Query 027519
Match_columns 222
No_of_seqs 133 out of 1114
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 11:08:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027519.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027519hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00075 rpl21 ribosomal prote 100.0 6.1E-43 1.3E-47 276.9 15.3 106 101-207 1-106 (108)
2 PRK05573 rplU 50S ribosomal pr 100.0 3.6E-42 7.9E-47 270.0 14.7 103 103-206 1-103 (103)
3 COG0261 RplU Ribosomal protein 100.0 6.3E-42 1.4E-46 268.7 13.5 103 103-206 1-103 (103)
4 TIGR00061 L21 ribosomal protei 100.0 3.7E-41 8E-46 263.9 14.1 101 104-205 1-101 (101)
5 PRK12278 50S ribosomal protein 100.0 1.1E-39 2.3E-44 285.5 15.3 106 103-209 1-106 (221)
6 PF00829 Ribosomal_L21p: Ribos 100.0 3.3E-40 7.1E-45 255.7 9.2 96 103-199 1-96 (96)
7 KOG1686 Mitochondrial/chloropl 99.9 2E-27 4.2E-32 196.3 11.1 118 98-215 21-138 (151)
8 PF12791 RsgI_N: Anti-sigma fa 87.5 1.2 2.5E-05 30.7 4.2 38 101-145 4-41 (56)
9 PF11356 Pilus_PilP: Type IV p 72.3 6.4 0.00014 28.9 3.9 40 98-143 36-78 (87)
10 TIGR03689 pup_AAA proteasome A 71.1 15 0.00032 36.6 7.2 39 104-145 60-98 (512)
11 PF02311 AraC_binding: AraC-li 69.3 7.6 0.00016 28.6 3.8 21 105-125 34-54 (136)
12 COG0662 {ManC} Mannose-6-phosp 66.9 8.5 0.00018 30.5 3.8 26 100-125 57-88 (127)
13 PF04351 PilP: Pilus assembly 66.3 7.3 0.00016 32.2 3.4 26 100-125 88-114 (149)
14 COG3264 Small-conductance mech 66.1 9.3 0.0002 40.3 4.8 79 119-211 652-730 (835)
15 COG3168 PilP Tfp pilus assembl 58.2 17 0.00036 31.6 4.2 26 100-125 107-132 (170)
16 KOG1686 Mitochondrial/chloropl 57.7 4.8 0.0001 34.2 0.9 57 100-157 92-151 (151)
17 PF07883 Cupin_2: Cupin domain 57.4 16 0.00036 24.7 3.4 20 107-126 32-51 (71)
18 cd04867 TGS_YchF_C TGS_YchF_C: 56.4 5.2 0.00011 31.0 0.8 21 104-124 61-81 (83)
19 PF06249 EutQ: Ethanolamine ut 53.7 24 0.00051 30.0 4.4 27 107-139 108-134 (152)
20 PRK06788 flagellar motor switc 53.0 61 0.0013 26.5 6.5 63 101-171 34-101 (119)
21 PRK09943 DNA-binding transcrip 50.6 23 0.00049 29.5 3.8 21 105-125 139-159 (185)
22 PRK08983 fliN flagellar motor 49.4 54 0.0012 27.0 5.7 61 100-168 50-115 (127)
23 KOG0126 Predicted RNA-binding 42.4 83 0.0018 28.2 6.2 32 104-139 35-66 (219)
24 PF06071 YchF-GTPase_C: Protei 42.1 4.9 0.00011 31.1 -1.3 19 106-124 63-81 (84)
25 PRK15457 ethanolamine utilizat 39.9 38 0.00083 30.7 3.8 21 106-126 187-207 (233)
26 PF02563 Poly_export: Polysacc 37.9 15 0.00032 27.0 0.8 43 112-162 9-51 (82)
27 PRK06033 hypothetical protein; 37.5 61 0.0013 24.5 4.1 40 129-168 27-71 (83)
28 cd04092 mtEFG2_II_like mtEFG2_ 36.6 39 0.00084 24.4 2.8 22 115-136 60-81 (83)
29 PF11699 CENP-C_C: Mif2/CENP-C 35.2 51 0.0011 25.2 3.4 22 106-127 45-66 (85)
30 PF11213 DUF3006: Protein of u 34.8 62 0.0014 23.5 3.6 31 102-138 9-42 (71)
31 PRK13501 transcriptional activ 33.3 98 0.0021 27.1 5.3 21 105-125 49-69 (290)
32 cd04088 EFG_mtEFG_II EFG_mtEFG 33.1 44 0.00096 23.9 2.6 21 116-136 61-81 (83)
33 PF01050 MannoseP_isomer: Mann 33.1 65 0.0014 26.9 3.9 21 105-125 95-115 (151)
34 TIGR03214 ura-cupin putative a 32.7 58 0.0013 29.2 3.8 22 105-126 211-232 (260)
35 PF05896 NQRA: Na(+)-transloca 31.8 73 0.0016 29.3 4.3 55 113-174 28-84 (257)
36 cd03691 BipA_TypA_II BipA_TypA 29.9 52 0.0011 23.8 2.6 21 116-136 64-84 (86)
37 PF00717 Peptidase_S24: Peptid 29.0 51 0.0011 22.5 2.3 36 102-145 14-50 (70)
38 TIGR02480 fliN flagellar motor 28.4 1.6E+02 0.0035 21.4 5.0 43 126-168 25-72 (77)
39 cd03689 RF3_II RF3_II: this su 27.9 60 0.0013 24.1 2.6 21 116-136 62-82 (85)
40 PRK13500 transcriptional activ 27.2 1.3E+02 0.0028 27.0 5.1 22 105-126 79-100 (312)
41 PRK11171 hypothetical protein; 27.2 82 0.0018 28.3 3.8 20 106-125 217-236 (266)
42 PRK10371 DNA-binding transcrip 26.9 82 0.0018 28.3 3.8 21 105-125 57-77 (302)
43 TIGR01713 typeII_sec_gspC gene 26.9 1.3E+02 0.0027 27.2 5.0 24 100-123 94-117 (259)
44 COG2100 Predicted Fe-S oxidore 26.7 1.5E+02 0.0033 28.9 5.6 41 113-156 372-414 (414)
45 PRK10296 DNA-binding transcrip 26.2 92 0.002 27.0 3.8 21 105-125 54-74 (278)
46 TIGR00092 GTP-binding protein 26.1 40 0.00086 32.3 1.7 21 105-125 345-365 (368)
47 PRK05698 fliN flagellar motor 25.7 1.2E+02 0.0026 25.9 4.4 59 102-168 80-143 (155)
48 PF05899 Cupin_3: Protein of u 25.0 1.1E+02 0.0023 22.1 3.5 17 110-126 42-58 (74)
49 cd06530 S26_SPase_I The S26 Ty 24.5 81 0.0017 22.5 2.7 11 117-127 15-25 (85)
50 smart00841 Elong-fact-P_C Elon 23.6 1.2E+02 0.0025 21.8 3.3 26 112-139 22-47 (56)
51 cd05794 S1_EF-P_repeat_2 S1_EF 23.3 1.2E+02 0.0026 21.7 3.3 26 112-139 22-47 (56)
52 PF09285 Elong-fact-P_C: Elong 23.0 1.4E+02 0.003 21.4 3.6 26 112-139 22-47 (56)
53 PRK08433 flagellar motor switc 22.8 1.6E+02 0.0036 23.7 4.4 64 100-171 31-99 (111)
54 PRK14603 ruvA Holliday junctio 22.6 1.9E+02 0.0042 25.1 5.2 49 102-154 14-62 (197)
55 TIGR03021 pilP_fam type IV pil 22.4 1E+02 0.0023 24.9 3.2 25 98-122 76-101 (119)
56 TIGR02297 HpaA 4-hydroxyphenyl 22.3 1.1E+02 0.0023 26.5 3.5 22 105-126 55-76 (287)
57 PF09956 DUF2190: Uncharacteri 21.9 2.8E+02 0.006 22.0 5.5 33 113-146 3-35 (106)
58 TIGR02988 YaaA_near_RecF S4 do 21.9 62 0.0013 22.2 1.6 12 113-124 47-58 (59)
59 cd03690 Tet_II Tet_II: This su 21.8 82 0.0018 23.2 2.3 21 116-136 63-83 (85)
60 PF12961 DUF3850: Domain of Un 21.0 1.8E+02 0.004 21.9 4.1 33 102-141 8-40 (72)
61 PF01330 RuvA_N: RuvA N termin 21.0 2.8E+02 0.0061 19.2 4.8 49 101-153 13-61 (61)
62 PRK14604 ruvA Holliday junctio 20.9 1.4E+02 0.0029 26.0 3.8 49 102-153 14-62 (195)
63 PRK09601 GTP-binding protein Y 20.8 68 0.0015 30.7 2.1 19 107-125 343-361 (364)
64 PRK09685 DNA-binding transcrip 20.8 1.3E+02 0.0028 26.3 3.7 22 105-126 82-103 (302)
65 PRK12795 fliM flagellar motor 20.4 1.8E+02 0.0039 28.0 4.9 66 101-174 302-372 (388)
66 PRK13290 ectC L-ectoine syntha 20.4 1.3E+02 0.0029 24.2 3.4 18 109-126 71-89 (125)
No 1
>CHL00075 rpl21 ribosomal protein L21
Probab=100.00 E-value=6.1e-43 Score=276.90 Aligned_cols=106 Identities=34% Similarity=0.493 Sum_probs=102.6
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEe
Q 027519 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKY 180 (222)
Q Consensus 101 ~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~ 180 (222)
|.|||||++|||||||++||+|.||+|+ +++||.|+|++|||+++++.+.+|.|||+||+|+|+|++|+|++||++|||
T Consensus 1 ~~myAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~i~l~~VL~~~~~~~~~iG~P~v~~a~V~a~V~~h~r~~Ki~vfK~ 79 (108)
T CHL00075 1 MMTYAIIEAGGKQLWVEPGRFYDINHFP-LEPGTKILLNRVLLIRNESEILIGKPWLENATVKGRILHHFRGKKITVYKM 79 (108)
T ss_pred CcEEEEEEECCEEEEEeCCCEEEEEEcC-CCCCCEEEEEEEEEEecCCCeEECCcEecCcEEEEEEEeecCCCCEEEEEe
Confidence 4799999999999999999999999995 899999999999999988899999999999999999999999999999999
Q ss_pred cCCCCceeccCccCCceEEEEeeEeeC
Q 027519 181 KKKKNYRRNIGHRQPNTRIRITGITGY 207 (222)
Q Consensus 181 KRRK~yrRk~GHRQ~~TrLrI~~I~~~ 207 (222)
||||+|||++||||+||+|+|++|...
