Query gi|254780470|ref|YP_003064883.1| translation initiation factor IF-1 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 110
No_of_seqs 112 out of 663
Neff 2.4
Searched_HMMs 39220
Date Sun May 29 16:49:51 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780470.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12442 translation initiatio 100.0 6.4E-36 1.6E-40 229.9 10.6 72 1-110 1-72 (87)
2 CHL00010 infA translation init 100.0 8.3E-36 2.1E-40 229.3 10.2 72 1-110 1-72 (78)
3 PRK00276 infA translation init 100.0 8.2E-35 2.1E-39 223.5 10.4 72 1-110 1-72 (72)
4 TIGR00008 infA translation ini 100.0 1.5E-30 3.9E-35 198.7 8.8 69 3-109 1-69 (69)
5 cd04451 S1_IF1 S1_IF1: Transla 100.0 1.8E-30 4.5E-35 198.3 8.8 64 7-108 1-64 (64)
6 COG0361 InfA Translation initi 99.9 4.6E-27 1.2E-31 178.5 9.4 72 1-110 1-72 (75)
7 pfam01176 eIF-1a Translation i 99.7 2.5E-17 6.3E-22 121.9 9.2 64 6-108 2-65 (65)
8 cd05793 S1_IF1A S1_IF1A: Trans 98.7 7E-08 1.8E-12 67.0 8.4 63 9-110 2-64 (77)
9 smart00652 eIF1a eukaryotic tr 98.6 2.9E-07 7.5E-12 63.4 9.0 68 3-110 2-69 (83)
10 PRK04012 translation initiatio 98.3 4.3E-06 1.1E-10 56.6 8.8 65 7-110 20-84 (99)
11 PTZ00329 translation initiatio 97.9 9.5E-05 2.4E-09 48.8 8.6 68 3-110 29-96 (155)
12 cd04456 S1_IF1A_like S1_IF1A_l 97.5 0.00081 2.1E-08 43.4 8.3 61 11-110 4-65 (78)
13 PRK00098 ribosome-associated G 96.7 0.0054 1.4E-07 38.6 6.3 60 9-109 1-60 (298)
14 PRK12289 ribosome-associated G 96.7 0.0081 2.1E-07 37.5 7.1 69 5-107 5-73 (351)
15 cd04466 S1_YloQ_GTPase S1_YloQ 96.5 0.0076 1.9E-07 37.7 5.9 59 9-108 1-59 (68)
16 KOG3403 consensus 94.6 0.021 5.3E-07 35.2 2.1 51 58-109 45-95 (145)
17 cd04471 S1_RNase_R S1_RNase_R: 94.5 0.18 4.5E-06 29.8 6.7 76 8-109 4-82 (83)
18 cd01854 YjeQ_engC YjeQ/EngC. 93.9 0.21 5.3E-06 29.4 6.0 41 67-109 17-57 (287)
19 PRK05054 exoribonuclease II; P 92.7 0.49 1.3E-05 27.2 6.4 71 8-109 564-643 (644)
20 TIGR02063 RNase_R ribonuclease 92.0 0.71 1.8E-05 26.3 6.5 71 7-109 674-753 (755)
21 PRK11642 exoribonuclease R; Pr 91.9 0.98 2.5E-05 25.5 7.1 75 8-109 646-724 (813)
22 PRK07252 hypothetical protein; 72.9 8.6 0.00022 20.0 4.9 63 8-109 6-72 (120)
23 smart00316 S1 Ribosomal protei 70.6 10 0.00026 19.6 5.7 67 8-110 5-72 (72)
24 TIGR00523 eIF-1A translation i 70.6 3 7.8E-05 22.6 2.1 49 61-110 35-84 (99)
25 PRK12696 flgH flagellar basal 69.4 9.1 0.00023 19.8 4.3 20 7-26 152-171 (238)
26 pfam07202 Tcp10_C T-complex pr 68.6 7.3 0.00019 20.4 3.7 23 57-79 144-166 (179)
27 cd00164 S1_like S1_like: Ribos 67.2 12 0.00031 19.1 5.2 60 9-107 1-64 (65)
28 cd05692 S1_RPS1_repeat_hs4 S1_ 66.9 12 0.00031 19.1 5.1 63 8-110 3-69 (69)
29 PRK05807 hypothetical protein; 64.6 13 0.00034 18.8 5.0 66 1-108 1-71 (136)
30 pfam00575 S1 S1 RNA binding do 61.0 16 0.0004 18.5 5.0 68 8-110 7-74 (74)
31 smart00675 DM11 Domains in hyp 60.6 8.5 0.00022 20.0 2.8 39 64-104 37-75 (164)
32 cd04472 S1_PNPase S1_PNPase: P 54.9 20 0.00051 17.8 4.0 59 8-106 3-65 (68)
33 cd04452 S1_IF2_alpha S1_IF2_al 54.5 20 0.00052 17.8 5.4 70 8-110 6-75 (76)
34 cd05708 S1_Rrp5_repeat_sc12 S1 52.6 22 0.00056 17.6 5.8 65 8-110 5-73 (77)
35 cd05689 S1_RPS1_repeat_ec4 S1_ 51.1 23 0.00059 17.5 6.0 60 8-106 6-70 (72)
36 pfam11858 DUF3378 Domain of un 50.5 14 0.00037 18.7 2.6 14 66-79 38-51 (82)
37 PRK12699 flgH flagellar basal 50.3 19 0.00049 17.9 3.2 62 8-109 162-223 (246)
38 pfam02107 FlgH Flagellar L-rin 48.2 26 0.00065 17.2 3.7 63 7-108 96-158 (181)
39 PRK12697 flgH flagellar basal 48.0 22 0.00056 17.6 3.2 20 7-26 141-160 (227)
40 PRK12407 flgH flagellar basal 47.5 26 0.00067 17.1 3.6 20 7-26 133-152 (220)
41 COG1162 Predicted GTPases [Gen 46.4 27 0.0007 17.1 4.0 37 69-108 29-65 (301)
42 COG0557 VacB Exoribonuclease R 45.4 28 0.00073 17.0 5.6 79 5-109 622-703 (706)
43 cd05690 S1_RPS1_repeat_ec5 S1_ 44.1 30 0.00076 16.8 5.7 60 8-106 3-67 (69)
44 cd05697 S1_Rrp5_repeat_hs5 S1_ 43.7 30 0.00077 16.8 3.8 64 8-107 3-67 (69)
45 PRK12788 flgH flagellar basal 43.6 30 0.00077 16.8 3.7 20 7-26 145-164 (231)
46 cd04460 S1_RpoE S1_RpoE: RpoE, 43.5 30 0.00078 16.8 6.1 66 8-103 2-72 (99)
47 PRK00249 flgH flagellar basal 40.9 33 0.00085 16.5 3.7 20 7-26 145-164 (231)
48 PRK12700 flgH flagellar basal 40.3 34 0.00086 16.5 3.2 19 8-26 145-163 (230)
49 PRK08059 general stress protei 38.0 37 0.00095 16.3 5.0 64 8-110 9-76 (119)
50 PRK12698 flgH flagellar basal 37.7 38 0.00096 16.2 3.6 20 7-26 137-156 (224)
51 cd05688 S1_RPS1_repeat_ec3 S1_ 37.3 38 0.00098 16.2 5.3 59 8-106 4-66 (68)
52 TIGR01531 glyc_debranch glycog 36.9 8.8 0.00022 19.9 -0.2 16 94-109 586-602 (1584)
53 TIGR02464 ribofla_fusion conse 36.0 16 0.00042 18.3 1.1 21 81-101 124-144 (180)
54 cd05691 S1_RPS1_repeat_ec6 S1_ 35.3 41 0.0011 16.0 6.1 64 8-110 3-70 (73)
55 COG1451 Predicted metal-depend 35.1 41 0.0011 16.0 4.2 38 65-103 7-44 (223)
56 PRK06676 rpsA 30S ribosomal pr 34.9 42 0.0011 16.0 6.2 25 85-109 322-346 (390)
57 cd05685 S1_Tex S1_Tex: The C-t 34.8 42 0.0011 16.0 5.4 60 8-106 3-66 (68)
58 COG2063 FlgH Flagellar basal b 34.7 42 0.0011 16.0 3.7 21 6-26 146-166 (230)
59 PRK12701 flgH flagellar basal 34.2 43 0.0011 15.9 3.6 19 8-26 144-162 (230)
60 TIGR03591 polynuc_phos polyrib 33.4 44 0.0011 15.8 5.3 58 8-106 621-683 (684)
61 PRK07400 30S ribosomal protein 33.1 45 0.0011 15.8 5.7 21 87-107 160-180 (314)
62 COG2872 Predicted metal-depend 32.6 46 0.0012 15.8 6.9 69 6-97 12-89 (241)
63 pfam01079 Hint Hint module. Th 32.2 46 0.0012 15.7 3.2 13 81-93 102-114 (214)
64 PRK11824 polynucleotide phosph 31.9 47 0.0012 15.7 5.6 60 8-108 624-688 (694)
65 CHL00051 rps12 ribosomal prote 30.7 49 0.0013 15.6 3.1 45 65-109 58-115 (123)
66 pfam06257 DUF1021 Protein of u 30.0 51 0.0013 15.5 4.2 26 2-28 27-52 (76)
67 PTZ00115 40S ribosomal protein 29.6 51 0.0013 15.5 3.3 48 62-109 150-210 (288)
68 cd05698 S1_Rrp5_repeat_hs6_sc5 29.0 53 0.0013 15.4 5.9 68 8-110 3-70 (70)
69 PRK05163 rpsL 30S ribosomal pr 28.2 55 0.0014 15.3 3.1 46 65-110 58-116 (124)
70 PRK12764 hypothetical protein; 27.9 55 0.0014 15.3 2.9 25 84-108 198-225 (498)
71 cd04473 S1_RecJ_like S1_RecJ_l 27.9 55 0.0014 15.3 5.8 57 8-108 19-75 (77)
72 pfam01828 Peptidase_A4 Peptida 26.5 58 0.0015 15.1 3.1 28 81-108 87-114 (208)
73 pfam00164 Ribosomal_S12 Riboso 24.8 63 0.0016 14.9 3.3 45 66-110 48-105 (112)
74 TIGR01750 fabZ beta-hydroxyacy 24.3 38 0.00097 16.2 1.3 28 71-98 85-113 (142)
75 TIGR00370 TIGR00370 conserved 22.3 59 0.0015 15.1 1.9 37 56-92 175-215 (217)
76 COG1471 RPS4A Ribosomal protei 22.3 71 0.0018 14.6 5.2 41 5-45 87-131 (241)
77 pfam12158 DUF3592 Protein of u 20.9 76 0.0019 14.5 2.6 22 85-106 85-106 (134)
78 COG3745 CpaB Flp pilus assembl 20.3 67 0.0017 14.8 1.9 11 85-95 146-156 (276)
79 cd03448 HDE_HSD HDE_HSD The R 20.2 78 0.002 14.4 2.8 26 81-109 79-104 (122)
80 TIGR01245 trpD anthranilate ph 20.1 79 0.002 14.4 2.9 30 54-83 215-244 (331)
No 1
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=100.00 E-value=6.4e-36 Score=229.92 Aligned_cols=72 Identities=53% Similarity=0.930 Sum_probs=70.1
Q ss_pred CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf 97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK 80 (110)
Q Consensus 1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk 80 (110)
|||||.||++|+|+|+|||++|+|+| +|||.|+||+|||||+
T Consensus 1 MaKed~ie~eG~V~e~lpn~~FrV~L--------------------------------------eNg~~Vla~~sGKmR~ 42 (87)
T PRK12442 1 MAKEELIELDGIVDEVLPDSRYRVTL--------------------------------------ENGVEVGAYASGRMRK 42 (87)
T ss_pred CCCCCEEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEEECCEEE
T ss_conf 98655499878999987998799997--------------------------------------7998999998550133
Q ss_pred EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 164770299699997467578435988429
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
|+|||++||+|+||||||||||||||||||
T Consensus 43 ~~IrIl~GD~V~VElSpYDltkGRIvyR~k 72 (87)
T PRK12442 43 HRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEECCCCEEEEEECCCCCCCEEEEEEEC
T ss_conf 027776899899998877788748998847
No 2
>CHL00010 infA translation initiation factor 1
Probab=100.00 E-value=8.3e-36 Score=229.27 Aligned_cols=72 Identities=46% Similarity=0.870 Sum_probs=70.0
Q ss_pred CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf 97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK 80 (110)
Q Consensus 1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk 80 (110)
|||||.||++|+|+|+||||+|+|+| +|||.|+||+|||||+
T Consensus 1 MaKed~ie~eG~V~e~Lpn~~F~V~L--------------------------------------eng~~Vla~~sGKmR~ 42 (78)
T CHL00010 1 MMKENKIIMEGLVTESLPNGMFRVRL--------------------------------------DNGDLVLGYISGKIRR 42 (78)
T ss_pred CCCCCEEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCHHEE
T ss_conf 98655599989999986998899997--------------------------------------8999999999805200
Q ss_pred EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 164770299699997467578435988429
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
|+|||++||+|+||||||||||||||||||
T Consensus 43 ~~Iril~GD~V~VE~SpYDltkGRI~~R~k 72 (78)
T CHL00010 43 NSIRILPGDRVKVELSPYDLTKGRIIYRLR 72 (78)
T ss_pred CEEEECCCCEEEEEECCCCCCCEEEEEEEC
T ss_conf 318974899899998756788578999904
No 3
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=100.00 E-value=8.2e-35 Score=223.49 Aligned_cols=72 Identities=54% Similarity=0.864 Sum_probs=70.1
Q ss_pred CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf 97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK 80 (110)
Q Consensus 1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk 80 (110)
|||||.|+++|+|+|+|||++|||+|+ ||++|+||+|||||+
T Consensus 1 maKed~i~~~G~V~e~lpn~~F~V~Le--------------------------------------ng~~v~a~~sGKmR~ 42 (72)
T PRK00276 1 MAKEDVIEMEGTVLETLPNAMFRVELE--------------------------------------NGHEVLAHISGKMRK 42 (72)
T ss_pred CCCCCEEEEEEEEEEECCCCEEEEEEC--------------------------------------CCCEEEEEECHHEEE
T ss_conf 996554999999999859988999978--------------------------------------999999997413110
Q ss_pred EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 164770299699997467578435988429
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
|+|||++||+|+||||||||||||||||||
T Consensus 43 ~~Iril~GD~V~vE~spYDltkGRIv~R~k 72 (72)
T PRK00276 43 NYIRILPGDKVTVELSPYDLTKGRITYRYK 72 (72)
T ss_pred EEEEECCCCEEEEEECCCCCCCEEEEEECC
T ss_conf 169975899899998866799578999749
No 4
>TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (IPR003029 from INTERPRO).; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=99.97 E-value=1.5e-30 Score=198.65 Aligned_cols=69 Identities=54% Similarity=0.837 Sum_probs=66.6
Q ss_pred CCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEE
Q ss_conf 56459997899981589817999816677653332335443334455554445555544555688289999125112016
Q gi|254780470|r 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHR 82 (110)
Q Consensus 3 Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~ 82 (110)
||+.|+++|.|+|.|||++|+|+| +|++.|.||+|||||+++
T Consensus 1 K~~~i~~~G~v~e~l~n~~f~V~L--------------------------------------eN~~~v~a~iSGk~r~~~ 42 (69)
T TIGR00008 1 KEDKIEVEGKVVESLPNAMFRVEL--------------------------------------ENGHEVLAHISGKIRKNY 42 (69)
T ss_pred CCCEEEECCEEEECCCCCEEEEEE--------------------------------------CCCCEEEEEECCEEECCE
T ss_conf 975277423898543698269994--------------------------------------799789899710341351
Q ss_pred EEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 477029969999746757843598842
Q gi|254780470|r 83 IRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 83 IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
|||||||+|+||+||||||||||+||+
T Consensus 43 iriLpGD~V~ve~SpYdl~~GRI~yR~ 69 (69)
T TIGR00008 43 IRILPGDKVKVELSPYDLTRGRIIYRL 69 (69)
T ss_pred EEECCCCEEEEEECCCCCCCCCEEEEC
T ss_conf 755479878998713648775087749
No 5
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=99.97 E-value=1.8e-30 Score=198.34 Aligned_cols=64 Identities=52% Similarity=0.871 Sum_probs=61.7
Q ss_pred EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEE
Q ss_conf 99978999815898179998166776533323354433344555544455555445556882899991251120164770
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRIS 86 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl 86 (110)
||++|+|+|+||||+|+|+|+ ||+.|+||+|||||+|+|||+
T Consensus 1 ie~~G~V~e~lpn~~F~V~Le--------------------------------------ng~~v~a~~sGKmr~~~Iril 42 (64)
T cd04451 1 IEMEGVVTEALPNAMFRVELE--------------------------------------NGHEVLAHISGKMRMNYIRIL 42 (64)
T ss_pred CEEEEEEEEECCCCEEEEEEC--------------------------------------CCCEEEEEECCHHEEEEEEEC
T ss_conf 978899999879988999978--------------------------------------998999997233041269845
Q ss_pred CCCEEEEEECCCCCCCCEEEEE
Q ss_conf 2996999974675784359884
Q gi|254780470|r 87 LGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 87 ~GDkV~Ve~SPYDLtkGRItyR 108 (110)
+||+|+||||||||||||||||
T Consensus 43 ~GD~V~VE~SpYDltkGRI~~R 64 (64)
T cd04451 43 PGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred CCCEEEEEECCCCCCCEEEEEC
T ss_conf 8998999988667885789859
No 6
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4.6e-27 Score=178.48 Aligned_cols=72 Identities=49% Similarity=0.828 Sum_probs=69.7
Q ss_pred CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf 97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK 80 (110)
Q Consensus 1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk 80 (110)
|+|+|.+|++|+|.|+|||++|+|++ +||++++||+|||||+
T Consensus 1 m~~~d~~e~~g~V~e~L~~~~f~v~~--------------------------------------eng~~~~ahI~GKmr~ 42 (75)
T COG0361 1 MAKPDEIEMEGTVIEMLPNGRFRVEL--------------------------------------ENGHERLAHISGKMRK 42 (75)
T ss_pred CCCCCCCEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEECCCCCCE
T ss_conf 95564428999999973897899994--------------------------------------6996999882587440
Q ss_pred EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 164770299699997467578435988429
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
|+|||++||+|.||+||||++||||+|||+
T Consensus 43 ~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 43 NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred EEEEECCCCEEEEEECCCCCCCCCEEEEEC
T ss_conf 048857999999974566533355899833
No 7
>pfam01176 eIF-1a Translation initiation factor 1A / IF-1. This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
Probab=99.72 E-value=2.5e-17 Score=121.91 Aligned_cols=64 Identities=42% Similarity=0.609 Sum_probs=59.7
Q ss_pred EEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEE
Q ss_conf 59997899981589817999816677653332335443334455554445555544555688289999125112016477
Q gi|254780470|r 6 TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRI 85 (110)
Q Consensus 6 ~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRI 85 (110)
--|+.|+|+++|||++|+|++ +||+.++|+++|||| ++|+|
T Consensus 2 e~e~~g~V~~~lg~~~~~V~~--------------------------------------~dg~~~l~~i~GK~r-kriwi 42 (65)
T pfam01176 2 EGEMIGQVTEMLGNGRFEVEL--------------------------------------EDGHERLAHIPGKRR-KRIWI 42 (65)
T ss_pred CCEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCCEE-EEEEE
T ss_conf 986999999982998899997--------------------------------------999999999822054-57997
Q ss_pred ECCCEEEEEECCCCCCCCEEEEE
Q ss_conf 02996999974675784359884
Q gi|254780470|r 86 SLGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 86 l~GDkV~Ve~SPYDLtkGRItyR 108 (110)
.+||.|.|+++|||++||+|+||
T Consensus 43 ~~GD~VlV~~~~~~~~kg~Ii~r 65 (65)
T pfam01176 43 LRGDFVLVELSPYDKVKGRIIYR 65 (65)
T ss_pred CCCCEEEEEECCCCCCEEEEEEC
T ss_conf 49999999967877863999969
No 8
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=98.73 E-value=7e-08 Score=67.00 Aligned_cols=63 Identities=32% Similarity=0.478 Sum_probs=57.7
Q ss_pred EEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEECC
Q ss_conf 97899981589817999816677653332335443334455554445555544555688289999125112016477029
Q gi|254780470|r 9 FSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLG 88 (110)
Q Consensus 9 ~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~G 88 (110)
.=|+|++.|.|++|+|.. .||.+.+|++.||||+ |+.|-+|
T Consensus 2 ~y~~V~k~lG~~r~~v~c--------------------------------------~Dg~~ri~~IrGk~rk-R~wi~~g 42 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRC--------------------------------------FDGKKRLCRIRGKMRK-RVWINEG 42 (77)
T ss_pred CCEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCCEEE-EEEECCC
T ss_conf 419987511993699996--------------------------------------8999999998462020-3696489
Q ss_pred CEEEEEECCCCCCCCEEEEEEC
Q ss_conf 9699997467578435988429
Q gi|254780470|r 89 DKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 89 DkV~Ve~SPYDLtkGRItyR~K 110 (110)
|-|.|++-+|+-+|+.|+|+|.
T Consensus 43 diVLV~~rd~q~~K~DIi~kY~ 64 (77)
T cd05793 43 DIVLVAPWDFQDDKADIIYKYT 64 (77)
T ss_pred CEEEEECCCCCCCCEEEEEECC
T ss_conf 9999975677688488999829
No 9
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=98.62 E-value=2.9e-07 Score=63.38 Aligned_cols=68 Identities=29% Similarity=0.409 Sum_probs=60.5
Q ss_pred CCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEE
Q ss_conf 56459997899981589817999816677653332335443334455554445555544555688289999125112016
Q gi|254780470|r 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHR 82 (110)
Q Consensus 3 Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~ 82 (110)
||+. |+-|.|+.+|.|..|.|.. .||...+|.+.||||+ +
T Consensus 2 ~ee~-e~y~~V~k~lG~~~~~V~c--------------------------------------~dg~~rl~~i~gk~rk-r 41 (83)
T smart00652 2 KEDG-QEIAQVVKMLGNGRLEVMC--------------------------------------ADGKERLARIPGKMRK-K 41 (83)
T ss_pred CCCC-CEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECHHCEE-E
T ss_conf 8788-0999999944996799991--------------------------------------9999999998303030-2
Q ss_pred EEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 4770299699997467578435988429
Q gi|254780470|r 83 IRISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 83 IRIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
+.|-.||-|.|+..+|+-.||-|+|+|.
T Consensus 42 ~wi~~Gd~VlV~~r~~~~~K~DIi~~y~ 69 (83)
T smart00652 42 VWIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred EEEECCCEEEEEECCCCCCEEEEEEECC
T ss_conf 7984799999981367784699999479
No 10
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=98.33 E-value=4.3e-06 Score=56.59 Aligned_cols=65 Identities=31% Similarity=0.473 Sum_probs=58.4
Q ss_pred EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEE
Q ss_conf 99978999815898179998166776533323354433344555544455555445556882899991251120164770
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRIS 86 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl 86 (110)
=|+=|+|+..|-++.|.|.- .||..-+|.+.||||+ ++.|-
T Consensus 20 ~e~yg~V~k~lG~~r~~v~C--------------------------------------~Dg~~R~~~I~Gkmrk-r~WI~ 60 (99)
T PRK04012 20 GEVFGVVEQMLGANRVRVRC--------------------------------------MDGVERMGRIPGKMKK-RMWIR 60 (99)
T ss_pred CEEEEEEEECCCCCEEEEEE--------------------------------------CCCCEEEEEECCCCCC-CEEEE
T ss_conf 86999991061994299994--------------------------------------8999999997687512-34972
Q ss_pred CCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 299699997467578435988429
Q gi|254780470|r 87 LGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 87 ~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
.||-|.|.+-.|.-.|+-|+|+|.
T Consensus 61 ~gDiVLV~~refqd~K~DIi~kY~ 84 (99)
T PRK04012 61 EGDVVIVAPWDFQDEKADIIWRYT 84 (99)
T ss_pred CCCEEEEEEECCCCCEEEEEEECC
T ss_conf 799999985546686187999669
No 11
>PTZ00329 translation initiation factor eIF-1A; Provisional
Probab=97.90 E-value=9.5e-05 Score=48.78 Aligned_cols=68 Identities=25% Similarity=0.416 Sum_probs=58.2
Q ss_pred CCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEE
Q ss_conf 56459997899981589817999816677653332335443334455554445555544555688289999125112016
Q gi|254780470|r 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHR 82 (110)
Q Consensus 3 Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~ 82 (110)
||+- +.-|.|+.+|-|++|.|.. .+|..-+|++.||||+ |
T Consensus 29 keeg-qeYa~V~kmLG~gr~~v~C--------------------------------------~Dg~~Rl~~IrGk~Rk-r 68 (155)
T PTZ00329 29 KEED-QEYAQVLRMLGNGRLEAYC--------------------------------------FDGEKRLCHIRGKMRK-R 68 (155)
T ss_pred CCCC-CEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCCCEE-E
T ss_conf 7999-6899998604892599996--------------------------------------7998999997486301-1
Q ss_pred EEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 4770299699997467578435988429
Q gi|254780470|r 83 IRISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 83 IRIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
..|-.||-|.|.+-.|.-.|+-|+|+|.
