~ 537 (543)
-+|||-...
T Consensus 524 ~~~~~~~~~ 532 (1355)
T PRK10263 524 AAWYQPIPE 532 (1355)
T ss_pred cccccCCCc
Confidence 478776543
No 39
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=33.14 E-value=73 Score=27.47 Aligned_cols=38 Identities=18% Similarity=0.160 Sum_probs=28.3
Q ss_pred CCccCCcEEEEeecCc-----------ceEEEEEEEcceeEEEEEeCCCc
Q 009110 294 QPFVINEWIQTKIQGY-----------EVSGTVEHVGWWSPTIIRGDDRE 332 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~-----------~~~G~VeeIgl~sTT~ir~~d~~ 332 (543)
+-|++||.|.|+||.- |-.|+|+...=++ -.+...||.
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 4599999999976642 4578898888777 666666654
No 40
>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=32.96 E-value=4.2e+02 Score=28.75 Aligned_cols=80 Identities=13% Similarity=0.220 Sum_probs=56.6
Q ss_pred EEEEEeccCCHHHHHHHHHHHHHHHHcCC------CccccccccEEEEEeeCCCCCeEEEEEEEEEec---CChhhHHHH
Q 009110 358 KTYLAISHLDVHKVNSIVADMRKVLAKNP------QVEQQRLHRRVFLENINPESQSLNILVSCFVKT---SRFEEYLCV 428 (543)
Q Consensus 358 ~~~l~v~ytd~e~v~~l~~~l~e~l~~~p------~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~---~~~~~~~~i 428 (543)
++.++|.|.|....++++-++++.+.+.. .+=. -+.+-.+-. +..++++|-|-.-+ .+-++|.+.
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 47889999999999999999999998753 2211 133333332 34566666554332 256799999
Q ss_pred HHHHHHHHHHHHHHC
Q 009110 429 KEAILLDLLHVISHH 443 (543)
Q Consensus 429 r~~i~~~i~~~l~~~ 443 (543)
++++.+.+.+...+.
T Consensus 230 k~~v~~~v~~~a~~~ 244 (396)
T PF01941_consen 230 KEEVKEEVEDYAAKY 244 (396)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999988775
No 41
>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=32.64 E-value=1e+02 Score=28.04 Aligned_cols=25 Identities=16% Similarity=0.215 Sum_probs=19.4
Q ss_pred CCccCCcEEEEeecC--cceEEEEEEEc
Q 009110 294 QPFVINEWIQTKIQG--YEVSGTVEHVG 319 (543)
Q Consensus 294 rpfrVGD~I~i~i~g--~~~~G~VeeIg 319 (543)
..|++||+|+| ++| .|..|.|+++.
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 34999999999 443 36788999885
No 42
>PF13452 MaoC_dehydrat_N: N-terminal half of MaoC dehydratase; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1S9C_K 3OML_A 3KHP_A.
Probab=32.54 E-value=1.1e+02 Score=26.98 Aligned_cols=25 Identities=8% Similarity=0.042 Sum_probs=17.9
Q ss_pred hhhhhhhheeeeecCCccCCcEEEE
Q 009110 280 IFTNFLSSVMIHATQPFVINEWIQT 304 (543)
Q Consensus 280 ~l~N~~aGi~I~~~rpfrVGD~I~i 304 (543)
...-+-++--+-+-+|.++||.+.+
T Consensus 72 ~~~~vh~~~~~~~h~Pl~~Gd~l~~ 96 (132)
T PF13452_consen 72 LTRLVHGEQDIEFHRPLRPGDTLTA 96 (132)
T ss_dssp GGGEEEEEEEEEESS--BSSEEEEE
T ss_pred hhhEEecCcEEEEeCCCCCCCEEEE
Confidence 3444456777889999999999997
No 43
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=32.43 E-value=55 Score=27.41 Aligned_cols=27 Identities=22% Similarity=0.136 Sum_probs=20.6
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEccee
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVGWWS 322 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIgl~s 322 (543)
+++.||.|++ +.| .|..|.|.+|.--.
T Consensus 8 ~I~~GD~V~V-i~G~dKGK~G~V~~V~~~~ 36 (83)
T CHL00141 8 HVKIGDTVKI-ISGSDKGKIGEVLKIIKKS 36 (83)
T ss_pred cccCCCEEEE-eEcCCCCcEEEEEEEEcCC
Confidence 6899999998 543 46789998886543
No 44
>cd03455 SAV4209 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension.