T Consensus 80 krRK~yrrk~GHRQ~~T~i~I~~I~~~ 106 (108)
T CHL00075 80 RPKKKTRKKQGHRQKLTRFLIDSISFN 106 (108)
T ss_pred CCCCCccCCCccCCCcEEEEEEEEEcC
Confidence 999999999999999999999999863
No 2
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=100.00 E-value=3.6e-42 Score=270.04 Aligned_cols=103 Identities=46% Similarity=0.746 Sum_probs=100.6
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEecC
Q 027519 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (222)
Q Consensus 103 mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~KR 182 (222)
|||||++||+||||++||+|.||+|+ +++||.|+|++|||+++++++.+|.||+++|+|+|+|++|++++|+++|||||
T Consensus 1 MyAIi~~gGkQykV~~Gd~i~v~~l~-~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~A~V~~~~k~~Ki~vfK~kr 79 (103)
T PRK05573 1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEVGDTVEFDEVLLVGGGEEVKIGAPYVEGAKVTAEVVEHGRGKKVIVFKYKR 79 (103)
T ss_pred CEEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEeEEEEEeCCCCEEECCeEcCCCEEEEEEEeccCCCcEEEEEEcC
Confidence 89999999999999999999999995 89999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCCceEEEEeeEee
Q 027519 183 KKNYRRNIGHRQPNTRIRITGITG 206 (222)
Q Consensus 183 RK~yrRk~GHRQ~~TrLrI~~I~~ 206 (222)
||+|+|++||||+||+|+|++|.+
T Consensus 80 RK~y~r~~GHRQ~~T~i~I~~I~~ 103 (103)
T PRK05573 80 RKNYRKKQGHRQPYTKVKITSINA 103 (103)
T ss_pred CCCccccCCccCCcEEEEEEEEeC
Confidence 999999999999999999999963
No 3
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-42 Score=268.72 Aligned_cols=103 Identities=46% Similarity=0.759 Sum_probs=100.6
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEecC
Q 027519 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (222)
Q Consensus 103 mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~KR 182 (222)
|||||++|||||+|++||+|+||+|. +++||+|+||+|||+++++.+.+|.||++||+|.|+|++|+|++||++|||||
T Consensus 1 mYAii~tGGKQykV~~G~~i~vEkl~-~e~g~~v~f~~VL~v~~~~~v~iG~P~v~ga~V~aeV~~hgr~kKV~i~K~k~ 79 (103)
T COG0261 1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEPGDKVEFDEVLMVGGGEEVKIGAPYVEGAKVTAEVVEHGRGKKVIIFKYKR 79 (103)
T ss_pred CeEEEEECCEEEEEecCCEEEEEEcC-CCCCCEEEEEEEEEEcCCCceEECCceecCcEEEEEEhhhCCCceEEEEEecc
Confidence 89999999999999999999999994 89999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCCceEEEEeeEee
Q 027519 183 KKNYRRNIGHRQPNTRIRITGITG 206 (222)
Q Consensus 183 RK~yrRk~GHRQ~~TrLrI~~I~~ 206 (222)
||+|+|++||||+||+|+|++|.+
T Consensus 80 rK~~~rk~GHRQ~yT~vkI~~I~~ 103 (103)
T COG0261 80 RKNYRKKQGHRQPYTRVKITGIVA 103 (103)
T ss_pred CcCcccccCcccceEEEEEEEeeC
Confidence 999999999999999999999963
No 4
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=100.00 E-value=3.7e-41 Score=263.86 Aligned_cols=101 Identities=41% Similarity=0.660 Sum_probs=98.8
Q ss_pred EEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEecCC
Q 027519 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKKK 183 (222)
Q Consensus 104 YAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~KRR 183 (222)
||||++||+||||++||+|.||+|+ .++||.|+|++|||+++++++.+|+|+|++|+|+|+|++|+|++||++||||||
T Consensus 1 yAIi~~gGkQykV~~Gd~i~Ve~l~-~~~G~~i~l~~VLlv~~~~~~~iG~P~l~~a~V~a~V~~~~r~~Ki~vfK~krr 79 (101)
T TIGR00061 1 YAIVEIGGKQYKVEEGQTVRIEKLD-AAPGDTVEFDKVLMVNKGGDVKIGKPYVEGAKVVAEVEKHGRGKKVKVYKYRRR 79 (101)
T ss_pred CEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEEEEEEEecCCCeEECCeEcCCCEEEEEEEeecCCCCEEEEEeCCC
Confidence 8999999999999999999999995 799999999999999999999999999999999999999999999999999999
Q ss_pred CCceeccCccCCceEEEEeeEe
Q 027519 184 KNYRRNIGHRQPNTRIRITGIT 205 (222)
Q Consensus 184 K~yrRk~GHRQ~~TrLrI~~I~ 205 (222)
|+|||++||||+||+|+|++|.
T Consensus 80 K~y~r~~GHRQ~~T~i~I~~I~ 101 (101)
T TIGR00061 80 KHSRKKQGHRQPYTKVKVTKIV 101 (101)
T ss_pred CCccCCCccCCCcEEEEEEEeC
Confidence 9999999999999999999984
No 5
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=100.00 E-value=1.1e-39 Score=285.49 Aligned_cols=106 Identities=37% Similarity=0.544 Sum_probs=102.7
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEecC
Q 027519 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (222)
Q Consensus 103 mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~KR 182 (222)
|||||++|||||||++||+|.|++|. .++||+|.|++|||+++++++.||.|||+|++|+|+|++|+|++||++|||||
T Consensus 1 MyAVI~~gGKQykV~~Gd~i~Vekl~-~~~G~~i~~~~VL~v~~~~~~~iG~P~v~~a~V~A~V~~~~kg~Ki~vfK~kr 79 (221)
T PRK12278 1 MFAVIKTGGKQYKVQAGDLLRVEKLA-AEAGETVQFGEVLMLGEGDNVTVGAPFVDGAAVQAEVIEQIKGDKVIHFKKRR 79 (221)
T ss_pred CEEEEEeCCEEEEEeCCCEEEEeccC-CCCCCEEEEeEEEEEecCCCeEECCeEecCCEEEEEEEeecCCCCEEEEEeCC
Confidence 89999999999999999999999996 79999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCCceEEEEeeEeeCCC
Q 027519 183 KKNYRRNIGHRQPNTRIRITGITGYQD 209 (222)
Q Consensus 183 RK~yrRk~GHRQ~~TrLrI~~I~~~~~ 209 (222)
||+|||++||||+||+|||++|...+.