T Consensus 69 ~wI~~GDiVLV~lrdfqd~K~DIi~kY~ 96 (155)
T PTZ00329 69 VWINAGDIILVSLRDFQDSKADVIAKYT 96 (155)
T ss_pred EEEECCCEEEEEEECCCCCCEEEEEECC
T ss_conf 4785599999951526577242898478
No 12
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=97.50 E-value=0.00081 Score=43.36 Aligned_cols=61 Identities=25% Similarity=0.270 Sum_probs=52.0
Q ss_pred EEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEECCCE
Q ss_conf 89998158981799981667765333233544333445555444555554455568828999912511201647702996
Q gi|254780470|r 11 GIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDK 90 (110)
Q Consensus 11 G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~GDk 90 (110)
+.|+.+|-|..|.|.. .||...+|.+.||||+ ++-|-.||-
T Consensus 4 ~~V~~~lG~~r~~v~c--------------------------------------~DG~~rl~~ipGk~rk-rvWI~~gD~ 44 (78)
T cd04456 4 VRVLRMLGNNRHEVEC--------------------------------------ADGQRRLVSIPGKLRK-NIWIKRGDF 44 (78)
T ss_pred EEEEECCCCCEEEEEE--------------------------------------CCCCEEEEEECCCCEE-EEEEECCCE
T ss_conf 9999836997799991--------------------------------------8999999994063334-089836999
Q ss_pred EEEEECCC-CCCCCEEEEEEC
Q ss_conf 99997467-578435988429
Q gi|254780470|r 91 VKVAMNPY-DMTRARITYRFK 110 (110)
Q Consensus 91 V~Ve~SPY-DLtkGRItyR~K 110 (110)
|.|+.-+| +=.|+-|+|+|-
T Consensus 45 VlV~~~e~~~d~K~dIi~ky~ 65 (78)
T cd04456 45 LIVDPIEEGEDVKADIIFVYC 65 (78)
T ss_pred EEEEEHHHCCCCEEEEEEECC
T ss_conf 999881237984699999679
No 13
>PRK00098 ribosome-associated GTPase; Reviewed
Probab=96.72 E-value=0.0054 Score=38.59 Aligned_cols=60 Identities=22% Similarity=0.327 Sum_probs=46.6
Q ss_pred EEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEECC
Q ss_conf 97899981589817999816677653332335443334455554445555544555688289999125112016477029
Q gi|254780470|r 9 FSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLG 88 (110)
Q Consensus 9 ~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~G 88 (110)
|+|.|+... +..|.|+. ++|.++.|.+.|++|+..++.+.|
T Consensus 1 m~G~Vi~~~-~~~y~V~~--------------------------------------~~g~~~~c~~rG~~r~~~~~~~VG 41 (298)
T PRK00098 1 MEGKIIKAL-GGFYYVET--------------------------------------EDGTVYQCRARGKFRKKAITPTVG 41 (298)
T ss_pred CEEEEEEEE-CCEEEEEE--------------------------------------CCCCEEEEEECCEEECCCCCCCCC
T ss_conf 958999999-99999994--------------------------------------899699999330350579889988
Q ss_pred CEEEEEECCCCCCCCEEEEEE
Q ss_conf 969999746757843598842
Q gi|254780470|r 89 DKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 89 DkV~Ve~SPYDLtkGRItyR~ 109 (110)
|.|.++. .+-.+|.|+-.+
T Consensus 42 D~V~~~~--~~~~~g~I~~il 60 (298)
T PRK00098 42 DRVEISA--ENNSEGVILEIH 60 (298)
T ss_pred EEEEEEE--CCCCEEEEEEEE
T ss_conf 6999998--469849999981
No 14
>PRK12289 ribosome-associated GTPase; Reviewed
Probab=96.71 E-value=0.0081 Score=37.55 Aligned_cols=69 Identities=19% Similarity=0.250 Sum_probs=52.9
Q ss_pred CEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEE
Q ss_conf 45999789998158981799981667765333233544333445555444555554455568828999912511201647
Q gi|254780470|r 5 ETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIR 84 (110)
Q Consensus 5 d~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IR 84 (110)
..-.+-|+|+.+. +.-|+|+++++.. ..+..++|..-|++|+-.++
T Consensus 5 ~~~~l~G~Vi~~~-~~fY~V~~d~~~~---------------------------------~~~~~llC~~Rg~lrk~~~~ 50 (351)
T PRK12289 5 TTAQLLGTVVAVQ-ANFYQVRLDQPPL---------------------------------NPPSLLLCTRRTRLKKIGQQ 50 (351)
T ss_pred CCCCEEEEEEEEE-CCEEEEEECCCCC---------------------------------CCCCEEEEEEEEEECCCCCC
T ss_conf 5674389999777-8679999546766---------------------------------77734667875664268998
Q ss_pred EECCCEEEEEECCCCCCCCEEEE
Q ss_conf 70299699997467578435988
Q gi|254780470|r 85 ISLGDKVKVAMNPYDMTRARITY 107 (110)
Q Consensus 85 Il~GDkV~Ve~SPYDLtkGRIty 107 (110)
+++||+|.|+..++.-.+|-|.-
T Consensus 51 v~VGD~V~ve~~d~~~~~G~I~~ 73 (351)
T PRK12289 51 VMVGDRVVVEEPDWQGQRGAIAE 73 (351)
T ss_pred CCCCCEEEEEECCCCCCEEEEEE
T ss_conf 76577799964178898188968
No 15
>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=96.51 E-value=0.0076 Score=37.73 Aligned_cols=59 Identities=17% Similarity=0.252 Sum_probs=45.0
Q ss_pred EEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEECC
Q ss_conf 97899981589817999816677653332335443334455554445555544555688289999125112016477029
Q gi|254780470|r 9 FSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLG 88 (110)
Q Consensus 9 ~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~G 88 (110)
|+|.|+.... ..|.|+. ++|..+.|.+.||+|+....+++|
T Consensus 1 m~G~Vi~~~g-~~y~V~~--------------------------------------~~g~~~~c~~RG~~r~~~~~~~vG 41 (68)
T cd04466 1 MEGLIIKAIG-GFYYVET--------------------------------------EDGKIYECRLRGKFRKDKNPPAVG 41 (68)
T ss_pred CEEEEEEEEC-CEEEEEE--------------------------------------CCCCEEEEEEEEEECCCCCCCCCC
T ss_conf 9799999999-9999993--------------------------------------999799999734791579998642
Q ss_pred CEEEEEECCCCCCCCEEEEE
Q ss_conf 96999974675784359884
Q gi|254780470|r 89 DKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 89 DkV~Ve~SPYDLtkGRItyR 108 (110)
|.|.++... -..|.|+--
T Consensus 42 D~V~~~~~~--~~~g~I~~i 59 (68)
T cd04466 42 DRVEFEPED--DGEGVIEEI 59 (68)
T ss_pred EEEEEEECC--CCEEEEEEE
T ss_conf 399999998--996999899
No 16
>KOG3403 consensus
Probab=94.62 E-value=0.021 Score=35.19 Aligned_cols=51 Identities=24% Similarity=0.453 Sum_probs=43.4
Q ss_pred CCCCCCCCCCCEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 5544555688289999125112016477029969999746757843598842
Q gi|254780470|r 58 GVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 58 g~~~~s~~~~~~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
|-++++.-+|..-+||+-||+|+ +++|.+||-+.|.+--|+-.|+-|+..|
T Consensus 45 Gr~e~~CfDGvkR~~hiRGklrk-kVwi~~GDIiLv~lRD~qd~kaDvilKY 95 (145)
T KOG3403 45 GRLEASCFDGVKRLCHIRGKLRK-KVWINQGDIILVGLRDYQDDKADVILKY 95 (145)
T ss_pred CCEEEEEECCHHHHHHHHCCCEE-EEEECCCCEEEEEEECCCCCCCCEEEHH
T ss_conf 72789971243446420130101-4764378889997002665432431010
No 17
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=94.51 E-value=0.18 Score=29.76 Aligned_cols=76 Identities=26% Similarity=0.388 Sum_probs=47.7
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEEECCCE--EEEEEE
Q ss_conf 9978999815898179998166776533323354433344555544455555445556882-8999912511--201647
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNA-VVIAYTAGRM--RKHRIR 84 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~-~VlA~isGKm--Rk~~IR 84 (110)
+|+|+|+...|.+.| |+|++. +-+|.-|++...+. ...---...+ |+..=+
T Consensus 4 ~f~g~I~~v~~~GiF-V~l~~~-------------------------~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~ 57 (83)
T cd04471 4 EFDGVISGVTSFGLF-VELDNL-------------------------TVEGLVHVSTLGDDYYEFDEENHALVGERTGKV 57 (83)
T ss_pred EEEEEEEEEEEEEEE-EEEECC-------------------------CEEEEEECCCCCCCCEEECCCCEEEECCCCCCE
T ss_conf 999999989830699-998288-------------------------739999822145672244740218981347759
Q ss_pred EECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 7029969999746757843598842
Q gi|254780470|r 85 ISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 85 Il~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
.-+||+|+|.+.--|..++||.+.+
T Consensus 58 ~~lGd~v~V~i~~vd~~~~~I~f~l 82 (83)
T cd04471 58 FRLGDKVKVRVVRVDLDRRKIDFEL 82 (83)
T ss_pred EECCCEEEEEEEEEECCCCEEEEEE
T ss_conf 9789999999999943039898997
No 18
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=93.85 E-value=0.21 Score=29.38 Aligned_cols=41 Identities=24% Similarity=0.318 Sum_probs=33.3
Q ss_pred CCEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 8289999125112016477029969999746757843598842
Q gi|254780470|r 67 NAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 67 ~~~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
+.++.|.+.|++|+....+++||.|.++.. +-..|+|+-.+
T Consensus 17 ~~~~~~~~rg~~~~~~~~~~VGD~V~~~~~--~~~~g~I~~i~ 57 (287)
T cd01854 17 GGELRCRARGKLRKKGIKPVVGDWVEVEPD--DDGEGVIVRVL 57 (287)
T ss_pred CEEEEEEEEEECCCCCCCCCCCEEEEEEEC--CCCEEEEEEEE
T ss_conf 969999980010567999634659999974--79808999994
No 19
>PRK05054 exoribonuclease II; Provisional
Probab=92.71 E-value=0.49 Score=27.19 Aligned_cols=71 Identities=23% Similarity=0.336 Sum_probs=43.1
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---EE------EEEECCCE
Q ss_conf 9978999815898179998166776533323354433344555544455555445556882---89------99912511
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNA---VV------IAYTAGRM 78 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~---~V------lA~isGKm 78 (110)
.|+|+|+-+.+.+.| |+|.++ |-+|.-|++.+... .. .....|+
T Consensus 564 ~f~g~Is~vt~fG~f-V~L~~~-------------------------~~eG~V~~~~l~~~~~~~~~~~~~~~~~~~~~- 616 (644)
T PRK05054 564 RFAAEIIDISRGGMR-VRLLEN-------------------------GAIAFIPAPFLHAVRDELVCNQENGTVQIKGE- 616 (644)
T ss_pred EEEEEEEEEEECCEE-EEEECC-------------------------CEEEEEEEEECCCCCCEEEECCHHHHEECCCC-
T ss_conf 278999759817789-998668-------------------------50899981132567733898202210340586-
Q ss_pred EEEEEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 2016477029969999746757843598842
Q gi|254780470|r 79 RKHRIRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 79 Rk~~IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
| +.-+||+|+|.+.--|+.+++|+||-
T Consensus 617 ~----~yrlGd~v~V~v~~vd~~~r~I~~~p 643 (644)
T PRK05054 617 T----VYKLGDVIDVTLAEVRMETRSIIARP 643 (644)
T ss_pred E----EEECCCEEEEEEEEEECHHCEEEEEE
T ss_conf 8----99789999999999800018487697
No 20
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=92.04 E-value=0.71 Score=26.26 Aligned_cols=71 Identities=30% Similarity=0.494 Sum_probs=50.8
Q ss_pred EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CEEEEEECCC
Q ss_conf 9997899981589817999816677653332335443334455554445555544555688---------2899991251
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDN---------AVVIAYTAGR 77 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~---------~~VlA~isGK 77 (110)
=+|+|+|+-+..=++| |+|+++ .=+|.-+||.+.+ +...+-=+||
T Consensus 674 ~~f~G~Is~VT~FG~F-VeL~~~-------------------------~ieGLVhI~~L~dDYY~Fd~~~~~L~G~R~gk 727 (755)
T TIGR02063 674 EEFEGVISGVTSFGLF-VELENN-------------------------TIEGLVHISTLKDDYYVFDEKGLALVGERTGK 727 (755)
T ss_pred CEEEEEEEEEEEEEEE-EEECCC-------------------------EEEEEEECCCCCCCCCEECCCCCEEEEECCCC
T ss_conf 6887799756620138-973674-------------------------11102632789885630752207886432687
Q ss_pred EEEEEEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 12016477029969999746757843598842
Q gi|254780470|r 78 MRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 78 mRk~~IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
. .-+||+|+|-+--=|+-.|+|-|.+
T Consensus 728 ----~--frLGD~v~V~V~~ad~~~~~idF~L 753 (755)
T TIGR02063 728 ----V--FRLGDRVKVRVVKADLDTGKIDFEL 753 (755)
T ss_pred ----E--EECCCEEEEEEEEECCCCCEEEEEE
T ss_conf ----3--7248748999999610336698997
No 21
>PRK11642 exoribonuclease R; Provisional
Probab=91.90 E-value=0.98 Score=25.45 Aligned_cols=75 Identities=24% Similarity=0.351 Sum_probs=47.5
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCE----EEEEE
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511----20164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRM----RKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKm----Rk~~I 83 (110)
+|+|+|+-+-+-+.| |+|++ .+-+|.-+||.+.+---. |-+-.+ |++.-
T Consensus 646 ~f~G~IsgVt~fG~F-VeL~~-------------------------~~vEGLVhvs~L~dD~Y~-yd~~~~~LvG~rtg~ 698 (813)
T PRK11642 646 VFKGVIASVTGFGFF-VRLDD-------------------------LFIDGLVHVSSLDNDYYR-FDQVGQRLIGESSGQ 698 (813)
T ss_pred EEEEEEEEEEEEEEE-EEECC-------------------------CCEEEEEECCCCCCCEEE-ECCCCCEEEEEECCC
T ss_conf 788999607610089-99548-------------------------863788880128883189-833578898650797
Q ss_pred EEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 77029969999746757843598842
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
+.-+||+|+|.+.--|+.+..|-|.+
T Consensus 699 ~y~lGD~V~V~v~~Vd~~~~qIDfeL 724 (813)
T PRK11642 699 TYRLGDRVEVRVEAVNMDERKIDFSL 724 (813)
T ss_pred EEECCCEEEEEEEEECHHHCEEEEEE
T ss_conf 88269979999999742137355898
No 22
>PRK07252 hypothetical protein; Provisional
Probab=72.91 E-value=8.6 Score=19.96 Aligned_cols=63 Identities=13% Similarity=0.220 Sum_probs=41.8
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC----CEEEEEE
Q ss_conf 997899981589817999816677653332335443334455554445555544555688289999125----1120164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAG----RMRKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isG----KmRk~~I 83 (110)
.++|+|+...|.+.|- .|. +|..=+.|+|- ++..-.=
T Consensus 6 iv~G~V~~I~~fGaFV-~l~--------------------------------------~gv~GLiHISEis~~~v~~~~~ 46 (120)
T PRK07252 6 KLKGTITGIKPYGAFV-ALE--------------------------------------NGTTGLIHISEIKTGFIDNIHQ 46 (120)
T ss_pred EEEEEEEEEECCEEEE-EEC--------------------------------------CCCEEEEEHHHHCCCCCCCHHH
T ss_conf 9999999997545799-957--------------------------------------9957888866601020049999
Q ss_pred EEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 77029969999746757843598842
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
-+-+||.|+|-+---|-.++||..-+
T Consensus 47 ~~kvGd~V~vkVi~ID~e~~rIsLSi 72 (120)
T PRK07252 47 LLKVGNEVLVQVIDIDEYTKKASLSM 72 (120)
T ss_pred HCCCCCEEEEEEEEEECCCCEEECCH
T ss_conf 47899999999999868999886136
No 23
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=70.64 E-value=10 Score=19.57 Aligned_cols=67 Identities=28% Similarity=0.428 Sum_probs=43.2
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCC-EEEEEEEEE
Q ss_conf 9978999815898179998166776533323354433344555544455555445556882899991251-120164770
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGR-MRKHRIRIS 86 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGK-mRk~~IRIl 86 (110)
.+.|.|....+ ..+.|.+.. +-.|.-|+ .+++-+ ......+..