Probab=30.85 E-value=1.8e+02 Score=25.25 Aligned_cols=43 Identities=14% Similarity=0.135 Sum_probs=27.1
Q ss_pred hhheeeeecCCccCCcEEEEeecCcceEEEEEEEcc----eeEEEEEeCCCcEE
Q 009110 285 LSSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGW----WSPTIIRGDDREAV 334 (543)
Q Consensus 285 ~aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl----~sTT~ir~~d~~~v 334 (543)
+.++-+-+.+|..+||.+.+ .++|.+..- ...+.+++.+|+.+
T Consensus 69 ~~~~~~rf~~pv~~Gdtl~~-------~~~v~~~~~~~~v~~~~~~~nq~G~~v 115 (123)
T cd03455 69 VKSFAFRLGAPLYAGDTLRF-------GGRVTAKRDDEVVTVELWARNSEGDHV 115 (123)
T ss_pred EEEEEEEeeccccCCCEEEE-------EEEEEeeccCcEEEEEEEEEcCCCCEE
Confidence 34556788999999999987 345554321 11255566666643
No 45
>cd03453 SAV4209_like SAV4209_like. Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=30.76 E-value=2.1e+02 Score=25.10 Aligned_cols=18 Identities=17% Similarity=0.257 Sum_probs=14.8
Q ss_pred heeeeecCCccCCcEEEE
Q 009110 287 SVMIHATQPFVINEWIQT 304 (543)
Q Consensus 287 Gi~I~~~rpfrVGD~I~i 304 (543)
+.-+-+.+|..+||.+.+
T Consensus 72 ~~~~rf~~Pv~~Gdtl~~ 89 (127)
T cd03453 72 SFGVRFTKPVPVPDTLTC 89 (127)
T ss_pred EEEEEECCcCcCCCEEEE
Confidence 344678899999999986
No 46
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=30.62 E-value=1.7e+02 Score=31.61 Aligned_cols=80 Identities=13% Similarity=0.271 Sum_probs=55.8
Q ss_pred EEEEEeccCCHHHHHHHHHHHHHHHH------cCCCccccccccEEEEEeeCCCCCeEEEEEEEEEec---CChhhHHHH
Q 009110 358 KTYLAISHLDVHKVNSIVADMRKVLA------KNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKT---SRFEEYLCV 428 (543)
Q Consensus 358 ~~~l~v~ytd~e~v~~l~~~l~e~l~------~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~---~~~~~~~~i 428 (543)
++.++|.|.|....++++-++++.+. ++|.+=.+ +.+-.+-. +..+.++|-+-.-+ .+-++|.+.
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 47889999999999999999999994 44443332 33334432 34566666543332 256799999
Q ss_pred HHHHHHHHHHHHHHC
Q 009110 429 KEAILLDLLHVISHH 443 (543)
Q Consensus 429 r~~i~~~i~~~l~~~ 443 (543)
++++.+.+.+...+.
T Consensus 230 k~~v~~~v~~~a~~~ 244 (399)
T PRK04439 230 KEEVKEKVEDLAQKY 244 (399)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999987654
No 47
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=30.61 E-value=58 Score=25.90 Aligned_cols=42 Identities=24% Similarity=0.506 Sum_probs=17.0
Q ss_pred hhhhhhhee-eeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEE
Q 009110 281 FTNFLSSVM-IHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTII 326 (543)
Q Consensus 281 l~N~~aGi~-I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~i 326 (543)
+.|-.+|-+ +-....|..||+|+ |..|..-.|.| +||.+ |.+
T Consensus 8 v~~~vag~fa~ps~atf~~gdrvr-kksgaawqg~v--vgwy~-t~l 50 (78)
T PF06442_consen 8 VSNPVAGQFAFPSNATFGMGDRVR-KKSGAAWQGQV--VGWYC-TKL 50 (78)
T ss_dssp -------------S-SS-TT-EEE-ESSSS--EEEE--EEEE---SS
T ss_pred cccccccceecccccccccchhhh-hcccccccceE--eEEEe-ccc
Confidence 345555533 44667999999999 45555667887 47877 544
No 48
>PF13726 Na_H_antiport_2: Na+-H+ antiporter family
Probab=30.33 E-value=76 Score=26.95 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhCCch-HHHHHHHHHHHHHHHHhchhhhhhhhhhe
Q 009110 244 WVAAVSLFMELLGFST-QRWLTAGGLGTVLLTLAGREIFTNFLSSV 288 (543)
Q Consensus 244 ~vi~~~~~L~~lgi~~-~~lla~~Gi~glalgfAaq~~l~N~~aGi 288 (543)
+.+.++.+|..+-+|+ -+++.++-++|++-|+...++++-|.+|+
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 3445556666676775 57778888889999999999999888876
No 49
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=30.10 E-value=82 Score=38.25 Aligned_cols=47 Identities=21% Similarity=0.242 Sum_probs=35.9
Q ss_pred CCccCCcEEEEeecC------cceEEEEEEEcceeEEEEEeCCCcEEEEeCccc
Q 009110 294 QPFVINEWIQTKIQG------YEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKF 341 (543)
Q Consensus 294 rpfrVGD~I~i~i~g------~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l 341 (543)
+.|++||+|.+.-++ +|..|+|++|.=.. ..++..||+.+.+|...+
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 35689999998776 778888888888876544
No 50
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=29.30 E-value=8.5e+02 Score=30.23 Aligned_cols=31 Identities=13% Similarity=-0.001 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 009110 107 LRLIPAAALVAFAAWGLVPLVRLGRTIFLNR 137 (543)
Q Consensus 107 ~~ll~al~i~~~a~~~~~~l~~~~~~~~~~r 137 (543)
..++.+++++++++++.+++-+++.+.+.++
T Consensus 834 ~~ll~AllIliv~~~l~r~l~~lle~~l~~~ 864 (1109)
T PRK10929 834 GSVLIAILVFIITTQLVRNLPALLELALLQH 864 (1109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4567777777777777676666665544333
No 51
>cd03441 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.