T Consensus 80 RK~yrrk~GHRQ~~T~i~I~~I~~~g~ 106 (221)
T PRK12278 80 RQSSRRTKGHRQLLTLVRITEILASGA 106 (221)
T ss_pred CCCcccCCCcCCCcEEEEEEEEEcCCc
Confidence 999999999999999999999987554
No 6
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=100.00 E-value=3.3e-40 Score=255.72 Aligned_cols=96 Identities=51% Similarity=0.800 Sum_probs=93.8
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEecC
Q 027519 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (222)
Q Consensus 103 mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~KR 182 (222)
|||||++||+||+|++||+|.||+| ++++||+|+|++||++++++++.+|+|||++++|+|+|++|++++|+++|||||
T Consensus 1 myAIi~~ggkQykV~~gd~i~v~~l-~~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~v~K~kr 79 (96)
T PF00829_consen 1 MYAIIEIGGKQYKVEEGDVIDVERL-DAEVGDKIELDKVLLIGSEDFTLIGRPYLEGAKVEATVLEHGKGKKIIVFKKKR 79 (96)
T ss_dssp -EEEEESSSEEEEESSSEEEEEEST-SSSTTSEEEETTEEEEETSSSTCSSSSSSSSSEEEEEEEEEEEEEEEEEEEEET
T ss_pred CEEEEEECCEEEEEeCCCEEEECCc-CcCCCCEEEEEEEEEEecCCCeEECCccCCCcEEEEEEEeccCCCcEEEEEECC
Confidence 8999999999999999999999999 689999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCCceEE
Q 027519 183 KKNYRRNIGHRQPNTRI 199 (222)
Q Consensus 183 RK~yrRk~GHRQ~~TrL 199 (222)
||+|+|++||||+||+|
T Consensus 80 RK~y~r~~GhRq~~T~i 96 (96)
T PF00829_consen 80 RKRYRRKQGHRQPYTRI 96 (96)
T ss_dssp TTTEEEEEEEEEEEEEE
T ss_pred ccccccCCccCCCeEEC
Confidence 99999999999999986
No 7
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2e-27 Score=196.32 Aligned_cols=118 Identities=53% Similarity=0.634 Sum_probs=113.5
Q ss_pred CCCCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEE
Q 027519 98 PKREEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIV 177 (222)
Q Consensus 98 ~~~~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~V 177 (222)
.++...||||.+||+||+|..||.|+.++++..++||+|.|++|||+|+.+++++|+|.|++++|.|.|+|+++..|+++
T Consensus 21 ~kr~~~favv~v~srq~kvs~gd~iy~eg~~p~nv~d~i~l~kVlLvg~~~~T~~grpvv~~vtv~aVv~e~g~~~kvvh 100 (151)
T KOG1686|consen 21 IKRPSGFAVVSVGSRQRKVSSGDTIYTEGLKPKNVLDSIPLPKVLLVGPVEETRIGRPVVKKVTVHAVVEEYGLLFKVVH 100 (151)
T ss_pred cccCCccEEEEEcceeEEecCCCeeeecCccccccccccccceEEEecCcceeEecCcccccceEEEEeeeccccccEEE
Confidence 56889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCCceeccCccCCceEEEEeeEeeCCCCCcccc
Q 027519 178 FKYKKKKNYRRNIGHRQPNTRIRITGITGYQDYPAVTL 215 (222)
Q Consensus 178 fK~KRRK~yrRk~GHRQ~~TrLrI~~I~~~~~~p~~~~ 215 (222)
||+|++|.|||..||||..|+|||++|.+++..+-.++
T Consensus 101 fk~k~~k~tr~~~~~~qe~t~LrIt~it~ie~e~~~~v 138 (151)
T KOG1686|consen 101 FKSKQWKVTRRDLGHRQEATELRITCITGIELEKVLLV 138 (151)
T ss_pred EEecchhhhhhhhcccCcccEEEEeeeeeeeeccceec
Confidence 99999999999999999999999999999998875544
No 8
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=87.45 E-value=1.2 Score=30.73 Aligned_cols=38 Identities=24% Similarity=0.466 Sum_probs=30.8
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEe
Q 027519 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVG 145 (222)
Q Consensus 101 ~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvg 145 (222)
.+.||||.+. .|+++.+.+-.+.++||+|.|+..-...
T Consensus 4 ~~~~aiVlT~-------dGeF~~ik~~~~~~vG~eI~~~~~~~~~ 41 (56)
T PF12791_consen 4 KKKYAIVLTP-------DGEFIKIKRKPGMEVGQEIEFDEKDIIN 41 (56)
T ss_pred cCCEEEEEcC-------CCcEEEEeCCCCCcccCEEEEechhhcc
Confidence 3578888875 5889999998889999999998865443
No 9
>PF11356 Pilus_PilP: Type IV pilus biogenesis; InterPro: IPR022753 Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation []. PilP is an inner membrane protein, required for pilus expression and transformation []. PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction []. ; PDB: 3OSS_C 2LNV_A.
Probab=72.32 E-value=6.4 Score=28.86 Aligned_cols=40 Identities=23% Similarity=0.153 Sum_probs=27.3
Q ss_pred CCCCCeEEEEE-ECCEEEEEcCCCEEE--EcccCCCCCCCeEEEceEEE
Q 027519 98 PKREEIFAVVM-IGSRQYIVFPGRFIY--TQRLKGANVNDKIILNKVLL 143 (222)
Q Consensus 98 ~~~~~mYAIVe-igGkQYkV~~GD~I~--Verlk~~~~Gd~I~l~kVLl 143 (222)
......+|||+ .+|.|+.+..||.|. =-++. .|.-|+|++
T Consensus 36 ~~~~~~~Aii~~~~~~~~~~~~Gd~i~~~g~~v~------~I~~d~Vvl 78 (87)
T PF11356_consen 36 GGGGRSSAIIRPSGGEQRTYRVGDTIPGSGWTVK------SISPDRVVL 78 (87)
T ss_dssp SCSSS-EEEEE-CTTEEEEE-TTEE-SSSSEEEE------EEETTEEEE
T ss_pred cCCCceEEEEEeCCCcEEEEECcCEeCCCCEEEE------EEeCCEEEE
Confidence 35678999999 999999999999874 22332 455667776
No 10
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=71.06 E-value=15 Score=36.60 Aligned_cols=39 Identities=23% Similarity=0.166 Sum_probs=31.2
Q ss_pred EEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEe
Q 027519 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVG 145 (222)
Q Consensus 104 YAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvg 145 (222)
-|-|..+|+.|+|...-.|....| .+|+.|.|+.-+.+-
T Consensus 60 ~~~v~~~g~~~~~~~~~~~~~~~l---~~g~~v~l~e~~~~v 98 (512)
T TIGR03689 60 TAEVFTAGRRMRVTVSPNVNAAEL---VPGQTVRLNEALQVV 98 (512)
T ss_pred eEEEEeCCceEEEEeCCCCCHHHC---CCCCEEEECCcceee
Confidence 367788899999988887777766 599999999777653
No 11
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=69.29 E-value=7.6 Score=28.63 Aligned_cols=21 Identities=19% Similarity=0.453 Sum_probs=16.1
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
..+.++|++|.|.+||++.++
T Consensus 34 ~~~~~~~~~~~l~~g~~~li~ 54 (136)
T PF02311_consen 34 GTLHIDGQEYPLKPGDLFLIP 54 (136)
T ss_dssp EEEEETTEEEEE-TT-EEEE-
T ss_pred EEEEECCEEEEEECCEEEEec
Confidence 457899999999999999887
No 12
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=66.87 E-value=8.5 Score=30.52 Aligned_cols=26 Identities=31% Similarity=0.445 Sum_probs=22.5
Q ss_pred CCCeEE------EEEECCEEEEEcCCCEEEEc