T Consensus 5 iv~g~V~~v~~-~g~~v~i~~--------------------------~~~g~l~~---------~~l~~~~~~~~~~~~~ 48 (72)
T smart00316 5 VVEGTVTEITP-FGAFVDLGN--------------------------GVEGLIPI---------SELSDKRVKDPEEVLK 48 (72)
T ss_pred EEEEEEEEEEC-CEEEEEECC--------------------------CCEEEEEH---------HHCCCCCCCCHHHEEC
T ss_conf 99999999978-739999769--------------------------98999980---------7505555478468363
Q ss_pred CCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 299699997467578435988429
Q gi|254780470|r 87 LGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 87 ~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
+||.|++.+.-++..+++|..-+|
T Consensus 49 ~G~~v~~~V~~~~~~~~~i~ls~k 72 (72)
T smart00316 49 VGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 898999999999999999999859
No 24
>TIGR00523 eIF-1A translation initiation factor eIF-1A; InterPro: IPR001253 Eukaryotic translation initiation factor A (eIF-1A) (formerly known as eiF-4C) is a protein that seems to be required for maximal rate of protein biosynthesis. It enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA to 40S ribosomal subunits . Archaebacteria also seem to possess an eIF-1A homolog.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=70.56 E-value=3 Score=22.59 Aligned_cols=49 Identities=22% Similarity=0.427 Sum_probs=38.6
Q ss_pred CCCCCCCCEEEEEECCCEEEEEEEEECCCEEEEEECCCC-CCCCEEEEEEC
Q ss_conf 455568828999912511201647702996999974675-78435988429
Q gi|254780470|r 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYD-MTRARITYRFK 110 (110)
Q Consensus 61 ~~s~~~~~~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYD-LtkGRItyR~K 110 (110)
.+...+|+.-++++.|++++ +|-+-.||-+.+..-.+. -.+.-|+|||.
T Consensus 35 ~~~c~dg~~~~~~~~g~~~~-~~w~~~gd~~~~~~~~~~~~~~~d~~~~~~ 84 (99)
T TIGR00523 35 KVRCLDGNKRLGRIPGKLKK-KIWVREGDVVLVKPWEFQGDDKCDIVWRYT 84 (99)
T ss_pred EEEECCCCCHHHHCCCHHHH-HEECCCCCEEEEEECCCCCCCCCEEEEECC
T ss_conf 45412341011111100110-001036866787402346754320111023
No 25
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=69.42 E-value=9.1 Score=19.82 Aligned_cols=20 Identities=15% Similarity=0.242 Sum_probs=16.1
Q ss_pred EEEEEEEEECCCCCCEEEEE
Q ss_conf 99978999815898179998
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L 26 (110)
-.+...|+++|||+++.|+=
T Consensus 152 ~tIaa~Vv~VLpNGnL~I~G 171 (238)
T PRK12696 152 ATIAARVLRVMPGGLLQVEG 171 (238)
T ss_pred EEEEEEEEEECCCCCEEEEE
T ss_conf 99999999987799599999
No 26
>pfam07202 Tcp10_C T-complex protein 10 C-terminus. This family represents the C-terminus (approximately 180 residues) of eukaryotic T-complex protein 10. The T-complex is involved in spermatogenesis in mice.
Probab=68.63 E-value=7.3 Score=20.38 Aligned_cols=23 Identities=30% Similarity=0.553 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCCEEEEEECCCEE
Q ss_conf 55544555688289999125112
Q gi|254780470|r 57 DGVDPISYLDNAVVIAYTAGRMR 79 (110)
Q Consensus 57 ~g~~~~s~~~~~~VlA~isGKmR 79 (110)
+|+--+.|.||....-|.+||.|
T Consensus 144 dGtvk~vy~~G~qet~y~~Grvr 166 (179)
T pfam07202 144 DGTVKTVYCNGRQETKYSSGRVR 166 (179)
T ss_pred CCCEEEEECCCCEEEECCCCCEE
T ss_conf 99699992698688874896489
No 27
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=67.16 E-value=12 Score=19.14 Aligned_cols=60 Identities=23% Similarity=0.263 Sum_probs=41.7
Q ss_pred EEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE----EEEE
Q ss_conf 978999815898179998166776533323354433344555544455555445556882899991251120----1647
Q gi|254780470|r 9 FSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK----HRIR 84 (110)
Q Consensus 9 ~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk----~~IR 84 (110)
++|.|....+.+.| |++. ++..-++|+|.-... ..-.
T Consensus 1 v~G~V~~i~~~G~f-V~~~--------------------------------------~~~~gli~~s~~s~~~~~~~~~~ 41 (65)
T cd00164 1 VTGKVVSITKFGVF-VELE--------------------------------------DGVEGLVHISELSDKFVKDPSEV 41 (65)
T ss_pred CEEEEEEEECCEEE-EEEC--------------------------------------CCEEEEEEHHHHCCCCCCCHHHE
T ss_conf 98999999784599-9989--------------------------------------87178898889167653595109
Q ss_pred EECCCEEEEEECCCCCCCCEEEE
Q ss_conf 70299699997467578435988
Q gi|254780470|r 85 ISLGDKVKVAMNPYDMTRARITY 107 (110)
Q Consensus 85 Il~GDkV~Ve~SPYDLtkGRIty 107 (110)
+-+||.|++.+-..|..++||..
T Consensus 42 ~~~G~~V~~~Vi~vd~~~~~i~L 64 (65)
T cd00164 42 FKVGDEVEVKVLEVDPEKGRISL 64 (65)
T ss_pred ECCCCEEEEEEEEEECCCCEEEC
T ss_conf 85999999999999899998976
No 28
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=66.94 E-value=12 Score=19.11 Aligned_cols=63 Identities=30% Similarity=0.380 Sum_probs=40.3
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCE--EEEEE--
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511--20164--
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRM--RKHRI-- 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKm--Rk~~I-- 83 (110)
.++|+|....|-+.| |++. ++-.=+.|+|-=- |...+
T Consensus 3 vv~G~V~~I~~fGaF-V~l~--------------------------------------~g~~GL~HiSeis~~~v~~~~~ 43 (69)
T cd05692 3 VVEGTVTRLKPFGAF-VELG--------------------------------------GGISGLVHISQIAHKRVKDVKD 43 (69)
T ss_pred EEEEEEEEEECCEEE-EEEC--------------------------------------CCCEEEEEHHHHCCCCCCCHHH
T ss_conf 999999999853899-9968--------------------------------------9988999969834565579889
Q ss_pred EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 770299699997467578435988429
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
.+-+||.|++-+---| .++||..-.|
T Consensus 44 ~~~~Gd~v~vkVi~id-~~~ri~LS~K 69 (69)
T cd05692 44 VLKEGDKVKVKVLSID-ARGRISLSIK 69 (69)
T ss_pred HCCCCCEEEEEEEEEC-CCCCEEECCC
T ss_conf 1789999999999999-9996680159
No 29
>PRK05807 hypothetical protein; Provisional
Probab=64.59 E-value=13 Score=18.84 Aligned_cols=66 Identities=18% Similarity=0.205 Sum_probs=43.1
Q ss_pred CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf 97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK 80 (110)
Q Consensus 1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk 80 (110)
|+=+.--.++|+|+.+.|-+.|-- |. |..=|.|+|- +-.
T Consensus 1 MslevG~iv~G~V~~I~~fGaFV~-l~---------------------------------------g~~GLvHISE-is~ 39 (136)
T PRK05807 1 MTLEAGSILEGTVVNITNFGAFVE-VE---------------------------------------GKTGLVHISE-VAD 39 (136)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEE-EC---------------------------------------CEEEEEEHHH-HCC
T ss_conf 974578899999999972447999-78---------------------------------------9276898567-077
Q ss_pred EEE-----EEECCCEEEEEECCCCCCCCEEEEE
Q ss_conf 164-----7702996999974675784359884
Q gi|254780470|r 81 HRI-----RISLGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 81 ~~I-----RIl~GDkV~Ve~SPYDLtkGRItyR 108 (110)
.+| -+-.||.|+|-+--.| .+|||-.-
T Consensus 40 ~~Vk~i~d~lk~Gd~V~vkVl~iD-~~gkI~LS 71 (136)
T PRK05807 40 TYVKDIREHLKEQDKVKVKVISID-DNGKISLS 71 (136)
T ss_pred CCCCCHHHHCCCCCEEEEEEEEEC-CCCCCEEE
T ss_conf 643699996789999999999989-99981433
No 30
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=60.96 E-value=16 Score=18.45 Aligned_cols=68 Identities=28% Similarity=0.443 Sum_probs=42.4
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL 87 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~ 87 (110)
.++|+|...-+.+.| |+|.. |-+|.-|+|-.... +...-.=.+.+
T Consensus 7 iv~G~V~~i~~~G~f-V~l~~--------------------------~~~g~v~~s~ls~~--------~~~~~~~~~~~ 51 (74)
T pfam00575 7 VVKGTVTRVTKGGAF-VDLGN--------------------------GVEGFIPISEISDD--------RVEDPDEVLKV 51 (74)
T ss_pred EEEEEEEEEECCEEE-EEECC--------------------------CCEEEEEHHHCCCC--------CCCCHHHHHCC
T ss_conf 999999999877599-99789--------------------------97999984461365--------55677683059
Q ss_pred CCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 99699997467578435988429
Q gi|254780470|r 88 GDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 88 GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
||+|++-+.-.|..++||..-.|
T Consensus 52 G~~v~~~V~~vd~~~~~i~lS~k 74 (74)
T pfam00575 52 GDEVEVKVLKVDKERGRIILSIR 74 (74)
T ss_pred CCEEEEEEEEEECCCCEEEEEEC
T ss_conf 99999999999999999999839
No 31
>smart00675 DM11 Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329.
Probab=60.63 E-value=8.5 Score=20.02 Aligned_cols=39 Identities=8% Similarity=0.055 Sum_probs=30.9
Q ss_pred CCCCCEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCCE
Q ss_conf 56882899991251120164770299699997467578435
Q gi|254780470|r 64 YLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRAR 104 (110)
Q Consensus 64 ~~~~~~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYDLtkGR 104 (110)
+...... -|+||-+..-- .|.|+||+.+.++.|-+.||.