Probab=29.05 E-value=2.2e+02 Score=24.33 Aligned_cols=20 Identities=15% Similarity=0.214 Sum_probs=16.6
Q ss_pred hhheeeeecCCccCCcEEEE
Q 009110 285 LSSVMIHATQPFVINEWIQT 304 (543)
Q Consensus 285 ~aGi~I~~~rpfrVGD~I~i 304 (543)
++..-+-+.+|..+||.+.+
T Consensus 70 ~~~~~~~f~~Pv~~Gd~l~~ 89 (127)
T cd03441 70 LGSQSVRFLAPVFPGDTLRV 89 (127)
T ss_pred eEEeEEEEeCCcCCCCEEEE
Confidence 34566788999999999987
No 52
>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=28.18 E-value=67 Score=27.88 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=13.9
Q ss_pred CCccCCcEEEEeecCc-----------ceEEEEEEEcce
Q 009110 294 QPFVINEWIQTKIQGY-----------EVSGTVEHVGWW 321 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~-----------~~~G~VeeIgl~ 321 (543)
+.|++||.|.|++++. |-.|+|..++=.
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 5699999999976643 457888866553
No 53
>cd03454 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=28.11 E-value=2.1e+02 Score=25.37 Aligned_cols=16 Identities=6% Similarity=0.109 Sum_probs=14.3
Q ss_pred eeeecCCccCCcEEEE
Q 009110 289 MIHATQPFVINEWIQT 304 (543)
Q Consensus 289 ~I~~~rpfrVGD~I~i 304 (543)
-+-+.+|..+||.+.+
T Consensus 82 ~~~f~~pv~~Gd~l~~ 97 (140)
T cd03454 82 ELRWPRPVRPGDTLSV 97 (140)
T ss_pred eeEeCCCCCCCCEEEE
Confidence 5778999999999987
No 54
>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=28.02 E-value=2e+02 Score=23.10 Aligned_cols=38 Identities=16% Similarity=0.059 Sum_probs=28.2
Q ss_pred eEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEEc
Q 009110 311 VSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRNL 349 (543)
Q Consensus 311 ~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N~ 349 (543)
+.|+|.+|.=.. ..+....+-.=.+|-+.++...+.|.
T Consensus 7 V~g~V~~i~~~G-~fV~l~~~v~G~v~~~~ls~~~~~~~ 44 (74)
T cd05705 7 LRGYVSSVTKQG-VFFRLSSSIVGRVLFQNVTKYFVSDP 44 (74)
T ss_pred EEEEEEEEeCCc-EEEEeCCCCEEEEEHHHccCccccCh
Confidence 347888887655 66666678888889888887776664
No 55
>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=27.94 E-value=1.7e+02 Score=24.71 Aligned_cols=45 Identities=13% Similarity=0.239 Sum_probs=26.2
Q ss_pred CccCCcEEEEeecCcceEEEEEEEcceeE-------EEEEeCCCcEEEEeCcccc
Q 009110 295 PFVINEWIQTKIQGYEVSGTVEHVGWWSP-------TIIRGDDREAVHIPNHKFT 342 (543)
Q Consensus 295 pfrVGD~I~i~i~g~~~~G~VeeIgl~sT-------T~ir~~d~~~v~IPNs~l~ 342 (543)
.|++||+|.- ++.| -|+|++|.-... -.++-.++..++||-....