Q 027519 100 REEIFA------VVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 100 ~~~mYA------IVeigGkQYkV~~GD~I~Ve 125 (222)
+.++|. +|.++|+++.|.+||.++|+
T Consensus 57 ~dE~~~Vl~G~g~v~~~~~~~~v~~gd~~~iP 88 (127)
T COG0662 57 RDEHWYVLEGTGKVTIGGEEVEVKAGDSVYIP 88 (127)
T ss_pred cceEEEEEeeEEEEEECCEEEEecCCCEEEEC
Confidence 567775 46799999999999999999
No 13
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=66.30 E-value=7.3 Score=32.17 Aligned_cols=26 Identities=23% Similarity=0.273 Sum_probs=22.6
Q ss_pred CCCeEEEEEE-CCEEEEEcCCCEEEEc
Q 027519 100 REEIFAVVMI-GSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 100 ~~~mYAIVei-gGkQYkV~~GD~I~Ve 125 (222)
....+|+|+. .|+=|+|..||+|-.+
T Consensus 88 ~~~~~ALv~~pdg~v~~V~~G~yiG~n 114 (149)
T PF04351_consen 88 GGQPWALVQDPDGKVYRVKVGDYIGQN 114 (149)
T ss_dssp TTEEEEEEEE-TTEEEEEETTEEETTT
T ss_pred CCEEEEEEEeCCCCEEEecCCCEeccC
Confidence 5679999999 9999999999998443
No 14
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=66.12 E-value=9.3 Score=40.26 Aligned_cols=79 Identities=25% Similarity=0.226 Sum_probs=59.5
Q ss_pred CCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEEEEEEEeeccCCcEEEEEecCCCCceeccCccCCceE
Q 027519 119 GRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKKKKNYRRNIGHRQPNTR 198 (222)
Q Consensus 119 GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~KI~VfK~KRRK~yrRk~GHRQ~~Tr 198 (222)
|=+|.+||- +++||.|++..+. | +|....|.||.++.+.++.|+|=-.-==.+--..+-||-.++|
T Consensus 652 GlIiL~Erp--vkvGD~It~g~~~----------G--~V~~I~vRAT~I~~fd~~~vIVPNs~fI~~qV~NWs~~~~~~R 717 (835)
T COG3264 652 GLIILFERP--VKVGDTVTIGTVS----------G--TVRKISVRATTIRTFDRKEVIVPNSAFITEQVINWSLRDTTTR 717 (835)
T ss_pred hhhhheecC--cccCCEEEECCce----------E--EEEEEEeeEEEEEeCCCCeEEeccHHHHhhheeeeeccCceEE
Confidence 456677763 7899999987741 1 6788999999999999999987443333455678999999999
Q ss_pred EEEeeEeeCCCCC
Q 027519 199 IRITGITGYQDYP 211 (222)
Q Consensus 199 LrI~~I~~~~~~p 211 (222)
+.|.==..|+.-|
T Consensus 718 ~~i~v~vay~sD~ 730 (835)
T COG3264 718 LVIPVGVAYGSDP 730 (835)
T ss_pred EEEEecccCCCCH
Confidence 9987655565544
No 15
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=58.23 E-value=17 Score=31.55 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=22.9
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEc
Q 027519 100 REEIFAVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 100 ~~~mYAIVeigGkQYkV~~GD~I~Ve 125 (222)
..+.+|+|+..|+-|+|..|++|-.+
T Consensus 107 g~~~~A~i~~~~~v~~V~vG~YlGqN 132 (170)
T COG3168 107 GQGVSALIEAPGGVYRVRVGQYLGQN 132 (170)
T ss_pred CCceEEEEEcCCceEEEeeccEeecc
Confidence 34789999999999999999998655
No 16
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=57.71 E-value=4.8 Score=34.25 Aligned_cols=57 Identities=35% Similarity=0.402 Sum_probs=46.3
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEc---ccCCCCCCCeEEEceEEEEecCCceEeccccc
Q 027519 100 REEIFAVVMIGSRQYIVFPGRFIYTQ---RLKGANVNDKIILNKVLLVGTKTTTYIGKPVV 157 (222)
Q Consensus 100 ~~~mYAIVeigGkQYkV~~GD~I~Ve---rlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v 157 (222)
..-.|+++....+|+++..-|....+ +| ...-+.-|++.++++++.++++.+|.|.+
T Consensus 92 ~g~~~kvvhfk~k~~k~tr~~~~~~qe~t~L-rIt~it~ie~e~~~~v~~~nf~~vgk~~l 151 (151)
T KOG1686|consen 92 YGLLFKVVHFKSKQWKVTRRDLGHRQEATEL-RITCITGIELEKVLLVGAPNFTAVGKPLL 151 (151)
T ss_pred ccccccEEEEEecchhhhhhhhcccCcccEE-EEeeeeeeeeccceeccCccceeeccccC
Confidence 45678999999999999988877665 23 13467889999999999999999999863
No 17
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=57.36 E-value=16 Score=24.70 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=17.3
Q ss_pred EEECCEEEEEcCCCEEEEcc
Q 027519 107 VMIGSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 107 VeigGkQYkV~~GD~I~Ver 126 (222)
+.++|..|.+.+||.+.++.
T Consensus 32 ~~~~~~~~~l~~Gd~~~i~~ 51 (71)
T PF07883_consen 32 LTVDGERVELKPGDAIYIPP 51 (71)
T ss_dssp EEETTEEEEEETTEEEEEET
T ss_pred EEEccEEeEccCCEEEEECC
Confidence 44899999999999999883
No 18
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=56.37 E-value=5.2 Score=30.95 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=18.1
Q ss_pred EEEEEECCEEEEEcCCCEEEE
Q 027519 104 FAVVMIGSRQYIVFPGRFIYT 124 (222)
Q Consensus 104 YAIVeigGkQYkV~~GD~I~V 124 (222)
-..+++.||.|.|..||++.+
T Consensus 61 ~Gkir~eGK~Yiv~DGDi~~f 81 (83)
T cd04867 61 AGKYRQEGKDYVVQDGDIIFF 81 (83)
T ss_pred cChhhhhCCceEeeCCeEEEE
Confidence 346789999999999999876
No 19
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=53.70 E-value=24 Score=29.97 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.1
Q ss_pred EEECCEEEEEcCCCEEEEcccCCCCCCCeEEEc
Q 027519 107 VMIGSRQYIVFPGRFIYTQRLKGANVNDKIILN 139 (222)
Q Consensus 107 VeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~ 139 (222)
|.+.|+-|...+||+|+++ .|.+|.|.
T Consensus 108 i~~~G~~~~A~~GDvi~iP------kGs~I~fs 134 (152)
T PF06249_consen 108 ISIDGQTVTAKPGDVIFIP------KGSTITFS 134 (152)
T ss_dssp EEETTEEEEEETT-EEEE-------TT-EEEEE
T ss_pred EEECCEEEEEcCCcEEEEC------CCCEEEEe
Confidence 4589999999999999987 36788884
No 20
>PRK06788 flagellar motor switch protein; Validated
Probab=53.00 E-value=61 Score=26.47 Aligned_cols=63 Identities=19% Similarity=0.176 Sum_probs=35.2
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEc-----eEEEEecCCceEeccccccCcEEEEEEEeecc
Q 027519 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILN-----KVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGL 171 (222)
Q Consensus 101 ~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~-----kVLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k 171 (222)
-.+=..+++|..+..+. | +-+.++||.|.|+ .|-+.-++-..+.|.|.+.+.+.-..|.+-..