T Consensus 37 ~~~~~d~-v~vSGn~T~~W-diqP~DrI~~~~~v~~~dRG~ 75 (164)
T smart00675 37 VDMDPDG-LHISGNITVIW-DVQPTDRISARVSVMHFERGT 75 (164)
T ss_pred EEECCCE-EEEECEEEEEE-ECCCCCEEEEEEEEEEECCCE
T ss_conf 9864875-99945098999-528999899999999973873
No 32
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=54.89 E-value=20 Score=17.84 Aligned_cols=59 Identities=22% Similarity=0.345 Sum_probs=38.2
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCE--EEEEE--
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511--20164--
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRM--RKHRI-- 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKm--Rk~~I-- 83 (110)
.++|+|....|-+.|- +|. .+..-+.|+|-=- |..++
T Consensus 3 iv~G~V~~i~~fG~FV-~l~--------------------------------------~g~~GLiHiSeis~~~v~~~~~ 43 (68)
T cd04472 3 IYEGKVVKIKDFGAFV-EIL--------------------------------------PGKDGLVHISELSDERVEKVED 43 (68)
T ss_pred EEEEEEEEEECCEEEE-EEC--------------------------------------CCCEEEEEHHHHCCCCCCCHHH
T ss_conf 9999999997329999-957--------------------------------------9962488868934565469889
Q ss_pred EEECCCEEEEEECCCCCCCCEEE
Q ss_conf 77029969999746757843598
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRIt 106 (110)
-+-+||+|++.+--.| .++||.
T Consensus 44 ~~~~Gd~v~vkVi~iD-~~~ri~ 65 (68)
T cd04472 44 VLKVGDEVKVKVIEVD-DRGRIS 65 (68)
T ss_pred HCCCCCEEEEEEEEEC-CCCCCC
T ss_conf 0789999999999999-999720
No 33
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=54.53 E-value=20 Score=17.81 Aligned_cols=70 Identities=20% Similarity=0.196 Sum_probs=44.5
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL 87 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~ 87 (110)
-++|.|+...|.+.|- .|..- .|-+|.-++|-.. .++++.-+=.+-+
T Consensus 6 iv~G~V~~i~~~GafV-~l~e~------------------------~g~eGlihiSEis--------~~~v~~~~d~~~~ 52 (76)
T cd04452 6 LVVVTVKSIADMGAYV-SLLEY------------------------GNIEGMILLSELS--------RRRIRSIRKLVKV 52 (76)
T ss_pred EEEEEEEEEECCEEEE-EECCC------------------------CCCEEEEEHHHCC--------CCCCCCHHHHCCC
T ss_conf 9999999997346999-97336------------------------9919999979968--------4511599995589
Q ss_pred CCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 99699997467578435988429
Q gi|254780470|r 88 GDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 88 GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
||+|++.+--.|..++||..-.|
T Consensus 53 G~~v~~kVi~vD~~k~~i~LS~K 75 (76)
T cd04452 53 GRKEVVKVIRVDKEKGYIDLSKK 75 (76)
T ss_pred CCEEEEEEEEEECCCCEEEEEEC
T ss_conf 99999999999789999982236
No 34
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=52.59 E-value=22 Score=17.62 Aligned_cols=65 Identities=18% Similarity=0.297 Sum_probs=41.9
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC----CEEEEEE
Q ss_conf 997899981589817999816677653332335443334455554445555544555688289999125----1120164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAG----RMRKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isG----KmRk~~I 83 (110)
.++|+|....|-+.| |+|+..+ ..=++|+|- +...-.=
T Consensus 5 ~v~G~V~~i~~fG~F-V~l~g~~-------------------------------------i~GLvHiSels~~~~~~~~~ 46 (77)
T cd05708 5 KIDGTVRRVEDYGVF-IDIDGTN-------------------------------------VSGLCHKSEISDNRVADASK 46 (77)
T ss_pred EEEEEEEEEECEEEE-EEECCCC-------------------------------------EEEEEEHHHHCCCCCCCHHH
T ss_conf 999999999641789-9967898-------------------------------------07998878817565689889
Q ss_pred EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 770299699997467578435988429
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
..-.||+|++-+---|..++||..-.|
T Consensus 47 ~~~~Gd~V~vkVl~iD~e~~rI~LSiK 73 (77)
T cd05708 47 LFRVGDKVRAKVLKIDAEKKRISLGLK 73 (77)
T ss_pred HCCCCCEEEEEEEEEECCCCEEEEEEE
T ss_conf 168999999999999899999998984
No 35
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=51.12 E-value=23 Score=17.49 Aligned_cols=60 Identities=27% Similarity=0.303 Sum_probs=40.9
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCE--EEE--EE
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511--201--64
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRM--RKH--RI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKm--Rk~--~I 83 (110)
.++|.|+...+-+.|- +|. +|-.-+.|+|-=- +++ --
T Consensus 6 ~v~G~V~~It~fG~FV-~i~--------------------------------------~g~eGLvHiSelsw~~~~~~p~ 46 (72)
T cd05689 6 RLFGKVTNLTDYGCFV-ELE--------------------------------------EGVEGLVHVSEMDWTNKNIHPS 46 (72)
T ss_pred EEEEEEEEEECCEEEE-EEC--------------------------------------CCCEEEEEHHHCCCCCCCCCHH
T ss_conf 9999998994762399-966--------------------------------------9938999976631654667963
Q ss_pred -EEECCCEEEEEECCCCCCCCEEE
Q ss_conf -77029969999746757843598
Q gi|254780470|r 84 -RISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 84 -RIl~GDkV~Ve~SPYDLtkGRIt 106 (110)
-+-+||.|++.+--.|..+.||.
T Consensus 47 ~~~~~Gd~v~vkIl~iD~e~~rIs 70 (72)
T cd05689 47 KVVSLGDEVEVMVLDIDEERRRIS 70 (72)
T ss_pred HHCCCCCEEEEEEEEEECCCCEEC
T ss_conf 603899999999999959979953
No 36
>pfam11858 DUF3378 Domain of unknown function (DUF3378). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 80 amino acids in length.
Probab=50.54 E-value=14 Score=18.66 Aligned_cols=14 Identities=36% Similarity=0.646 Sum_probs=11.9
Q ss_pred CCCEEEEEECCCEE
Q ss_conf 88289999125112
Q gi|254780470|r 66 DNAVVIAYTAGRMR 79 (110)
Q Consensus 66 ~~~~VlA~isGKmR 79 (110)
+|..|.+|.|||..
T Consensus 38 ~~~tIt~Y~SGKV~ 51 (82)
T pfam11858 38 PGATITAYTSGKVL 51 (82)
T ss_pred CCEEEEEEECCEEE
T ss_conf 98199998056189
No 37
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=50.34 E-value=19 Score=17.94 Aligned_cols=62 Identities=21% Similarity=0.328 Sum_probs=38.1
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL 87 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~ 87 (110)
.+...|+++|||+++.|+=. -.|.. |+-.=.-.++|-.|-.-| .
T Consensus 162 tItatVv~VLpNGNLvI~Ge--------------------------------K~v~v-N~e~e~IrlsGiVRP~DI---~ 205 (246)
T PRK12699 162 TITVTVVDILPNGNLLVSGE--------------------------------KQIGI-NQGHEFIRLSGVINPINV---I 205 (246)
T ss_pred EEEEEEEEECCCCCEEEEEE--------------------------------EEEEE-CCCEEEEEEEEEECHHHC---C
T ss_conf 99999999878998899987--------------------------------99998-898799999999783436---7
Q ss_pred CCEEEEEECCCCCCCCEEEEEE
Q ss_conf 9969999746757843598842
Q gi|254780470|r 88 GDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 88 GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
... ++---+.-+||.|.-
T Consensus 206 dNt----V~St~IAdArI~Y~G 223 (246)
T PRK12699 206 NNT----VSSIQVADARIEYRG 223 (246)
T ss_pred CCE----ECHHEEEEEEEEECC
T ss_conf 870----830012548999823
No 38
>pfam02107 FlgH Flagellar L-ring protein.
Probab=48.24 E-value=26 Score=17.22 Aligned_cols=63 Identities=19% Similarity=0.298 Sum_probs=36.3
Q ss_pred EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEE
Q ss_conf 99978999815898179998166776533323354433344555544455555445556882899991251120164770
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRIS 86 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl 86 (110)
-.+...|+++|||+++.|+=. + .|. .|+-.-.-.++|-+|-.-|.
T Consensus 96 ~~ita~V~~VlpNGnLvI~G~-------K-------------------------~i~-vn~e~e~i~lsGiVRp~DI~-- 140 (181)
T pfam02107 96 GTITVTVTDVLPNGNLVIRGE-------K-------------------------EVR-VNQGDEYIRLSGIVRPEDIS-- 140 (181)
T ss_pred EEEEEEEEEECCCCCEEEEEE-------E-------------------------EEE-ECCCEEEEEEEEEECHHHCC--
T ss_conf 999999999868998999999-------9-------------------------999-89988999999999989979--
Q ss_pred CCCEEEEEECCCCCCCCEEEEE
Q ss_conf 2996999974675784359884
Q gi|254780470|r 87 LGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 87 ~GDkV~Ve~SPYDLtkGRItyR 108 (110)
++.. ++-..+--+||.|.
T Consensus 141 ~~Nt----V~S~~IAdA~I~y~ 158 (181)
T pfam02107 141 PDNT----VSSTRIADARIEYG 158 (181)
T ss_pred CCCE----ECCCEEEEEEEEEE
T ss_conf 9975----96003355899980
No 39
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=47.98 E-value=22 Score=17.61 Aligned_cols=20 Identities=30% Similarity=0.343 Sum_probs=16.0
Q ss_pred EEEEEEEEECCCCCCEEEEE
Q ss_conf 99978999815898179998
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L 26 (110)
-.+...|+++|||+++.|+=
T Consensus 141 gtItatV~~VLPNGNLvI~G 160 (227)
T PRK12697 141 GTITVTVTNVLPNGNLVVSG 160 (227)
T ss_pred EEEEEEEEEECCCCCEEEEE
T ss_conf 99999999987799399999
No 40
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=47.45 E-value=26 Score=17.15 Aligned_cols=20 Identities=20% Similarity=0.268 Sum_probs=16.4
Q ss_pred EEEEEEEEECCCCCCEEEEE
Q ss_conf 99978999815898179998
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L 26 (110)
-.+...|+++|||+++.|+=
T Consensus 133 g~itvtV~~VlpNGNLvI~G 152 (220)
T PRK12407 133 GSITVAVHQVLPNGVLVIRG 152 (220)
T ss_pred EEEEEEEEEECCCCCEEEEE
T ss_conf 89999999987899689999
No 41
>COG1162 Predicted GTPases [General function prediction only]
Probab=46.43 E-value=27 Score=17.05 Aligned_cols=37 Identities=22% Similarity=0.287 Sum_probs=29.5
Q ss_pred EEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCCEEEEE
Q ss_conf 8999912511201647702996999974675784359884
Q gi|254780470|r 69 VVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 69 ~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYDLtkGRItyR 108 (110)
..-|..-|++|+.....+.||+|.++-.+-. |-|...
T Consensus 29 ~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~~---g~I~~i 65 (301)
T COG1162 29 VYRCRARGNLRKKDLKPVVGDRVVFEDENNN---GVIEKI 65 (301)
T ss_pred EEEEEEECCEECCCCCCCCCCEEEEECCCCC---CEEEEE
T ss_conf 5511762132316766320576997147765---027887
No 42
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=45.39 E-value=28 Score=16.96 Aligned_cols=79 Identities=24% Similarity=0.232 Sum_probs=45.8
Q ss_pred CEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEC---CCEEEE
Q ss_conf 45999789998158981799981667765333233544333445555444555554455568828999912---511201
Q gi|254780470|r 5 ETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTA---GRMRKH 81 (110)
Q Consensus 5 d~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~is---GKmRk~ 81 (110)
-.-+++|+|+.+...+.|- .|... .+++. -.++.+++-...---. =.-.+.
T Consensus 622 vg~~f~g~V~~v~~~g~~V-~l~~~--------~iegl-----------------V~~s~L~~d~y~~~~~~~~l~~~~~ 675 (706)
T COG0557 622 VGEEFDGVVTGVTSFGFFV-ELPEL--------GLEGL-----------------VHISSLPDDYYHFDERGQALVGEKS 675 (706)
T ss_pred CCCEEEEEEEEEECCCEEE-EECCC--------CEEEE-----------------EECCCCCCCEEECCHHHHHHHCCCC
T ss_conf 5876889999873275799-96275--------40334-----------------7635588610302301123203556
Q ss_pred EEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 6477029969999746757843598842
Q gi|254780470|r 82 RIRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 82 ~IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
....-+||+|+|.+.--|...+.|.+..
T Consensus 676 ~~~~~lgd~v~v~v~~v~~~~~~i~~~~ 703 (706)
T COG0557 676 GKVYRLGDEVKVKVTSVDLDERKIDFEL 703 (706)
T ss_pred CCCCCCCCEEEEEEEEECCCCCCEEEEE
T ss_conf 6542338869999998705656135885
No 43
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=44.14 E-value=30 Score=16.84 Aligned_cols=60 Identities=18% Similarity=0.166 Sum_probs=40.1
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCC-----EEEEE
Q ss_conf 9978999815898179998166776533323354433344555544455555445556882899991251-----12016
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGR-----MRKHR 82 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGK-----mRk~~ 82 (110)
.++|+|+...+-+.|- +|. ++-.=++|+|-- ...-.