T Consensus 1 mf~~GD~VVh--~~~G-v~~i~~i~~~~~~~~~~~yy~L~~~~~~~i~vPv~~~~ 52 (98)
T PF02559_consen 1 MFKIGDYVVH--PNHG-VGRIEGIEEIEFGGEKQEYYVLEYADDDTIYVPVDNAD 52 (98)
T ss_dssp T--TTSEEEE--TTTE-EEEEEEEEEEECTTEEEEEEEEEECCCEEEEEECCCGG
T ss_pred CCCCCCEEEE--CCCc-eEEEEEEEEEeeCCeeEEEEEEEECCCCEEEEEcCChh
Confidence 3899999985 3333 377777654330 3455555557777777643
No 56
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=27.28 E-value=73 Score=27.86 Aligned_cols=26 Identities=19% Similarity=0.021 Sum_probs=20.3
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEcce
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVGWW 321 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIgl~ 321 (543)
+++.||.|++ +.| .|..|.|.+|.-.
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 543 4678999988643
No 57
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=26.96 E-value=46 Score=25.91 Aligned_cols=18 Identities=22% Similarity=0.433 Sum_probs=15.2
Q ss_pred HHHHHHHHHcCCCccccc
Q 009110 375 VADMRKVLAKNPQVEQQR 392 (543)
Q Consensus 375 ~~~l~e~l~~~p~i~~~~ 392 (543)
-+.|++++++||+|++++
T Consensus 11 ~~~m~~fie~hP~WDQ~R 28 (57)
T PF10929_consen 11 HQAMKDFIETHPNWDQYR 28 (57)
T ss_pred HHHHHHHHHcCCCchHHH
Confidence 345999999999999875
No 58
>COG1607 Acyl-CoA hydrolase [Lipid metabolism]
Probab=26.77 E-value=87 Score=29.51 Aligned_cols=30 Identities=13% Similarity=0.141 Sum_probs=24.5
Q ss_pred eeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEEE
Q 009110 290 IHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR 327 (543)
Q Consensus 290 I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir 327 (543)
+.|.+|+++||.|.+ .+.|.++|=+| ..+.
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 688999999999987 58899988877 4443
No 59
>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=26.69 E-value=1.2e+02 Score=23.56 Aligned_cols=30 Identities=13% Similarity=-0.021 Sum_probs=19.5
Q ss_pred ecCCccCCcEEEEeecCcceEEEEEEEcce
Q 009110 292 ATQPFVINEWIQTKIQGYEVSGTVEHVGWW 321 (543)
Q Consensus 292 ~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~ 321 (543)
.++|+..||.|.+.+.|+...-.|.++.-.
T Consensus 15 ~~~pv~~Gd~i~~~~~~~~~~~~V~~~~P~ 44 (64)
T PF02933_consen 15 EGRPVTKGDTIVFPFFGQALPFKVVSTEPS 44 (64)
T ss_dssp TTEEEETT-EEEEEETTEEEEEEEEEECSS
T ss_pred cCCCccCCCEEEEEeCCcEEEEEEEEEEcC
Confidence 458999999999865554455555555443
No 60
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=26.48 E-value=1e+02 Score=26.80 Aligned_cols=33 Identities=21% Similarity=0.146 Sum_probs=22.5
Q ss_pred CCccCCcEEEEeecCc-----------ceEEEEEEEcceeEEEEE
Q 009110 294 QPFVINEWIQTKIQGY-----------EVSGTVEHVGWWSPTIIR 327 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~-----------~~~G~VeeIgl~sTT~ir 327 (543)
+.|++||.|.|++++. |-.|+|..++=++ ..+.
T Consensus 33 ~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A-~~V~ 76 (98)
T PRK04306 33 QEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRA-YIVE 76 (98)
T ss_pred HhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeE-EEEE
Confidence 4599999999976642 2357777776666 4443
No 61
>PRK11281 hypothetical protein; Provisional
Probab=26.37 E-value=1.3e+03 Score=28.61 Aligned_cols=8 Identities=0% Similarity=-0.035 Sum_probs=5.0
Q ss_pred EEEEcCCc
Q 009110 72 RSVLAPGG 79 (543)
Q Consensus 72 ~~~~~~~~ 79 (543)
|+|=+|++
T Consensus 454 ~lfWv~s~ 461 (1113)
T PRK11281 454 QIFWVNSN 461 (1113)
T ss_pred hhhccCCC
Confidence 45666776
No 62
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=26.36 E-value=81 Score=25.88 Aligned_cols=28 Identities=11% Similarity=0.243 Sum_probs=19.9
Q ss_pred hheeeeec--CCccCCcEEEEeecCcceEEEEEEEcc
Q 009110 286 SSVMIHAT--QPFVINEWIQTKIQGYEVSGTVEHVGW 320 (543)
Q Consensus 286 aGi~I~~~--rpfrVGD~I~i~i~g~~~~G~VeeIgl 320 (543)
.|+++... ...++||+|++ .|+|.|-.=
T Consensus 33 ~gifV~~~~~~~~~~Gd~V~v-------tG~v~ey~g 62 (78)
T cd04486 33 EGIFVYTGSGADVAVGDLVRV-------TGTVTEYYG 62 (78)
T ss_pred ceEEEecCCCCCCCCCCEEEE-------EEEEEeeCC
Confidence 35555544 36899999997 589988654
No 63
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=26.35 E-value=1.1e+03 Score=28.29 Aligned_cols=23 Identities=13% Similarity=0.176 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhC
Q 009110 234 FAGKAVYTAVWVAAVSLFMELLG 256 (543)
Q Consensus 234 ~l~~i~~~iv~vi~~~~~L~~lg 256 (543)
...++.+.+++.+++..++..+|
T Consensus 510 ~~~~~~rl~~~~~~i~l~l~~wg 532 (835)
T COG3264 510 QLLRLIRLLLLLIAIPLVLYVWG 532 (835)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHh
Confidence 44556677777777777777777
No 64
>TIGR02286 PaaD phenylacetic acid degradation protein PaaD. Sequences scoring between trusted and noise include those from archaea and other species not known to catabolize phenylacetic acid and which are not adjacent to other genes potentially involved with such a pathway.