T Consensus 34 v~V~v~aeLG~t~ltl~--D------lL~L~vGDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~~~~AVrItei~~ 101 (119)
T PRK06788 34 ISIELGVKLGKASITLG--D------VKQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMDEKFGIIISEIEA 101 (119)
T ss_pred CceEEEEEEecceecHH--H------HhCCCCCCEEEeCCcCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEecC
Confidence 45666777887665432 1 1134566666665 22222233445667777777776667766443
No 21
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=50.65 E-value=23 Score=29.54 Aligned_cols=21 Identities=19% Similarity=0.339 Sum_probs=18.5
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
+.+.++|+.|.+.+||.++++
T Consensus 139 ~~~~~~~~~~~l~~Gd~~~~~ 159 (185)
T PRK09943 139 IVLTINGQDYHLVAGQSYAIN 159 (185)
T ss_pred EEEEECCEEEEecCCCEEEEc
Confidence 346799999999999999988
No 22
>PRK08983 fliN flagellar motor switch protein; Validated
Probab=49.41 E-value=54 Score=26.97 Aligned_cols=61 Identities=15% Similarity=0.136 Sum_probs=36.6
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEce-----EEEEecCCceEeccccccCcEEEEEEEe
Q 027519 100 REEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (222)
Q Consensus 100 ~~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~k-----VLlvgs~~~t~iG~P~v~~a~V~A~Vle 168 (222)
.-.+=..+++|..+..+ ..|-+.++||.|.|++ |-+.-++-..+.|.+.+.+.+.-.+|.+
T Consensus 50 ~v~V~v~v~LG~t~ltl--------~dlL~L~~GDVI~Ld~~~ddpv~v~Vng~~~f~G~~G~~~~k~AVrI~~ 115 (127)
T PRK08983 50 DIPVTISMEVGRSFISI--------RNLLQLNQGSVVELDRVAGEPLDVMVNGTLIAHGEVVVVNDKFGIRLTD 115 (127)
T ss_pred cCeeEEEEEEecCcccH--------HHHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 34566667777665533 2333467788888776 4444444556667777777665555554
No 23
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=42.43 E-value=83 Score=28.22 Aligned_cols=32 Identities=19% Similarity=0.288 Sum_probs=25.6
Q ss_pred EEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEc
Q 027519 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILN 139 (222)
Q Consensus 104 YAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~ 139 (222)
-|-|.+||-.|-+++||+|-|-. +-|..|.++
T Consensus 35 sA~Iyiggl~~~LtEgDil~VFS----qyGe~vdin 66 (219)
T KOG0126|consen 35 SAYIYIGGLPYELTEGDILCVFS----QYGEIVDIN 66 (219)
T ss_pred ceEEEECCCcccccCCcEEEEee----ccCceEEEE
Confidence 48899999999999999998842 466666444
No 24
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=42.07 E-value=4.9 Score=31.08 Aligned_cols=19 Identities=26% Similarity=0.408 Sum_probs=13.3
Q ss_pred EEEECCEEEEEcCCCEEEE
Q 027519 106 VVMIGSRQYIVFPGRFIYT 124 (222)
Q Consensus 106 IVeigGkQYkV~~GD~I~V 124 (222)
.++..||.|.|+.||+|.+
T Consensus 63 k~r~eGK~YivqDGDIi~f 81 (84)
T PF06071_consen 63 KLRLEGKDYIVQDGDIIHF 81 (84)
T ss_dssp -SEEEETT-B--TTEEEEE
T ss_pred CccccCCceeEeCCCEEEE
Confidence 4678899999999999976
No 25
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=39.95 E-value=38 Score=30.74 Aligned_cols=21 Identities=14% Similarity=0.229 Sum_probs=18.1
Q ss_pred EEEECCEEEEEcCCCEEEEcc
Q 027519 106 VVMIGSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 106 IVeigGkQYkV~~GD~I~Ver 126 (222)
.+.++|+.|.+.+||++++++
T Consensus 187 ~l~IdG~t~~l~pGDvlfIPk 207 (233)
T PRK15457 187 HVRHEGETMIAKAGDVMFIPK 207 (233)
T ss_pred EEEECCEEEEeCCCcEEEECC
Confidence 367899999999999999884
No 26
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=37.91 E-value=15 Score=27.04 Aligned_cols=43 Identities=19% Similarity=0.241 Sum_probs=19.7
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEeccccccCcEE
Q 027519 112 RQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAV 162 (222)
Q Consensus 112 kQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~P~v~~a~V 162 (222)
..|++.+||.|.|.-....+ |+.-..|+.++.+ --|++....|
T Consensus 9 ~~y~l~pGD~l~i~v~~~~~------l~~~~~V~~dG~I--~lP~iG~v~v 51 (82)
T PF02563_consen 9 PEYRLGPGDVLRISVFGWPE------LSGEYTVDPDGTI--SLPLIGPVKV 51 (82)
T ss_dssp ------TT-EEEEEETT-HH------HCCSEE--TTSEE--EETTTEEEE-
T ss_pred CCCEECCCCEEEEEEecCCC------cccceEECCCCcE--eecccceEEE
Confidence 57999999999998553211 5556667666544 3466655444
No 27
>PRK06033 hypothetical protein; Validated
Probab=37.47 E-value=61 Score=24.51 Aligned_cols=40 Identities=13% Similarity=0.173 Sum_probs=23.3
Q ss_pred CCCCCCeEEEce-----EEEEecCCceEeccccccCcEEEEEEEe
Q 027519 129 GANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (222)
Q Consensus 129 ~~~~Gd~I~l~k-----VLlvgs~~~t~iG~P~v~~a~V~A~Vle 168 (222)
+.++||.|.|++ |-+.-++-..+.|.|...+.+.-.+|.+
T Consensus 27 ~L~~GDVI~L~~~~~~~v~v~V~~~~~f~g~~G~~~~~~AV~I~~ 71 (83)
T PRK06033 27 RMGRGAVIPLDATEADEVWILANNHPIARGEVLIDRNRIAVEVTR 71 (83)
T ss_pred CCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 456777777654 4444444555667777777655555543
No 28
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=36.57 E-value=39 Score=24.43 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=15.7
Q ss_pred EEcCCCEEEEcccCCCCCCCeE
Q 027519 115 IVFPGRFIYTQRLKGANVNDKI 136 (222)
Q Consensus 115 kV~~GD~I~Verlk~~~~Gd~I 136 (222)
.+..||++.+..++++..||+|
T Consensus 60 ~~~aGdI~~i~gl~~~~~Gdtl 81 (83)
T cd04092 60 SLSAGNIGVITGLKQTRTGDTL 81 (83)
T ss_pred eeCCCCEEEEECCCCcccCCEE
Confidence 4567777777777667777766
No 29
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=35.18 E-value=51 Score=25.16 Aligned_cols=22 Identities=23% Similarity=0.224 Sum_probs=17.5
Q ss_pred EEEECCEEEEEcCCCEEEEccc
Q 027519 106 VVMIGSRQYIVFPGRFIYTQRL 127 (222)
Q Consensus 106 IVeigGkQYkV~~GD~I~Verl 127 (222)
-|.+++.+|.+.+||..+||+-
T Consensus 45 ~Vti~~~~f~v~~G~~F~VP~g 66 (85)
T PF11699_consen 45 EVTIHETSFVVTKGGSFQVPRG 66 (85)
T ss_dssp EEEETTEEEEEETT-EEEE-TT
T ss_pred EEEEcCcEEEEeCCCEEEECCC
Confidence 3678999999999999999964
No 30
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=34.75 E-value=62 Score=23.50 Aligned_cols=31 Identities=26% Similarity=0.358 Sum_probs=22.2
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcc--c-CCCCCCCeEEE
Q 027519 102 EIFAVVMIGSRQYIVFPGRFIYTQR--L-KGANVNDKIIL 138 (222)
Q Consensus 102 ~mYAIVeigGkQYkV~~GD~I~Ver--l-k~~~~Gd~I~l 138 (222)
+-|||+++.+.+ +.+.|++ | .++..||.+.+
T Consensus 9 ~~~AVl~~~~~~------~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 9 GDYAVLELEDGE------KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CCEEEEEECCCe------EEEEEEHHHCCCCCCcccEEEE
Confidence 679999998776 3455553 4 45789998877
No 31
>PRK13501 transcriptional activator RhaR; Provisional
Probab=33.30 E-value=98 Score=27.12 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=19.0
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
+.+.++|+.|.+.+||.+.|+
T Consensus 49 ~~~~i~~~~~~l~~g~~~~I~ 69 (290)
T PRK13501 49 GLHVLNDHPYRITCGDVFYIQ 69 (290)
T ss_pred eEEEECCeeeeecCCeEEEEc
Confidence 467789999999999999997
No 32
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=33.14 E-value=44 Score=23.92 Aligned_cols=21 Identities=19% Similarity=0.164 Sum_probs=13.7
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 027519 116 VFPGRFIYTQRLKGANVNDKI 136 (222)
Q Consensus 116 V~~GD~I~Verlk~~~~Gd~I 136 (222)
+..||+..+..++++.+||++
T Consensus 61 ~~aGdI~~i~g~~~~~~Gdtl 81 (83)
T cd04088 61 AGAGDIGAVAGLKDTATGDTL 81 (83)
T ss_pred eCCCCEEEEECCCCCccCCEe
Confidence 456777776666666666665
No 33
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=33.12 E-value=65 Score=26.90 Aligned_cols=21 Identities=19% Similarity=0.396 Sum_probs=19.1