T Consensus 3 ~v~G~V~~i~~fG~FV-~l~--------------------------------------~gieGLvHiselsw~~~~~~~~ 43 (69)
T cd05690 3 VVSGKIKSITDFGIFV-GLD--------------------------------------GGIDGLVHISDISWTQRVRHPS 43 (69)
T ss_pred EEEEEEEEECCCEEEE-EEC--------------------------------------CCCEEEEEHHHHCCCCCCCCHH
T ss_conf 9999999991318999-976--------------------------------------9965999948824566667976
Q ss_pred EEEECCCEEEEEECCCCCCCCEEE
Q ss_conf 477029969999746757843598
Q gi|254780470|r 83 IRISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 83 IRIl~GDkV~Ve~SPYDLtkGRIt 106 (110)
=..-.||+|++-+--.|..+.||.
T Consensus 44 ~~~~~Gd~V~vkVl~iD~e~~ris 67 (69)
T cd05690 44 EIYKKGQEVEAVVLNIDVERERIS 67 (69)
T ss_pred HCCCCCCEEEEEEEEEECCCCEEC
T ss_conf 825899999999999979868863
No 44
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=43.75 E-value=30 Score=16.80 Aligned_cols=64 Identities=27% Similarity=0.354 Sum_probs=39.6
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC-CEEEEEEEEE
Q ss_conf 997899981589817999816677653332335443334455554445555544555688289999125-1120164770
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAG-RMRKHRIRIS 86 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isG-KmRk~~IRIl 86 (110)
.++|.|..+.|-+.| |+|.. |-+|.-|+| |+|- ++..-.=..-
T Consensus 3 iv~G~V~~i~~fG~f-V~l~~--------------------------~i~Glv~~s---------~lsd~~v~~p~~~fk 46 (69)
T cd05697 3 VVKGTIRKLRPSGIF-VKLSD--------------------------HIKGLVPPM---------HLADVRLKHPEKKFK 46 (69)
T ss_pred EEEEEEEEECCCEEE-EEECC--------------------------CEEEEEEHH---------HHCCCCCCCHHHCCC
T ss_conf 999999997384279-99579--------------------------906998789---------908652069889089
Q ss_pred CCCEEEEEECCCCCCCCEEEE
Q ss_conf 299699997467578435988
Q gi|254780470|r 87 LGDKVKVAMNPYDMTRARITY 107 (110)
Q Consensus 87 ~GDkV~Ve~SPYDLtkGRIty 107 (110)
+||+|++-+---|..+.||.-
T Consensus 47 ~G~~Vk~rVl~vD~~~~ri~L 67 (69)
T cd05697 47 PGLKVKCRVLSVEPERKRLVL 67 (69)
T ss_pred CCCEEEEEEEEEECCCCEEEE
T ss_conf 999999999999488799886
No 45
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=43.65 E-value=30 Score=16.80 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=16.3
Q ss_pred EEEEEEEEECCCCCCEEEEE
Q ss_conf 99978999815898179998
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L 26 (110)
..+..+|+++|||++..|+=
T Consensus 145 ~tIaa~V~~VLPNGNLvI~G 164 (231)
T PRK12788 145 FSVAAIVVDVLPNGNLLISG 164 (231)
T ss_pred EEEEEEEEEECCCCCEEEEE
T ss_conf 99999999987899589999
No 46
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=43.46 E-value=30 Score=16.78 Aligned_cols=66 Identities=18% Similarity=0.260 Sum_probs=37.4
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-E----EECCCEEEEE
Q ss_conf 9978999815898179998166776533323354433344555544455555445556882899-9----9125112016
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVI-A----YTAGRMRKHR 82 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~Vl-A----~isGKmRk~~ 82 (110)
.|+|+|+.+-.-+.|- +|.. -+|.-.||.+..--+. - .+-| ++..
T Consensus 2 v~eG~Vs~Vt~fG~FV-~L~~---------------------------ieGLvHiS~l~dD~~~fd~~~~~liG--~r~~ 51 (99)
T cd04460 2 VVEGEVVEVVDFGAFV-RIGP---------------------------VDGLLHISQIMDDYISYDPKNKRLIG--EETK 51 (99)
T ss_pred EEEEEEEEEEECCEEE-EECC---------------------------CEEEEEHHHCCCCEEEECHHHCEEEE--CCCC
T ss_conf 7999999588256699-9328---------------------------10689936757843998124468985--1278
Q ss_pred EEEECCCEEEEEECCCCCCCC
Q ss_conf 477029969999746757843
Q gi|254780470|r 83 IRISLGDKVKVAMNPYDMTRA 103 (110)
Q Consensus 83 IRIl~GDkV~Ve~SPYDLtkG 103 (110)
-.+-+||+|+|-+.--|+.+-
T Consensus 52 ~~~~~GD~V~vrV~~V~~~~r 72 (99)
T cd04460 52 RVLKVGDVVRARIVAVSLKER 72 (99)
T ss_pred CEECCCCEEEEEEEEEECCCC
T ss_conf 698479999999999806206
No 47
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=40.92 E-value=33 Score=16.54 Aligned_cols=20 Identities=25% Similarity=0.395 Sum_probs=16.5
Q ss_pred EEEEEEEEECCCCCCEEEEE
Q ss_conf 99978999815898179998
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L 26 (110)
-.+...|+++|||++..|+=
T Consensus 145 gtIta~V~~VlpNGnL~I~G 164 (231)
T PRK00249 145 GTITVTVTQVLPNGNLVIRG 164 (231)
T ss_pred EEEEEEEEEECCCCCEEEEE
T ss_conf 99999999987899689999
No 48
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=40.35 E-value=34 Score=16.53 Aligned_cols=19 Identities=26% Similarity=0.436 Sum_probs=14.4
Q ss_pred EEEEEEEECCCCCCEEEEE
Q ss_conf 9978999815898179998
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L 26 (110)
.+.-.|+++|||+++.|+=
T Consensus 145 tItvtV~~VlpNGNL~I~G 163 (230)
T PRK12700 145 TITTTVIGVLPNGNLQIAG 163 (230)
T ss_pred EEEEEEEEECCCCCEEEEE
T ss_conf 9999999986699589999
No 49
>PRK08059 general stress protein 13; Validated
Probab=37.99 E-value=37 Score=16.27 Aligned_cols=64 Identities=17% Similarity=0.238 Sum_probs=42.8
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC----CEEEEEE
Q ss_conf 997899981589817999816677653332335443334455554445555544555688289999125----1120164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAG----RMRKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isG----KmRk~~I 83 (110)
.++|.|+...|.+.|- ++. ++-.-+.|+|- +...-+=
T Consensus 9 iv~G~V~~I~~fG~FV-~l~--------------------------------------~gv~GLihiSEls~~~v~~~~~ 49 (119)
T PRK08059 9 VVTGKVTGIQDYGAFV-ALD--------------------------------------EETQGLVHISEITHGFVKDIHD 49 (119)
T ss_pred EEEEEEEEEECEEEEE-EEE--------------------------------------CCCEEEEEHHHHCCCCCCCHHH
T ss_conf 9999999997404899-994--------------------------------------3953788878824566679999
Q ss_pred EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 770299699997467578435988429
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
.+-.||+|++.+--.|..++||..-.|
T Consensus 50 ~~~vGd~V~vkVi~iD~e~~ri~LSlK 76 (119)
T PRK08059 50 FLKVGDEVKVKVLSVDEEHGKISLSIR 76 (119)
T ss_pred HHCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 705899899999999899999987503
No 50
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=37.73 E-value=38 Score=16.25 Aligned_cols=20 Identities=30% Similarity=0.390 Sum_probs=15.8
Q ss_pred EEEEEEEEECCCCCCEEEEE
Q ss_conf 99978999815898179998
Q gi|254780470|r 7 LEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 7 ie~~G~V~E~LPna~FrV~L 26 (110)
-.+...|+|+|||+++.|+=
T Consensus 137 gtIta~V~~VlpNGNL~I~G 156 (224)
T PRK12698 137 GSISANVMQVLPNGNLVIRG 156 (224)
T ss_pred EEEEEEEEEECCCCCEEEEE
T ss_conf 99999999986698099999
No 51
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=37.29 E-value=38 Score=16.21 Aligned_cols=59 Identities=24% Similarity=0.320 Sum_probs=38.1
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEC----CCEEEEEE
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912----51120164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTA----GRMRKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~is----GKmRk~~I 83 (110)
.++|+|+...|.+-|- .+. +-.-+.|+| .+.+.-+=
T Consensus 4 iv~g~V~~i~~fG~FV-~l~---------------------------------------gi~Glihisels~~~~~~~~~ 43 (68)
T cd05688 4 VVEGTVKSITDFGAFV-DLG---------------------------------------GVDGLLHISDMSWGRVKHPSE 43 (68)
T ss_pred EEEEEEEEEECCEEEE-EEC---------------------------------------CEEEEEECHHHCCCCCCCHHH
T ss_conf 9999999995638899-979---------------------------------------989999843646666689889
Q ss_pred EEECCCEEEEEECCCCCCCCEEE
Q ss_conf 77029969999746757843598
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRIt 106 (110)
.+-.||+|++-+---|..|+||.
T Consensus 44 ~~k~Gd~v~~kVi~iD~~k~rIs 66 (68)
T cd05688 44 VVNVGDEVEVKVLKIDKERKRIS 66 (68)
T ss_pred HCCCCCEEEEEEEEEECCCCEEC
T ss_conf 14799999999999999979864
No 52
>TIGR01531 glyc_debranch glycogen debranching enzymye; InterPro: IPR006421 Glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (2.4.1.25 from EC) and amylo-1,6-glucosidase (3.2.1.33 from EC). Site-directed mutagenesis studies in Saccharomyces cerevisiae indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this family belong to the larger alpha-amylase family. The family contains eukaryotic proteins.; GO: 0004134 4-alpha-glucanotransferase activity, 0004135 amylo-alpha-16-glucosidase activity, 0005978 glycogen biosynthetic process.
Probab=36.94 E-value=8.8 Score=19.92 Aligned_cols=16 Identities=38% Similarity=0.877 Sum_probs=10.6
Q ss_pred EECCCCCC-CCEEEEEE
Q ss_conf 97467578-43598842
Q gi|254780470|r 94 AMNPYDMT-RARITYRF 109 (110)
Q Consensus 94 e~SPYDLt-kGRItyR~ 109 (110)
+||-||+. .||.+|||
T Consensus 586 A~sA~~shE~GRLVYrY 602 (1584)
T TIGR01531 586 AMSAWDSHEQGRLVYRY 602 (1584)
T ss_pred HHHHHCCCCCCEEEECC
T ss_conf 98762114376017702
No 53
>TIGR02464 ribofla_fusion conserved hypothetical protein; InterPro: IPR012816 This entry describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (IPR000926 from INTERPRO), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (IPR004794 from INTERPRO) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from Escherichia coli currently is named YbiA. The function(s) of members of this family is unknown..
Probab=36.01 E-value=16 Score=18.35 Aligned_cols=21 Identities=38% Similarity=0.545 Sum_probs=16.4
Q ss_pred EEEEEECCCEEEEEECCCCCC
Q ss_conf 164770299699997467578
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMT 101 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLt 101 (110)
..|=...++++.||-||||.-
T Consensus 124 r~~LL~T~~~~LVEaSP~D~i 144 (180)
T TIGR02464 124 REILLSTGGKKLVEASPYDKI 144 (180)
T ss_pred HHHHHCCCCCCEEEECCCCCE
T ss_conf 998644787403310788860
No 54
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=35.32 E-value=41 Score=16.02 Aligned_cols=64 Identities=22% Similarity=0.256 Sum_probs=41.0
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC----CEEEEEE
Q ss_conf 997899981589817999816677653332335443334455554445555544555688289999125----1120164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAG----RMRKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isG----KmRk~~I 83 (110)
-++|.|++..|.+.|- .|.. +..-+.|+|- +.....=
T Consensus 3 iV~G~V~~i~~~G~fV-~l~~--------------------------------------~v~G~ih~sels~~~~~~~~~ 43 (73)
T cd05691 3 IVTGKVTEVDAKGATV-KLGD--------------------------------------GVEGFLRAAELSRDRVEDATE 43 (73)
T ss_pred EEEEEEEEEECCCEEE-EECC--------------------------------------CCEEEEEHHHCCCCHHHCHHH
T ss_conf 9999999997786899-9289--------------------------------------969999989978211329254
Q ss_pred EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 770299699997467578435988429
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
+.-.||+|++-+---|..+.||..-.|
T Consensus 44 ~~~vGd~v~akIi~iD~~~~ri~LSiK 70 (73)
T cd05691 44 RFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCCCCCEEEEEEEEEECCCCEEEEEEE
T ss_conf 389999999999999788999986742
No 55
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=35.13 E-value=41 Score=16.00 Aligned_cols=38 Identities=24% Similarity=0.293 Sum_probs=28.6
Q ss_pred CCCCEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCC
Q ss_conf 688289999125112016477029969999746757843
Q gi|254780470|r 65 LDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRA 103 (110)
Q Consensus 65 ~~~~~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYDLtkG 103 (110)
.+|..+......+.|+..||+.+||.|.| ..|+.++..