Probab=26.00 E-value=2.3e+02 Score=24.31 Aligned_cols=41 Identities=15% Similarity=0.162 Sum_probs=26.9
Q ss_pred hheeeeecCCccCCcEEEEeecCcceEEEEEEEc----ceeEEEEEeCCCcEE
Q 009110 286 SSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVG----WWSPTIIRGDDREAV 334 (543)
Q Consensus 286 aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIg----l~sTT~ir~~d~~~v 334 (543)
..+-+-+-+|.+.||++.+ .++|.+.| ... +.+.+.+|+.+
T Consensus 60 ~~~~i~f~rp~~~G~~l~~-------~a~v~~~g~~~~~~~-~~i~~~~~~~v 104 (114)
T TIGR02286 60 AQCTIDFLRPGRAGERLEA-------EAVEVSRGGRTGTYD-VEVVNQEGELV 104 (114)
T ss_pred EEEEEEEecCCCCCCEEEE-------EEEEEEeCCcEEEEE-EEEEcCCCCEE
Confidence 3456788999999999986 36666643 333 44555555544
No 65
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=25.60 E-value=1.9e+02 Score=34.33 Aligned_cols=46 Identities=9% Similarity=0.105 Sum_probs=32.3
Q ss_pred CCccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccc
Q 009110 294 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFT 342 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~ 342 (543)
++|++||+|.+ .+.+..|+|.+|.=-....+ ..++-.+.+|-+.+.
T Consensus 635 ~~~~~Gd~V~v--~~~~~~g~v~~i~~~~~~~V-~~g~~k~~v~~~~l~ 680 (782)
T PRK00409 635 EELKVGDEVKY--LSLGQKGEVLSIPDDKEAIV-QAGIMKMKVPLSDLE 680 (782)
T ss_pred cCCCCCCEEEE--ccCCceEEEEEEcCCCeEEE-EECCEEEEEeHHHce
Confidence 56999999998 44568899999942111333 346777888888874
No 66
>PF11449 DUF2899: Protein of unknown function (DUF2899); InterPro: IPR021552 This is a bacterial family of uncharacterised proteins.
Probab=25.35 E-value=7.9e+02 Score=25.64 Aligned_cols=42 Identities=21% Similarity=0.299 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH----HhCCchHHHHHHHHHHHHH
Q 009110 231 GFNFAGKAVYTAVWVAAVSLFME----LLGFSTQRWLTAGGLGTVL 272 (543)
Q Consensus 231 ~i~~l~~i~~~iv~vi~~~~~L~----~lgi~~~~lla~~Gi~gla 272 (543)
..+.+....++.+|+++...+++ ..|.|...++...|..+-.