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
|.|.++|+.+.+.+||.++++
T Consensus 95 a~v~~~~~~~~~~~g~sv~Ip 115 (151)
T PF01050_consen 95 AEVTLDDEEFTLKEGDSVYIP 115 (151)
T ss_pred EEEEECCEEEEEcCCCEEEEC
Confidence 557799999999999999998
No 34
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=32.66 E-value=58 Score=29.16 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=18.7
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ver 126 (222)
+++.++|+-|.|++||++.++-
T Consensus 211 G~~~~~g~~~~V~~GD~i~i~~ 232 (260)
T TIGR03214 211 GVYNLDNNWVPVEAGDYIWMGA 232 (260)
T ss_pred EEEEECCEEEEecCCCEEEECC
Confidence 4567999999999999999873
No 35
>PF05896 NQRA: Na(+)-translocating NADH-quinone reductase subunit A (NQRA); InterPro: IPR008703 This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+ potential driven by aerobic respiration [].; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0006814 sodium ion transport, 0055114 oxidation-reduction process
Probab=31.80 E-value=73 Score=29.28 Aligned_cols=55 Identities=15% Similarity=0.236 Sum_probs=35.9
Q ss_pred EEEEcCCCEEEE-cccCCCCCCCeEEEceEEEEecCC-ceEeccccccCcEEEEEEEeeccCCc
Q 027519 113 QYIVFPGRFIYT-QRLKGANVNDKIILNKVLLVGTKT-TTYIGKPVVTNAAVHAVVEEQGLNPK 174 (222)
Q Consensus 113 QYkV~~GD~I~V-erlk~~~~Gd~I~l~kVLlvgs~~-~t~iG~P~v~~a~V~A~Vleh~k~~K 174 (222)
.|-|.+.|++-+ ++|. +++||+|.....|+.+..+ .+.+=.| |.++|.+--||.|
T Consensus 28 ~~al~~~Df~g~~Pkm~-VkeGD~Vk~Gq~LF~dK~~p~v~ftsP------vsG~V~~I~RG~r 84 (257)
T PF05896_consen 28 TVALLPDDFPGMKPKML-VKEGDRVKAGQPLFEDKKNPGVKFTSP------VSGTVKAINRGER 84 (257)
T ss_pred EEEEcCcccCCCCccEE-eccCCEEeCCCeeEeeCCCCCcEEecC------CCeEEEEEecCCC
Confidence 344456666654 4674 8999999999999997543 2333333 6677777656554
No 36
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=29.94 E-value=52 Score=23.78 Aligned_cols=21 Identities=14% Similarity=0.303 Sum_probs=14.7
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 027519 116 VFPGRFIYTQRLKGANVNDKI 136 (222)
Q Consensus 116 V~~GD~I~Verlk~~~~Gd~I 136 (222)
+..||+..+..++++.+||.+
T Consensus 64 ~~aG~I~~i~gl~~~~~Gdtl 84 (86)
T cd03691 64 AEAGDIVAIAGIEDITIGDTI 84 (86)
T ss_pred ECCCCEEEEECCCCCccccee
Confidence 567777777777666777765
No 37
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=28.99 E-value=51 Score=22.47 Aligned_cols=36 Identities=14% Similarity=0.063 Sum_probs=15.6
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCC-eEEEceEEEEe
Q 027519 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVND-KIILNKVLLVG 145 (222)
Q Consensus 102 ~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd-~I~l~kVLlvg 145 (222)
+-+.+|+-.. .+..||++.+..- |+ ...+.+|....
T Consensus 14 Gd~v~v~~~~---~~~~gdivv~~~~-----~~~~~~iKrv~~~~ 50 (70)
T PF00717_consen 14 GDIVLVDPSS---EPKDGDIVVVKID-----GDEELYIKRVVGEP 50 (70)
T ss_dssp TEEEEEEETS------TTSEEEEEET-----TEESEEEEEEEEET
T ss_pred CCEEEEEEcC---CCccCeEEEEEEC-----CceeeEEEEEEEeC
Confidence 4455555333 5556665555321 11 25556655443
No 38
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=28.39 E-value=1.6e+02 Score=21.44 Aligned_cols=43 Identities=19% Similarity=0.118 Sum_probs=22.8
Q ss_pred ccCCCCCCCeEEEce-----EEEEecCCceEeccccccCcEEEEEEEe
Q 027519 126 RLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (222)
Q Consensus 126 rlk~~~~Gd~I~l~k-----VLlvgs~~~t~iG~P~v~~a~V~A~Vle 168 (222)
.+-+.++||.|.|++ |-+.-++-..+.|.+..-+.+.-.+|.+
T Consensus 25 ell~L~~Gdvi~L~~~~~~~v~l~v~g~~~~~g~lg~~~~~~avrI~~ 72 (77)
T TIGR02480 25 DLLKLGEGSVIELDKLAGEPLDILVNGRLIARGEVVVVEDKFGIRITE 72 (77)
T ss_pred HHhcCCCCCEEEcCCCCCCcEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 344456777777752 3333334445556665555554444444
No 39
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=27.87 E-value=60 Score=24.06 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=16.0
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 027519 116 VFPGRFIYTQRLKGANVNDKI 136 (222)
Q Consensus 116 V~~GD~I~Verlk~~~~Gd~I 136 (222)
+..||++.+-.++++..||++
T Consensus 62 a~aGdIv~v~gl~~~~~Gdtl 82 (85)
T cd03689 62 AYPGDIIGLVNPGNFQIGDTL 82 (85)
T ss_pred ECCCCEEEEECCCCccccCEe
Confidence 567888888877777778776
No 40
>PRK13500 transcriptional activator RhaR; Provisional
Probab=27.22 E-value=1.3e+02 Score=26.99 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ver 126 (222)
+.+.++|+.|.+.+||++.|+.
T Consensus 79 g~~~v~~~~~~l~~Gdl~~I~~ 100 (312)
T PRK13500 79 GLHVLNDRPYRITRGDLFYIHA 100 (312)
T ss_pred EEEEECCEEEeecCCeEEEECC
Confidence 4577889999999999999984
No 41
>PRK11171 hypothetical protein; Provisional
Probab=27.21 E-value=82 Score=28.26 Aligned_cols=20 Identities=25% Similarity=0.335 Sum_probs=17.1
Q ss_pred EEEECCEEEEEcCCCEEEEc
Q 027519 106 VVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 106 IVeigGkQYkV~~GD~I~Ve 125 (222)
++.++|+-|.|++||.|.++
T Consensus 217 ~~~~~~~~~~l~~GD~i~~~ 236 (266)
T PRK11171 217 VYRLNNDWVEVEAGDFIWMR 236 (266)
T ss_pred EEEECCEEEEeCCCCEEEEC
Confidence 45689999999999999886
No 42
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=26.88 E-value=82 Score=28.33 Aligned_cols=21 Identities=10% Similarity=0.107 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
+.+.++|++|.+.+||.+.++
T Consensus 57 ~~~~i~g~~~~l~~Gd~ili~ 77 (302)
T PRK10371 57 VEYLINNEKVQINQGHITLFW 77 (302)
T ss_pred EEEEECCEEEEEcCCcEEEEe
Confidence 468899999999999999997
No 43
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=26.88 E-value=1.3e+02 Score=27.22 Aligned_cols=24 Identities=21% Similarity=0.069 Sum_probs=20.9
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEE
Q 027519 100 REEIFAVVMIGSRQYIVFPGRFIY 123 (222)
Q Consensus 100 ~~~mYAIVeigGkQYkV~~GD~I~ 123 (222)
...-+|||+.+|+|.....||.|.
T Consensus 94 ~~~s~AiI~~~~~q~~y~iGd~i~ 117 (259)
T TIGR01713 94 RIRSIAIIEEGSEQVSLGINESFE 117 (259)
T ss_pred CcceEEEEEeCCeEEEEeCCCCcC
Confidence 456899999999999999999874
No 44
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=26.74 E-value=1.5e+02 Score=28.91 Aligned_cols=41 Identities=34% Similarity=0.402 Sum_probs=30.0
Q ss_pred EEEEcCCCEEEEcccC--CCCCCCeEEEceEEEEecCCceEecccc
Q 027519 113 QYIVFPGRFIYTQRLK--GANVNDKIILNKVLLVGTKTTTYIGKPV 156 (222)
Q Consensus 113 QYkV~~GD~I~Verlk--~~~~Gd~I~l~kVLlvgs~~~t~iG~P~ 156 (222)
-.-|..+++|.|...+ ...+||.+ +|-.+.+.++++||.|+
T Consensus 372 mlavArdRvIav~~~~~~~~~vG~~v---kvrIvr~khnI~Ia~p~ 414 (414)
T COG2100 372 MLAVARDRVIAVINSNEGALLVGDRV---KVRIVRTKHNIYIAVPV 414 (414)
T ss_pred EEEEecccEEEEecCchhhhccCceE---EEEEEEccCceEEeeeC
Confidence 3444458888888765 24689998 55567788999999885
No 45
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=26.15 E-value=92 Score=26.99 Aligned_cols=21 Identities=14% Similarity=0.344 Sum_probs=18.6
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
+.+.++|+.|.+.+||.+.++
T Consensus 54 ~~~~i~~~~~~l~~g~l~~i~ 74 (278)
T PRK10296 54 YYQEINGKRVLLERGDFVFIP 74 (278)
T ss_pred EEEEECCEEEEECCCcEEEeC
Confidence 457789999999999999987
No 46
>TIGR00092 GTP-binding protein YchF. This predicted GTP-binding protein is found in a single copy in every complete bacterial genome, and is found in Eukaryotes. A more distantly related protein, separated from this model, is found in the archaea. It is known to bind GTP and double-stranded nucleic acid. It is suggested to belong to a nucleoprotein complex and act as a translation factor.