T Consensus 7 ~~~~~~~v~~~r~~r~~~i~i~~~~~v~v-~~P~~~~~~ 44 (223)
T COG1451 7 GDGLPLEVQVKRRAKRLTIRIPPGGTVRV-SVPPGLSDE 44 (223)
T ss_pred CCCCCEEEEEEECCCCEEEEECCCCEEEE-EECCCCCHH
T ss_conf 26860899995044011688668985999-817888878
No 56
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=34.93 E-value=42 Score=15.98 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=13.1
Q ss_pred EECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 7029969999746757843598842
Q gi|254780470|r 85 ISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 85 Il~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
.-+||.|++-+---|..+.||..-+
T Consensus 322 ~~~Gd~V~~~Vl~id~e~~ri~LS~ 346 (390)
T PRK06676 322 LEEGQEVKVKVLEVDEEEKRISLSI 346 (390)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEEE
T ss_conf 7899999999999817789899881
No 57
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=34.81 E-value=42 Score=15.97 Aligned_cols=60 Identities=20% Similarity=0.237 Sum_probs=39.2
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEC----CCEEEEEE
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912----51120164
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTA----GRMRKHRI 83 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~is----GKmRk~~I 83 (110)
.++|.|.-.-|-+.|- .|.. +..-++|+| .++..-.=
T Consensus 3 iv~G~V~~i~~fG~FV-~l~~--------------------------------------~~~GLvhisels~~~~~~~~~ 43 (68)
T cd05685 3 VLEGVVTNVTDFGAFV-DIGV--------------------------------------KQDGLIHISKMADRFVSHPSD 43 (68)
T ss_pred EEEEEEEEEECEEEEE-EECC--------------------------------------CCEEEEECHHHCCCCCCCHHH
T ss_conf 9999999996528999-9149--------------------------------------978999818976787679868
Q ss_pred EEECCCEEEEEECCCCCCCCEEE
Q ss_conf 77029969999746757843598
Q gi|254780470|r 84 RISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 84 RIl~GDkV~Ve~SPYDLtkGRIt 106 (110)
..-+||+|++.+--.|..++||.
T Consensus 44 ~~~vGd~v~~kVi~id~e~~ri~ 66 (68)
T cd05685 44 VVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred CCCCCCEEEEEEEEEECCCCEEE
T ss_conf 57999999999999989999887
No 58
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=34.67 E-value=42 Score=15.96 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=17.3
Q ss_pred EEEEEEEEEECCCCCCEEEEE
Q ss_conf 599978999815898179998
Q gi|254780470|r 6 TLEFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 6 ~ie~~G~V~E~LPna~FrV~L 26 (110)
...+..+|+++|||++.-|+=
T Consensus 146 ~~tIta~V~~VLpNGNL~I~G 166 (230)
T COG2063 146 TGTITATVVQVLPNGNLVIEG 166 (230)
T ss_pred EEEEEEEEEEECCCCCEEEEE
T ss_conf 999999999986899789997
No 59
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=34.17 E-value=43 Score=15.91 Aligned_cols=19 Identities=32% Similarity=0.344 Sum_probs=12.8
Q ss_pred EEEEEEEECCCCCCEEEEE
Q ss_conf 9978999815898179998
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKL 26 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L 26 (110)
.+...|+++|||+++.|+=
T Consensus 144 tIta~V~~VLpNGNLvI~G 162 (230)
T PRK12701 144 SISVTVAKVLANGNMVVQG 162 (230)
T ss_pred EEEEEEEEECCCCCEEEEE
T ss_conf 9999999986699799999
No 60
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=33.35 E-value=44 Score=15.83 Aligned_cols=58 Identities=22% Similarity=0.328 Sum_probs=38.0
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEE---
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647---
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIR--- 84 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IR--- 84 (110)
.++|+|+...+-+-|--.+ .|..-|.|+|- +...|+.
T Consensus 621 ~y~g~V~~i~~fGafve~~---------------------------------------pg~~GLlHiSe-l~~~rv~~v~ 660 (684)
T TIGR03591 621 IYEGKVVRIMDFGAFVEIL---------------------------------------PGKDGLVHISE-IANERVEKVE 660 (684)
T ss_pred EEEEEEEEEEECEEEEEEC---------------------------------------CCCCEEEEEEC-CCCCCCCCHH
T ss_conf 7999999998440899967---------------------------------------99814787001-3653446864
Q ss_pred --EECCCEEEEEECCCCCCCCEEE
Q ss_conf --7029969999746757843598
Q gi|254780470|r 85 --ISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 85 --Il~GDkV~Ve~SPYDLtkGRIt 106 (110)
+-.||+|+|.+---| .+|||-
T Consensus 661 dv~~~Gd~i~Vk~~~id-~~Gri~ 683 (684)
T TIGR03591 661 DVLKEGDEVKVKVLEID-KQGRIK 683 (684)
T ss_pred HHCCCCCEEEEEEEEEC-CCCCCC
T ss_conf 52168988999999788-999828
No 61
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=33.14 E-value=45 Score=15.81 Aligned_cols=21 Identities=19% Similarity=0.420 Sum_probs=9.1
Q ss_pred CCCEEEEEECCCCCCCCEEEE
Q ss_conf 299699997467578435988
Q gi|254780470|r 87 LGDKVKVAMNPYDMTRARITY 107 (110)
Q Consensus 87 ~GDkV~Ve~SPYDLtkGRIty 107 (110)
.|+.+.+.+--.|..+.||+.
T Consensus 160 vG~~~~~kIieid~~~~rivl 180 (314)
T PRK07400 160 VGEELPLKFLEVDEERNRLVL 180 (314)
T ss_pred CCCEEEEEEEEEECCCCCEEE
T ss_conf 697688999997156682489
No 62
>COG2872 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]
Probab=32.65 E-value=46 Score=15.76 Aligned_cols=69 Identities=23% Similarity=0.355 Sum_probs=42.5
Q ss_pred EEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCEEEEEECC
Q ss_conf 5999789998158981799981667765333233544333445555444555554455---------5688289999125
Q gi|254780470|r 6 TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPIS---------YLDNAVVIAYTAG 76 (110)
Q Consensus 6 ~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s---------~~~~~~VlA~isG 76 (110)
..|+++.|.++.+| .+.|+. +.-+|++|.+.|.-|..-.- +..+..|+-+++.
T Consensus 12 ~~e~~~~v~~v~~~---~i~ld~---------------T~Fyp~~GGQp~D~G~l~~~~~~~~~~~~~~~~~~I~H~~~~ 73 (241)
T COG2872 12 LKEFEATVVDVEDN---EIVLDR---------------TIFYPTGGGQPGDTGTLIWAGGEYVVEDVTKDGEEIVHVLAE 73 (241)
T ss_pred CCCCEEEEEEEECC---EEEEEE---------------CCCCCCCCCCCCCCEEEEECCCEEEEEEEEECCEEEEEEECC
T ss_conf 10024899998287---389871---------------222479899868866898289469999887616199998167
Q ss_pred CEEEEEEEEECCCEEEEEECC
Q ss_conf 112016477029969999746
Q gi|254780470|r 77 RMRKHRIRISLGDKVKVAMNP 97 (110)
Q Consensus 77 KmRk~~IRIl~GDkV~Ve~SP 97 (110)
+ -...+||+|+.++.+
T Consensus 74 ----~-~~~~vG~~V~~~IDW 89 (241)
T COG2872 74 ----H-AKLKVGDKVKLKIDW 89 (241)
T ss_pred ----C-CCCCCCCEEEEEECC
T ss_conf ----6-667899789999790
No 63
>pfam01079 Hint Hint module. This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module.
Probab=32.18 E-value=46 Score=15.72 Aligned_cols=13 Identities=31% Similarity=0.301 Sum_probs=6.9
Q ss_pred EEEEEECCCEEEE
Q ss_conf 1647702996999
Q gi|254780470|r 81 HRIRISLGDKVKV 93 (110)
Q Consensus 81 ~~IRIl~GDkV~V 93 (110)
+-=++-+||.|-|
T Consensus 102 fAs~V~~Gd~v~v 114 (214)
T pfam01079 102 FASDVRPGDYVLV 114 (214)
T ss_pred ECCCCCCCCEEEE
T ss_conf 7222778988999
No 64
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=31.90 E-value=47 Score=15.69 Aligned_cols=60 Identities=23% Similarity=0.319 Sum_probs=38.8
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEE---
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647---
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIR--- 84 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IR--- 84 (110)
.++|+|+...+-+-|--.+ .|..-|.|+|- |...|+.
T Consensus 624 iy~g~V~~i~~fGafve~~---------------------------------------pg~~GLlHiSe-l~~~rv~~v~ 663 (694)
T PRK11824 624 IYEGKVVRIVDFGAFVEIL---------------------------------------PGKDGLVHISE-IANERVEKVE 663 (694)
T ss_pred EEEEEEEEEEECEEEEEEC---------------------------------------CCCEEEEEHHH-CCCCCCCCHH
T ss_conf 7999999998441899967---------------------------------------99806888002-4652346864
Q ss_pred --EECCCEEEEEECCCCCCCCEEEEE
Q ss_conf --702996999974675784359884
Q gi|254780470|r 85 --ISLGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 85 --Il~GDkV~Ve~SPYDLtkGRItyR 108 (110)
+-.||+|+|.+--.|- +|||-.-
T Consensus 664 d~~~~Gd~i~Vk~~~id~-~Gri~Ls 688 (694)
T PRK11824 664 DVLKEGDEVKVKVLEIDK-RGRIRLS 688 (694)
T ss_pred HHCCCCCEEEEEEEEECC-CCCEEEE
T ss_conf 511689889999998989-9986666
No 65
>CHL00051 rps12 ribosomal protein S12
Probab=30.73 E-value=49 Score=15.57 Aligned_cols=45 Identities=20% Similarity=0.247 Sum_probs=30.1
Q ss_pred CCCCEEEEEECCC-----------EEEEEEEEECCCEEEEEECCCCCC--CCEEEEEE
Q ss_conf 6882899991251-----------120164770299699997467578--43598842
Q gi|254780470|r 65 LDNAVVIAYTAGR-----------MRKHRIRISLGDKVKVAMNPYDMT--RARITYRF 109 (110)
Q Consensus 65 ~~~~~VlA~isGK-----------mRk~~IRIl~GDkV~Ve~SPYDLt--kGRItyR~ 109 (110)
.||..|+|||-|- +|--+.+=|||=+-++----||+. .+|.+-|-
T Consensus 58 sng~~v~ayIPGeghnlqehs~VLvrGGrv~DLPGVky~ivRG~~D~~gv~~R~~~RS 115 (123)
T CHL00051 58 TSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRS 115 (123)
T ss_pred CCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCC
T ss_conf 3898999981798768531578999388768799832799604202554465521343
No 66
>pfam06257 DUF1021 Protein of unknown function (DUF1021). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=30.00 E-value=51 Score=15.50 Aligned_cols=26 Identities=31% Similarity=0.437 Sum_probs=21.7
Q ss_pred CCCCEEEEEEEEEECCCCCCEEEEECC
Q ss_conf 756459997899981589817999816
Q gi|254780470|r 2 PKEETLEFSGIVSELLPNANFRVKLIT 28 (110)
Q Consensus 2 ~Ked~ie~~G~V~E~LPna~FrV~L~~ 28 (110)
-+...++-+|++.|..| +.|-|+|++
T Consensus 27 GRkK~~~~~GvL~etyP-svFvV~ld~ 52 (76)
T pfam06257 27 GRKKVTEREGILEETYP-SVFVVELDQ 52 (76)
T ss_pred CCEEEEEEEEEEEEECC-CEEEEEEEC
T ss_conf 95228999999931046-189999926
No 67
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=29.59 E-value=51 Score=15.46 Aligned_cols=48 Identities=23% Similarity=0.259 Sum_probs=34.0
Q ss_pred CCCCCCCEEEEEECCC-----------EEEEEEEEECCCEEEEEECCCCCC--CCEEEEEE
Q ss_conf 5556882899991251-----------120164770299699997467578--43598842
Q gi|254780470|r 62 ISYLDNAVVIAYTAGR-----------MRKHRIRISLGDKVKVAMNPYDMT--RARITYRF 109 (110)
Q Consensus 62 ~s~~~~~~VlA~isGK-----------mRk~~IRIl~GDkV~Ve~SPYDLt--kGRItyR~ 109 (110)
|-..||..|+|||-|- +|--+.+=|||=+-++----||+. ++|.+-|-
T Consensus 150 VrLsng~~v~aYIPGeGHnLQEHsvVLVRGGRvkDLPGVkY~iVRG~~D~~gV~~Rk~sRS 210 (288)
T PTZ00115 150 VRLSTGRTVTCHIPGIGHNLHTHSVVLVRGGRCQDVSGCHYKVVRGKYDLLPVKNRASSRS 210 (288)
T ss_pred EECCCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCCC
T ss_conf 9956998899972688757520327999588767799851799603023434465533332
No 68
>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=29.02 E-value=53 Score=15.40 Aligned_cols=68 Identities=25% Similarity=0.344 Sum_probs=42.2
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL 87 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~ 87 (110)
.++|.|..+.|.+.| |++..+ -+|.-|+|-.... ++..-.=..-.