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 56677778888888888876654 4588887777666655443
No 67
>PRK14725 pyruvate kinase; Provisional
Probab=24.96 E-value=1.1e+02 Score=35.11 Aligned_cols=82 Identities=10% Similarity=0.111 Sum_probs=49.0
Q ss_pred CccCCcEEEEeecCcceEEEEEEEccee-EEEEE--------eCCCcEEEEeCcccccCeEEEccCCC----ceEEEEEE
Q 009110 295 PFVINEWIQTKIQGYEVSGTVEHVGWWS-PTIIR--------GDDREAVHIPNHKFTVNVVRNLSQKT----HWRIKTYL 361 (543)
Q Consensus 295 pfrVGD~I~i~i~g~~~~G~VeeIgl~s-TT~ir--------~~d~~~v~IPNs~l~~~~I~N~sr~~----~~ri~~~l 361 (543)
-.++||.|-+ ++|...++|++++=.. .+++. -.+++=+.+|++.+.-..++---+.+ ... .-.+
T Consensus 372 ~v~~G~~Vli--dDG~I~l~V~~~~~~~v~~~V~~a~~~gg~L~s~KGiNlP~~~l~lp~LTekD~~dl~f~~~~-vD~V 448 (608)
T PRK14725 372 AARVGERVWF--DDGKIGAVVVKVEADEVELRITHARPGGSKLKAGKGINLPDSHLPLPALTDKDLEDLAFVAKH-ADIV 448 (608)
T ss_pred hcCCCCEEEE--eCCeEEEEEEEEECCEEEEEEEEecCCCCEecCCCceecCCCCCCCCCCCHHHHHHHHHHHHh-CCEE
Confidence 3899999987 7778999999886222 02222 12345566888886543332111111 011 2357
Q ss_pred Eecc-CCHHHHHHHHHHHH
Q 009110 362 AISH-LDVHKVNSIVADMR 379 (543)
Q Consensus 362 ~v~y-td~e~v~~l~~~l~ 379 (543)
.++| .+.++++.+.+.+.
T Consensus 449 alSFVrs~~DV~~lr~~L~ 467 (608)
T PRK14725 449 ALSFVRSPEDVRLLLDALE 467 (608)
T ss_pred EECCCCCHHHHHHHHHHHH
Confidence 8888 78888888654444
No 68
>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=24.92 E-value=1.8e+02 Score=23.51 Aligned_cols=43 Identities=9% Similarity=0.048 Sum_probs=33.1
Q ss_pred ccCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEE
Q 009110 296 FVINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRN 348 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N 348 (543)
+++||.+ .|+|.++.=+. ..+...++..-.+|.+.+....+.+
T Consensus 12 ~~~G~i~---------~g~V~~v~~~G-~fv~l~~~~~g~v~~~el~~~~~~~ 54 (83)
T cd04461 12 LKPGMVV---------HGYVRNITPYG-VFVEFLGGLTGLAPKSYISDEFVTD 54 (83)
T ss_pred CCCCCEE---------EEEEEEEeece-EEEEcCCCCEEEEEHHHCCcccccC
Confidence 6777755 47888887777 7777778888999999998766544
No 69
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=24.65 E-value=1.7e+02 Score=22.49 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=24.1
Q ss_pred hheeeeecCCccCCcEEEEeecCcceEEEEEEEcceeEEEE
Q 009110 286 SSVMIHATQPFVINEWIQTKIQGYEVSGTVEHVGWWSPTII 326 (543)
Q Consensus 286 aGi~I~~~rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~i 326 (543)
..+.+-+-+|.+.||.+++ .++|+++|=++ ..+
T Consensus 34 ~~~~i~f~~p~~~gd~l~~-------~~~v~~~g~~~-~~~ 66 (79)
T PF03061_consen 34 VELSIDFLRPVRPGDTLRV-------EARVVRVGRKS-FTV 66 (79)
T ss_dssp EEEEEEESS-BBTTSEEEE-------EEEEEEEESSE-EEE
T ss_pred EEEEEEEccccCCCeEEEE-------EEEEEEECCEE-EEE
Confidence 4456778899999999986 57888887666 443
No 70
>PHA02945 interferon resistance protein; Provisional
Probab=24.49 E-value=2.8e+02 Score=23.60 Aligned_cols=43 Identities=7% Similarity=0.010 Sum_probs=33.6
Q ss_pred cCCcEEEEeecCcceEEEEEEEcceeEEEEEeCCCcEEEEeCccc--ccCeEEE
Q 009110 297 VINEWIQTKIQGYEVSGTVEHVGWWSPTIIRGDDREAVHIPNHKF--TVNVVRN 348 (543)
Q Consensus 297 rVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l--~~~~I~N 348 (543)
.+||.+. |+|.+-+.-.++.+..+.|..=.+|+|.. ++.++.|
T Consensus 10 ~~Gelvi---------gtV~~~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~ 54 (88)
T PHA02945 10 NVGDVLK---------GKVYENGYALYIDLFDYPHSEAILAESVQMHMNRYFKY 54 (88)
T ss_pred CCCcEEE---------EEEEecCceEEEEecccCCcEEEEEeehhhhccceEee
Confidence 6777664 67766555555778888899999999955 9999999
No 71
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=24.15 E-value=80 Score=28.40 Aligned_cols=25 Identities=20% Similarity=0.338 Sum_probs=19.4
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEcc
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVGW 320 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIgl 320 (543)
+++.||.|+| +.| .|..|.|.+|.-
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 543 357899988844
No 72
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=23.64 E-value=94 Score=26.58 Aligned_cols=23 Identities=17% Similarity=0.459 Sum_probs=18.8
Q ss_pred CCccCCcEEEEeecCcceEEEEEEE
Q 009110 294 QPFVINEWIQTKIQGYEVSGTVEHV 318 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~~~~G~VeeI 318 (543)
+|+.+|+.|+- ++ -|..|.|.+|
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 58999999996 44 5788999887
No 73
>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=23.35 E-value=86 Score=27.95 Aligned_cols=24 Identities=21% Similarity=0.383 Sum_probs=19.4
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEc
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVG 319 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIg 319 (543)
+++.||.|.| +.| .|.+|.|.+|.