Probab=26.06 E-value=40 Score=32.30 Aligned_cols=21 Identities=14% Similarity=0.423 Sum_probs=17.9
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ve 125 (222)
..++..||.|.|..||+|.+-
T Consensus 345 Gk~r~eGK~YivqDGDIi~f~ 365 (368)
T TIGR00092 345 GLMRLEGKYYVVDDGDVLFFA 365 (368)
T ss_pred CchhhcCCeEEeeCCeEEEEe
Confidence 456889999999999999763
No 47
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=25.74 E-value=1.2e+02 Score=25.87 Aligned_cols=59 Identities=19% Similarity=0.169 Sum_probs=34.1
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEce-----EEEEecCCceEeccccccCcEEEEEEEe
Q 027519 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (222)
Q Consensus 102 ~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~k-----VLlvgs~~~t~iG~P~v~~a~V~A~Vle 168 (222)
.+-..+++|..+.. +..|-+.++||.|.|++ |-++-++-..+.|.+.+.+-+.-.+|.+
T Consensus 80 pV~lsveLG~t~it--------lrdLL~L~~GDVI~Ldk~~~epv~V~VnG~~~f~Ge~Gvvn~k~AVrIte 143 (155)
T PRK05698 80 PVSISMEVGSTDIN--------IRNLLQLNQGSVIELDRLAGEPLDVLVNGTLIAHGEVVVVNEKFGIRLTD 143 (155)
T ss_pred eeEEEEEEecCccc--------HHHHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 45566666655543 23333467788887776 4444444455667777666555555544
No 48
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=25.04 E-value=1.1e+02 Score=22.11 Aligned_cols=17 Identities=6% Similarity=0.151 Sum_probs=13.8
Q ss_pred CCEEEEEcCCCEEEEcc
Q 027519 110 GSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 110 gGkQYkV~~GD~I~Ver 126 (222)
+|.++.+.+||.+.+++
T Consensus 42 ~G~~~~~~aGD~~~~p~ 58 (74)
T PF05899_consen 42 DGETVTFKAGDAFFLPK 58 (74)
T ss_dssp TTEEEEEETTEEEEE-T
T ss_pred CCCEEEEcCCcEEEECC
Confidence 88889999999998873
No 49
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=24.55 E-value=81 Score=22.53 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=5.5
Q ss_pred cCCCEEEEccc
Q 027519 117 FPGRFIYTQRL 127 (222)
Q Consensus 117 ~~GD~I~Verl 127 (222)
..||++.+++.
T Consensus 15 ~~gd~v~v~~~ 25 (85)
T cd06530 15 QPGDLVLVNKL 25 (85)
T ss_pred cCCCEEEEEEe
Confidence 44555555543
No 50
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=23.58 E-value=1.2e+02 Score=21.75 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=17.3
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEEc
Q 027519 112 RQYIVFPGRFIYTQRLKGANVNDKIILN 139 (222)
Q Consensus 112 kQYkV~~GD~I~Verlk~~~~Gd~I~l~ 139 (222)
|.=.++-|-.|.||-+ .+.||+|.+|
T Consensus 22 K~A~letG~~i~VP~F--I~~Gd~I~V~ 47 (56)
T smart00841 22 KPATLETGAVVQVPLF--INEGDKIKVD 47 (56)
T ss_pred ceEEECCCCEEEcCCc--ccCCCEEEEE
Confidence 3344555667888866 5788887665
No 51
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=23.27 E-value=1.2e+02 Score=21.65 Aligned_cols=26 Identities=12% Similarity=0.144 Sum_probs=16.9
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEEc
Q 027519 112 RQYIVFPGRFIYTQRLKGANVNDKIILN 139 (222)
Q Consensus 112 kQYkV~~GD~I~Verlk~~~~Gd~I~l~ 139 (222)
|.=.++-|-.|.||-+ ++.||.|.+|
T Consensus 22 K~A~letG~~i~VP~F--I~~Gd~I~V~ 47 (56)
T cd05794 22 KPATLETGAEVQVPLF--IKEGEKIKVD 47 (56)
T ss_pred ceEEECCCCEEEcCCe--ecCCCEEEEE
Confidence 4444555666778866 5788887654
No 52
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=23.01 E-value=1.4e+02 Score=21.35 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=15.9
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEEc
Q 027519 112 RQYIVFPGRFIYTQRLKGANVNDKIILN 139 (222)
Q Consensus 112 kQYkV~~GD~I~Verlk~~~~Gd~I~l~ 139 (222)
|+=.++-|-.|.||.+ .+.||.|.+|
T Consensus 22 K~A~letG~~i~VP~F--I~~Gd~I~Vd 47 (56)
T PF09285_consen 22 KPATLETGAEIQVPLF--IEEGDKIKVD 47 (56)
T ss_dssp EEEEETTS-EEEEETT----TT-EEEEE
T ss_pred cEEEEcCCCEEEccce--ecCCCEEEEE
Confidence 4455666777899976 5799988655
No 53
>PRK08433 flagellar motor switch protein; Validated
Probab=22.85 E-value=1.6e+02 Score=23.66 Aligned_cols=64 Identities=17% Similarity=0.048 Sum_probs=39.2
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEce-----EEEEecCCceEeccccccCcEEEEEEEeecc
Q 027519 100 REEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEEQGL 171 (222)
Q Consensus 100 ~~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~k-----VLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k 171 (222)
.-.+-..+++|..+..+. .+-+.++||.|.|++ |-+.-++--.+.|.|.+.+.+.-.+|.+...
T Consensus 31 ~v~VeV~v~LG~t~itl~--------dlL~Lq~GDVI~Ld~~~~e~v~v~V~g~~~f~G~~G~~~~k~AVrI~e~i~ 99 (111)
T PRK08433 31 DIEVDFSAELGTTQISLL--------EILKFEKGSVIDLEKPAGESVELYINGRIIGKGEVMVYEKNLAIRINEILD 99 (111)
T ss_pred cceeEEEEEEecccccHH--------HHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEecC
Confidence 456777777887665432 222456777777763 3333344456678888888777667766544
No 54
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.61 E-value=1.9e+02 Score=25.06 Aligned_cols=49 Identities=20% Similarity=0.070 Sum_probs=36.4
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEecc
Q 027519 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGK 154 (222)
Q Consensus 102 ~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG~ 154 (222)
.-|+||+.+|--|.|..-... +...+.|+.+.|-.-+.+..+...+.|=
T Consensus 14 ~~~vvi~~~GvGY~V~vs~~~----~~~l~~g~~v~l~t~~~vrEd~~~LyGF 62 (197)
T PRK14603 14 EGSAVLLAGGVGLEVQCPAPT----LARLVEGQEAELHTRLVVREDALSLYGF 62 (197)
T ss_pred CCEEEEEECCEEEEEEcCHHH----HHHcCCCCeEEEEEEEEEccCCceeeCc
Confidence 458999999999998755332 1223579999998888888777777664
No 55
>TIGR03021 pilP_fam type IV pilus biogenesis protein PilP. Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP.
Probab=22.42 E-value=1e+02 Score=24.87 Aligned_cols=25 Identities=20% Similarity=0.260 Sum_probs=21.6
Q ss_pred CCCCCeEEEEEE-CCEEEEEcCCCEE
Q 027519 98 PKREEIFAVVMI-GSRQYIVFPGRFI 122 (222)
Q Consensus 98 ~~~~~mYAIVei-gGkQYkV~~GD~I 122 (222)
.....+.|.++. +|++.-|..||.|
T Consensus 76 G~~~~l~A~l~l~~G~~~~v~~G~~l 101 (119)
T TIGR03021 76 GRGGRLTATLRLPGGREVDVQVGDSL 101 (119)
T ss_pred ccCCCeEEEEEeCCCcEEEecCCCcc
Confidence 346789999999 8899999999975
No 56
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=22.28 E-value=1.1e+02 Score=26.55 Aligned_cols=22 Identities=14% Similarity=0.314 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ver 126 (222)
+.+.++|+.|.+.+||.+.++.