T Consensus 3 vv~G~V~~i~~~G~f-V~~~~~--------------------------i~Glvp~seis~~--------~v~~p~~~f~~ 47 (70)
T cd05698 3 KTHGTIVKVKPNGCI-VSFYNN--------------------------VKGFLPKSELSEA--------FIKDPEEHFRV 47 (70)
T ss_pred EEEEEEEEEECCCEE-EEECCC--------------------------CEEEEEHHHHCCC--------CCCCHHHHCCC
T ss_conf 999999999817189-994899--------------------------6999898992832--------02898993779
Q ss_pred CCEEEEEECCCCCCCCEEEEEEC
Q ss_conf 99699997467578435988429
Q gi|254780470|r 88 GDKVKVAMNPYDMTRARITYRFK 110 (110)
Q Consensus 88 GDkV~Ve~SPYDLtkGRItyR~K 110 (110)
|+.|++-+---|..+.||.--+|
T Consensus 48 Gq~V~v~Vl~vd~~~~ri~LS~K 70 (70)
T cd05698 48 GQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEECCCCEEEEECC
T ss_conf 99999999998089999999719
No 69
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=28.20 E-value=55 Score=15.31 Aligned_cols=46 Identities=24% Similarity=0.311 Sum_probs=29.7
Q ss_pred CCCCEEEEEECCC-----------EEEEEEEEECCCEEEEEECCCCCC--CCEEEEEEC
Q ss_conf 6882899991251-----------120164770299699997467578--435988429
Q gi|254780470|r 65 LDNAVVIAYTAGR-----------MRKHRIRISLGDKVKVAMNPYDMT--RARITYRFK 110 (110)
Q Consensus 65 ~~~~~VlA~isGK-----------mRk~~IRIl~GDkV~Ve~SPYDLt--kGRItyR~K 110 (110)
.||..|+|||-|- +|--+.+=|||=+-++----||+. .+|.+-|-|
T Consensus 58 sng~~v~ayIPGeGHnlqeHs~VLvrGGrvkDLPGVky~iVRG~~D~~gv~~R~~~RSk 116 (124)
T PRK05163 58 TNGFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQGRSK 116 (124)
T ss_pred CCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCC
T ss_conf 28989999808998776315789994887687998328996052025444655213431
No 70
>PRK12764 hypothetical protein; Provisional
Probab=27.94 E-value=55 Score=15.28 Aligned_cols=25 Identities=24% Similarity=0.359 Sum_probs=20.3
Q ss_pred EEECCCEEEEEEC---CCCCCCCEEEEE
Q ss_conf 7702996999974---675784359884
Q gi|254780470|r 84 RISLGDKVKVAMN---PYDMTRARITYR 108 (110)
Q Consensus 84 RIl~GDkV~Ve~S---PYDLtkGRItyR 108 (110)
.+.|||.|.||+. --++|.||.+-+
T Consensus 198 ~v~PGDvvEVEv~~~~~~~~~~g~l~~~ 225 (498)
T PRK12764 198 VAKPGDVVEVEVDSVAAGRLSTGRLCTR 225 (498)
T ss_pred CCCCCCEEEEEEECCCCCCCCCCEEEEE
T ss_conf 6899988999983167788765615777
No 71
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=27.94 E-value=55 Score=15.28 Aligned_cols=57 Identities=19% Similarity=0.269 Sum_probs=36.2
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf 99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL 87 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~ 87 (110)
.+.|+|+-..+=+.| |.|. ++..=|.|+|- |... .-.
T Consensus 19 ~y~G~V~~v~~fGaF-V~l~--------------------------------------~~~~GLiHiS~-l~~~---~~v 55 (77)
T cd04473 19 LYKGKVNGVAKYGVF-VDLN--------------------------------------DHVRGLIHRSN-LLRD---YEV 55 (77)
T ss_pred EEEEEEEEEEECCEE-EECC--------------------------------------CCCEEEEEEHH-CCCC---CCC
T ss_conf 999999889662889-9926--------------------------------------99879689316-6687---899
Q ss_pred CCEEEEEECCCCCCCCEEEEE
Q ss_conf 996999974675784359884
Q gi|254780470|r 88 GDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 88 GDkV~Ve~SPYDLtkGRItyR 108 (110)
||+|.|.+.--| .+|||-..
T Consensus 56 GD~V~VkV~~I~-~~Gki~L~ 75 (77)
T cd04473 56 GDEVIVQVTDIP-ENGNIDLI 75 (77)
T ss_pred CCEEEEEEEEEC-CCCCEEEE
T ss_conf 999999999999-99979318
No 72
>pfam01828 Peptidase_A4 Peptidase A4 family.
Probab=26.53 E-value=58 Score=15.13 Aligned_cols=28 Identities=25% Similarity=0.301 Sum_probs=23.7
Q ss_pred EEEEEECCCEEEEEECCCCCCCCEEEEE
Q ss_conf 1647702996999974675784359884
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMTRARITYR 108 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR 108 (110)
-.|.|.+||.+.+.+.....+.|.++.-
T Consensus 87 s~i~vs~GD~i~vtV~~ts~t~gt~tie 114 (208)
T pfam01828 87 SGISVSAGDTIVVNVTATSPTSGTATIE 114 (208)
T ss_pred CCCEECCCCEEEEEEEECCCCCEEEEEE
T ss_conf 5521089998999999657984799999
No 73
>pfam00164 Ribosomal_S12 Ribosomal protein S12.
Probab=24.78 E-value=63 Score=14.94 Aligned_cols=45 Identities=29% Similarity=0.366 Sum_probs=28.8
Q ss_pred CCCEEEEEECCC-----------EEEEEEEEECCCEEEEEECCCCCC--CCEEEEEEC
Q ss_conf 882899991251-----------120164770299699997467578--435988429
Q gi|254780470|r 66 DNAVVIAYTAGR-----------MRKHRIRISLGDKVKVAMNPYDMT--RARITYRFK 110 (110)
Q Consensus 66 ~~~~VlA~isGK-----------mRk~~IRIl~GDkV~Ve~SPYDLt--kGRItyR~K 110 (110)
|+..|.||+-|- +|-.+.+=+||=+-++----||+. .+|..-|.|
T Consensus 48 ng~~vtayIPG~Gh~lqehs~VLVrGgrv~DlPGVrykivrG~~D~~gv~~r~~~RSk 105 (112)
T pfam00164 48 NGKEVTAYIPGDGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDVAGVSDRKQARSK 105 (112)
T ss_pred CCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCC
T ss_conf 9989999828997785437889994887688997408997230026344632002311
No 74
>TIGR01750 fabZ beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ; InterPro: IPR010084 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes . FabZ is the primary dehydratase involved in fatty-acid elongation in type II FAS. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. ; GO: 0016836 hydro-lyase activity, 0006633 fatty acid biosynthetic process, 0005737 cytoplasm.
Probab=24.30 E-value=38 Score=16.22 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=19.3
Q ss_pred EEEECC-CEEEEEEEEECCCEEEEEECCC
Q ss_conf 999125-1120164770299699997467
Q gi|254780470|r 71 IAYTAG-RMRKHRIRISLGDKVKVAMNPY 98 (110)
Q Consensus 71 lA~isG-KmRk~~IRIl~GDkV~Ve~SPY 98 (110)
+.|.+| .==|||+.|+|||.-..++.=-
T Consensus 85 ~~~F~gid~akFr~pV~PGDqL~l~~e~~ 113 (142)
T TIGR01750 85 LVYFAGIDKAKFRKPVVPGDQLILEVEFL 113 (142)
T ss_pred EEEEEEECCCCCCCCCCCCCEEEEEEEEE
T ss_conf 89998862730356646782247878855
No 75
>TIGR00370 TIGR00370 conserved hypothetical protein TIGR00370; InterPro: IPR010016 This is an uncharacterised family of proteins of unknown function..
Probab=22.26 E-value=59 Score=15.12 Aligned_cols=37 Identities=27% Similarity=0.246 Sum_probs=28.3
Q ss_pred CCCCCCCCCCCCCEEEEEECCC----EEEEEEEEECCCEEE
Q ss_conf 5555445556882899991251----120164770299699
Q gi|254780470|r 56 NDGVDPISYLDNAVVIAYTAGR----MRKHRIRISLGDKVK 92 (110)
Q Consensus 56 ~~g~~~~s~~~~~~VlA~isGK----mRk~~IRIl~GDkV~ 92 (110)
--|+.|+|+.-|-..+.|++=- -+..=|=+-+||.|+
T Consensus 175 QTGvYP~stPGGWQLIG~T~laLFdp~~~~P~LLraGD~Vk 215 (217)
T TIGR00370 175 QTGVYPLSTPGGWQLIGKTKLALFDPAEDEPTLLRAGDIVK 215 (217)
T ss_pred CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEECCCCEEE
T ss_conf 65734366967420013565111462448673226886542
No 76
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=22.25 E-value=71 Score=14.65 Aligned_cols=41 Identities=20% Similarity=0.411 Sum_probs=23.9
Q ss_pred CEEEEE--EEEEECCCCCC--EEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 459997--89998158981--799981667765333233544333
Q gi|254780470|r 5 ETLEFS--GIVSELLPNAN--FRVKLITNDDDSSADCKLDSKVKS 45 (110)
Q Consensus 5 d~ie~~--G~V~E~LPna~--FrV~L~~~d~~~~~~~~l~~~~~~ 45 (110)
|+|++. |..--+|||.. |.+.-++.|....+.|+..+|...
T Consensus 87 DVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~v 131 (241)
T COG1471 87 DVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTV 131 (241)
T ss_pred EEEEECCCCCEEEEEECCCCCEEEEECCHHHCCCEEEEEEEEEEE
T ss_conf 999976889658988667850788754712045417998758982
No 77
>pfam12158 DUF3592 Protein of unknown function (DUF3592). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=20.94 E-value=76 Score=14.49 Aligned_cols=22 Identities=32% Similarity=0.546 Sum_probs=19.9
Q ss_pred EECCCEEEEEECCCCCCCCEEE
Q ss_conf 7029969999746757843598
Q gi|254780470|r 85 ISLGDKVKVAMNPYDMTRARIT 106 (110)
Q Consensus 85 Il~GDkV~Ve~SPYDLtkGRIt 106 (110)
.-.|++|+|..+|-|..+++|.
T Consensus 85 y~~G~~V~V~Y~P~~P~~a~i~ 106 (134)
T pfam12158 85 YRVGERVPVYYDPDNPEQARID 106 (134)
T ss_pred CCCCCEEEEEECCCCCCEEEEC
T ss_conf 8899989999999999677984
No 78
>COG3745 CpaB Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]
Probab=20.29 E-value=67 Score=14.79 Aligned_cols=11 Identities=36% Similarity=0.667 Sum_probs=8.0
Q ss_pred EECCCEEEEEE
Q ss_conf 70299699997
Q gi|254780470|r 85 ISLGDKVKVAM 95 (110)
Q Consensus 85 Il~GDkV~Ve~ 95 (110)
|+|||+|.|-|
T Consensus 146 VlPgDrVDVil 156 (276)
T COG3745 146 VLPGDRVDVIL 156 (276)
T ss_pred ECCCCEEEEEE
T ss_conf 25897378999
No 79
>cd03448 HDE_HSD HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit.
Probab=20.24 E-value=78 Score=14.40 Aligned_cols=26 Identities=12% Similarity=0.248 Sum_probs=19.5
Q ss_pred EEEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 16477029969999746757843598842
Q gi|254780470|r 81 HRIRISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
|.=-+.|||.+++++-. +.+++.|+.
T Consensus 79 F~~pV~pGd~l~v~iw~---~~~~v~~~~ 104 (122)
T cd03448 79 FSSPVFPGETLRTEMWK---EGNRVIFQT 104 (122)
T ss_pred ECCCCCCCCEEEEEEEE---ECCEEEEEE
T ss_conf 82653699989999999---799999999
No 80
>TIGR01245 trpD anthranilate phosphoribosyltransferase; InterPro: IPR005940 In many widely different species, including Escherichia coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzyme is a C-terminal part of a multifunctional protein together with glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (4.1.3.27 from EC).; GO: 0004048 anthranilate phosphoribosyltransferase activity, 0000162 tryptophan biosynthetic process.
Probab=20.10 E-value=79 Score=14.38 Aligned_cols=30 Identities=30% Similarity=0.510 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCCCEEEEEECCCEEEEEE
Q ss_conf 455555445556882899991251120164
Q gi|254780470|r 54 SGNDGVDPISYLDNAVVIAYTAGRMRKHRI 83 (110)
Q Consensus 54 ~g~~g~~~~s~~~~~~VlA~isGKmRk~~I 83 (110)
.|++|.||||+...-.|.---.|+++...|
T Consensus 215 hG~~GlDE~s~~g~t~v~el~~g~I~~~~~ 244 (331)
T TIGR01245 215 HGEDGLDEISLTGPTKVAELKDGEIREYTL 244 (331)
T ss_pred ECCCCCCEEECCCCCEEEEEECCCEEEEEE
T ss_conf 578896145316771699874893146664
Done!