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 543 46789998885
No 74
>PRK08187 pyruvate kinase; Validated
Probab=22.74 E-value=1.6e+02 Score=32.95 Aligned_cols=81 Identities=10% Similarity=0.181 Sum_probs=47.4
Q ss_pred CCccCCcEEEEeecCcceEEEEEEEcceeEEEEE----------eCCCcEEEEeCcccccCeEEEccCCC----ceEEEE
Q 009110 294 QPFVINEWIQTKIQGYEVSGTVEHVGWWSPTIIR----------GDDREAVHIPNHKFTVNVVRNLSQKT----HWRIKT 359 (543)
Q Consensus 294 rpfrVGD~I~i~i~g~~~~G~VeeIgl~sTT~ir----------~~d~~~v~IPNs~l~~~~I~N~sr~~----~~ri~~ 359 (543)
+-+++||.|-+ ++|...++|++++=.. ...+ -..++-+.+|+..+--+.++---..+ ...+ -
T Consensus 251 ~~v~~Gd~Ili--dDG~I~l~V~~v~~~~-v~~~V~~~~~~gg~L~~~KgiNlP~~~vrin~LtekD~~DL~f~~~~v-D 326 (493)
T PRK08187 251 ARLAVGARVWI--DDGKLGARVERVGPGG-ALLEVTHARPKGLKLKPEKGLNFPDTALDLPALTEKDRADLDFVARHA-D 326 (493)
T ss_pred HhcCCCCEEEE--eCCeEEEEEEEEeCCE-EEEEEEEecCCCeEecCCCcccccCceecCCCCCHhHHHHHHHHHhcC-C
Confidence 34899999987 7778999999986222 2221 12344456888876544332111111 0111 2
Q ss_pred EEEecc-CCHHHHHHHHHHH
Q 009110 360 YLAISH-LDVHKVNSIVADM 378 (543)
Q Consensus 360 ~l~v~y-td~e~v~~l~~~l 378 (543)
.+.+++ .+.++++.+.+.+
T Consensus 327 ~I~lSfV~saeDV~~l~~~L 346 (493)
T PRK08187 327 LVGYSFVQSPGDVEALQAAL 346 (493)
T ss_pred EEEECCCCCHHHHHHHHHHH
Confidence 377888 7888888764444
No 75
>COG4858 Uncharacterized membrane-bound protein conserved in bacteria [Function unknown]
Probab=22.09 E-value=7.5e+02 Score=24.18 Aligned_cols=18 Identities=11% Similarity=0.045 Sum_probs=11.6
Q ss_pred HHHHHHHHhHhcCchHHH
Q 009110 90 AAVLTRSYDTLRGNPVIL 107 (543)
Q Consensus 90 ~~~l~~~~~~~~~~~~~~ 107 (543)
+++|.....++++.....
T Consensus 107 ~~aLlsgitaff~~nA~~ 124 (226)
T COG4858 107 AMALLSGITAFFQKNAQV 124 (226)
T ss_pred HHHHHHHHHHHHhcCCcc
Confidence 477777777777754433
No 76
>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=22.02 E-value=4.1e+02 Score=26.51 Aligned_cols=58 Identities=16% Similarity=0.193 Sum_probs=34.5
Q ss_pred HHHHHHHcCCCccccccccEEEEEeeCCCCCeEEEEEEEEEecC-ChhhHHHHHHHHHHHHHHH
Q 009110 377 DMRKVLAKNPQVEQQRLHRRVFLENINPESQSLNILVSCFVKTS-RFEEYLCVKEAILLDLLHV 439 (543)
Q Consensus 377 ~l~e~l~~~p~i~~~~~~p~v~v~~~~~~~~~l~i~V~~~v~~~-~~~~~~~ir~~i~~~i~~~ 439 (543)
++++.+++.|.+.+-. .+++.+.|. ....+++.+.+++. +-.+..++++++.+.+.+.