T Consensus 55 ~~~~~~~~~~~l~~g~~~ii~~ 76 (287)
T TIGR02297 55 IALQLDEHEYSEYAPCFFLTPP 76 (287)
T ss_pred eEEEECCEEEEecCCeEEEeCC
Confidence 4678899999999999999883
No 57
>PF09956 DUF2190: Uncharacterized conserved protein (DUF2190); InterPro: IPR011231 This entry is represented by Bacteriophage VT1-Sakai, H0018. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised conserved proteins.
Probab=21.95 E-value=2.8e+02 Score=21.95 Aligned_cols=33 Identities=18% Similarity=0.242 Sum_probs=24.9
Q ss_pred EEEEcCCCEEEEcccCCCCCCCeEEEceEEEEec
Q 027519 113 QYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGT 146 (222)
Q Consensus 113 QYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs 146 (222)
.| |.+|+.|.+.--.++..||-+.+..++-+-.
T Consensus 3 Ny-vq~G~~i~~ta~~~V~sG~~V~vG~~~GVA~ 35 (106)
T PF09956_consen 3 NY-VQDGDTIDVTAPAAVASGDVVVVGSLFGVAL 35 (106)
T ss_pred cc-ccCCCEEEEecCcccccCCEEEECCEEEEEe
Confidence 45 7889999887555678888888888776643
No 58
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=21.89 E-value=62 Score=22.19 Aligned_cols=12 Identities=25% Similarity=0.456 Sum_probs=6.8
Q ss_pred EEEEcCCCEEEE
Q 027519 113 QYIVFPGRFIYT 124 (222)
Q Consensus 113 QYkV~~GD~I~V 124 (222)
.|+|..||.|.|
T Consensus 47 ~~~l~~Gd~v~i 58 (59)
T TIGR02988 47 GKKLYPGDVIEI 58 (59)
T ss_pred CCCCCCCCEEEe
Confidence 355666666554
No 59
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=21.76 E-value=82 Score=23.15 Aligned_cols=21 Identities=33% Similarity=0.438 Sum_probs=13.2
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 027519 116 VFPGRFIYTQRLKGANVNDKI 136 (222)
Q Consensus 116 V~~GD~I~Verlk~~~~Gd~I 136 (222)
+..||++-+..++++..||.|
T Consensus 63 ~~aGdI~ai~gl~~~~~Gdtl 83 (85)
T cd03690 63 VTAGDIAILTGLKGLRVGDVL 83 (85)
T ss_pred ECCCCEEEEECCCCCcCcccc
Confidence 556666666666666666654
No 60
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=21.03 E-value=1.8e+02 Score=21.85 Aligned_cols=33 Identities=21% Similarity=0.363 Sum_probs=24.5
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceE
Q 027519 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKV 141 (222)
Q Consensus 102 ~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kV 141 (222)
+.|.-|..|-|.|-+..+|. +.++||.+.|.+.
T Consensus 8 ~yF~~V~~G~KtfEiRkNDR-------df~VGD~L~L~E~ 40 (72)
T PF12961_consen 8 EYFEAVLSGRKTFEIRKNDR-------DFQVGDILVLREW 40 (72)
T ss_pred HHHHHHHCCCceEEEEecCC-------CCCCCCEEEEEEe
Confidence 34555667778888888773 5789999998874
No 61
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=20.99 E-value=2.8e+02 Score=19.19 Aligned_cols=49 Identities=18% Similarity=0.243 Sum_probs=33.0
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEec
Q 027519 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIG 153 (222)
Q Consensus 101 ~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG 153 (222)
..-|+|++.+|-=|+|..-+. .+...+.++.+.+-.-+.+..++..+.|
T Consensus 13 ~~~~vvi~~~GvGy~v~v~~~----~~~~l~~~~~v~l~t~~~vrEd~~~LyG 61 (61)
T PF01330_consen 13 NPDYVVIDVNGVGYEVFVPSN----TLSELPEGGEVKLYTYLIVREDAISLYG 61 (61)
T ss_dssp ESSEEEEEETTEEEEEEE-HH----HHHTS-TTSEEEEEEEEEEETTEEEEEE
T ss_pred cCCEEEEEECCEEEEEEeCCc----hHHhCCCCCEEEEEEEEEEeechhhcCC
Confidence 356899999999998863332 1223456678888888888776655544
No 62
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.85 E-value=1.4e+02 Score=26.04 Aligned_cols=49 Identities=18% Similarity=0.345 Sum_probs=36.4
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEceEEEEecCCceEec
Q 027519 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIG 153 (222)
Q Consensus 102 ~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~kVLlvgs~~~t~iG 153 (222)
..|+||+++|--|.|..-.... ..++ +.|+.+.|---+.+..+...+.|
T Consensus 14 ~~~viie~~GvGY~v~vs~~~~-~~l~--~~g~~v~l~t~~~vrEd~~~LyG 62 (195)
T PRK14604 14 NDHLIVETGGVGLLIYAPRSVL-AAIG--AIGDEVFLYTHLIVREDALTLYG 62 (195)
T ss_pred CCEEEEEECCEEEEEEeCHHHH-HHhc--cCCCeEEEEEEEEEecCCceeeC
Confidence 4699999999999987553321 1232 57999999998888877777665
No 63
>PRK09601 GTP-binding protein YchF; Reviewed
Probab=20.84 E-value=68 Score=30.66 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=15.9
Q ss_pred EEECCEEEEEcCCCEEEEc
Q 027519 107 VMIGSRQYIVFPGRFIYTQ 125 (222)
Q Consensus 107 VeigGkQYkV~~GD~I~Ve 125 (222)
+++-||.|.|+.||+|.+-
T Consensus 343 ~rleGkdY~v~DGDIi~f~ 361 (364)
T PRK09601 343 VRLEGKDYIVQDGDVMHFR 361 (364)
T ss_pred eeccCCceEecCCCEEEEE
Confidence 3477999999999999763
No 64
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=20.80 E-value=1.3e+02 Score=26.31 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=17.6
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 027519 105 AVVMIGSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 105 AIVeigGkQYkV~~GD~I~Ver 126 (222)
+.++.+|+.|.+.+||++.++.
T Consensus 82 ~~~~~~g~~~~l~~G~~~l~~~ 103 (302)
T PRK09685 82 AIIEQDDRQVQLAAGDITLIDA 103 (302)
T ss_pred EEEEECCeEEEEcCCCEEEEEC
Confidence 4467888899999999988863
No 65
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=20.44 E-value=1.8e+02 Score=28.01 Aligned_cols=66 Identities=17% Similarity=0.186 Sum_probs=42.8
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEEce-----EEEEecCCceEeccccccCcEEEEEEEeeccCCc
Q 027519 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPK 174 (222)
Q Consensus 101 ~~mYAIVeigGkQYkV~~GD~I~Verlk~~~~Gd~I~l~k-----VLlvgs~~~t~iG~P~v~~a~V~A~Vleh~k~~K 174 (222)
..+=..+..+..+. .+..+-+.++||.|.|+. |-+.-++--.+.|.|-..|.+.-++|.+....++
T Consensus 302 ~~V~l~a~L~~~~i--------tl~dlL~LkvGDVI~Ld~~~~~~v~v~v~g~p~F~g~~G~~~g~~AvrI~~~l~~~~ 372 (388)
T PRK12795 302 TDVEVDAVLDEQTL--------PLKRVLNLKVGDTLMLDARPDALVTLRCGDVPLTEGRMGRVGDRVAVRVEKPLRKPR 372 (388)
T ss_pred CeeEEEEEEeccEE--------eHHHHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEeccCCCEEEEEEEeecCCcc
Confidence 34445555554443 233333567888888873 5555555667789999899888888887665444
No 66
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=20.42 E-value=1.3e+02 Score=24.15 Aligned_cols=18 Identities=11% Similarity=0.207 Sum_probs=15.8
Q ss_pred E-CCEEEEEcCCCEEEEcc
Q 027519 109 I-GSRQYIVFPGRFIYTQR 126 (222)
Q Consensus 109 i-gGkQYkV~~GD~I~Ver 126 (222)
+ +|+.|.+.+||.++++.
T Consensus 71 i~~g~~~~L~aGD~i~~~~ 89 (125)
T PRK13290 71 LATGEVHPIRPGTMYALDK 89 (125)
T ss_pred cCCCEEEEeCCCeEEEECC
Confidence 6 49999999999999873
Done!