T Consensus 209 ~i~~~i~~~~~v~~v~---~~~~~~~g~--~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~ 267 (284)
T PF01545_consen 209 KIRRIIESVPGVIEVH---DLRVWQVGR--NKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREK 267 (284)
T ss_dssp HHHHHHHHTSS-SEEE---EEEEEEETT---EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhccCCceEecc---ceEEEEecC--CcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHh
Confidence 3566676677766532 578888883 45666777766654 3345555566655555554
No 77
>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=21.91 E-value=1.1e+02 Score=26.80 Aligned_cols=26 Identities=19% Similarity=0.069 Sum_probs=20.0
Q ss_pred CccCCcEEEEeecC--cceEEEEEEEcce
Q 009110 295 PFVINEWIQTKIQG--YEVSGTVEHVGWW 321 (543)
Q Consensus 295 pfrVGD~I~i~i~g--~~~~G~VeeIgl~ 321 (543)
+++.||.|++ +.| .|..|.|.+|.-.
T Consensus 3 ~ikkGD~V~V-i~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKV-ISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEE-eEcCCCCcEEEEEEEEcC
Confidence 6899999998 543 4678999988543
No 78
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.67 E-value=2.2e+02 Score=21.92 Aligned_cols=35 Identities=17% Similarity=0.171 Sum_probs=24.8
Q ss_pred eEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEE
Q 009110 311 VSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVR 347 (543)
Q Consensus 311 ~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~ 347 (543)
+.|+|+++.-.- ..+.- +|-.-.+|++.+....+.
T Consensus 4 v~g~V~~v~~~G-~~v~l-~g~~gfip~s~~~~~~~~ 38 (67)
T cd04465 4 VEGKVTEKVKGG-LIVDI-EGVRAFLPASQVDLRPVE 38 (67)
T ss_pred EEEEEEEEECCe-EEEEE-CCEEEEEEHHHCCCcccC
Confidence 467888886655 55555 788889999988765443
No 79
>PF14221 DUF4330: Domain of unknown function (DUF4330)
Probab=21.48 E-value=2.4e+02 Score=26.75 Aligned_cols=43 Identities=19% Similarity=0.243 Sum_probs=30.4
Q ss_pred ccCCcEEEEeecCcceEE--EEEEEcceeE-EEEEeCCCcEEEEeCc
Q 009110 296 FVINEWIQTKIQGYEVSG--TVEHVGWWSP-TIIRGDDREAVHIPNH 339 (543)
Q Consensus 296 frVGD~I~i~i~g~~~~G--~VeeIgl~sT-T~ir~~d~~~v~IPNs 339 (543)
++.||...+.+. +...| +|+++..... +...+.||+.+..|.-
T Consensus 72 ~~~gd~~~~~~r-nqp~G~v~V~~V~~~p~~~~~~~~dG~v~~~~dP 117 (168)
T PF14221_consen 72 IKEGDKTNIVIR-NQPAGQVTVKDVQVLPRTVVVPQPDGSVVEAPDP 117 (168)
T ss_pred ccCCCEEEEecc-CccccceEEEEEEEEccceEEECCCCeEEEccCC
Confidence 899999987433 45567 8888877652 3344579998887765
No 80
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=21.00 E-value=2.6e+02 Score=24.62 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=14.3
Q ss_pred eeeecCCccCCcEEEE
Q 009110 289 MIHATQPFVINEWIQT 304 (543)
Q Consensus 289 ~I~~~rpfrVGD~I~i 304 (543)
-+-+.+|..+||.+.+
T Consensus 84 ~~~f~~pv~~GD~l~~ 99 (140)
T cd03446 84 NLRFLNPVFIGDTIRA 99 (140)
T ss_pred eEEEcCCCCCCCEEEE
Confidence 5679999999999987
No 81
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.25 E-value=2.4e+02 Score=21.67 Aligned_cols=38 Identities=13% Similarity=0.202 Sum_probs=29.3
Q ss_pred ceEEEEEEEcceeEEEEEeCCCcEEEEeCcccccCeEEE
Q 009110 310 EVSGTVEHVGWWSPTIIRGDDREAVHIPNHKFTVNVVRN 348 (543)
Q Consensus 310 ~~~G~VeeIgl~sTT~ir~~d~~~v~IPNs~l~~~~I~N 348 (543)
-+.|+|.++.=.- ..++-.++-.-.+|.+.+..+.+.|
T Consensus 3 ~~~g~V~~v~~~G-~~V~l~~~~~gli~~s~l~~~~~~~ 40 (70)
T cd05698 3 KTHGTIVKVKPNG-CIVSFYNNVKGFLPKSELSEAFIKD 40 (70)
T ss_pred EEEEEEEEEecCc-EEEEECCCCEEEEEHHHcChhhcCC
Confidence 3568999988776 7788777888899999887655544
Done!