Query 028995
Match_columns 200
No_of_seqs 172 out of 1086
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:48:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028995.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028995hhsearch_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 3.3E-42 7.2E-47 268.8 13.6 97 101-198 1-97 (108)
2 COG0261 RplU Ribosomal protein 100.0 9.8E-42 2.1E-46 264.0 12.0 95 103-198 1-95 (103)
3 PRK05573 rplU 50S ribosomal pr 100.0 2.6E-41 5.5E-46 261.4 13.1 95 103-198 1-95 (103)
4 PF00829 Ribosomal_L21p: Ribos 100.0 1.1E-41 2.4E-46 260.0 7.5 95 103-198 1-95 (96)
5 TIGR00061 L21 ribosomal protei 100.0 1.2E-40 2.7E-45 257.1 12.8 94 104-198 1-94 (101)
6 PRK12278 50S ribosomal protein 100.0 6.1E-39 1.3E-43 276.5 13.2 95 103-198 1-95 (221)
7 KOG1686 Mitochondrial/chloropl 99.9 1.8E-24 3.9E-29 176.4 9.7 101 98-198 21-121 (151)
8 PF12791 RsgI_N: Anti-sigma fa 88.4 0.95 2.1E-05 30.7 4.1 37 101-144 4-40 (56)
9 PF11356 Pilus_PilP: Type IV p 83.6 1.7 3.6E-05 31.5 3.6 40 98-143 36-78 (87)
10 PF02311 AraC_binding: AraC-li 74.4 5.1 0.00011 29.0 3.8 21 105-125 34-54 (136)
11 PF04351 PilP: Pilus assembly 73.5 4.4 9.5E-05 32.9 3.6 24 100-123 88-112 (149)
12 COG0662 {ManC} Mannose-6-phosp 70.9 6.4 0.00014 30.7 3.8 26 100-125 57-88 (127)
13 COG3168 PilP Tfp pilus assembl 68.7 8.2 0.00018 32.9 4.2 26 100-125 107-132 (170)
14 PF07883 Cupin_2: Cupin domain 63.9 11 0.00024 25.1 3.4 20 107-126 32-51 (71)
15 PRK06788 flagellar motor switc 62.5 30 0.00064 27.8 6.1 63 100-171 33-101 (119)
16 TIGR03689 pup_AAA proteasome A 59.7 25 0.00054 34.4 6.3 38 104-144 60-97 (512)
17 cd04867 TGS_YchF_C TGS_YchF_C: 59.3 4.4 9.4E-05 30.9 0.8 21 104-124 61-81 (83)
18 PF06249 EutQ: Ethanolamine ut 56.9 20 0.00044 29.9 4.5 27 107-139 108-134 (152)
19 PRK09943 DNA-binding transcrip 56.0 17 0.00037 29.8 3.9 21 106-126 140-160 (185)
20 KOG1686 Mitochondrial/chloropl 52.2 6.5 0.00014 33.0 0.8 57 100-157 92-151 (151)
21 KOG0126 Predicted RNA-binding 47.3 65 0.0014 28.5 6.2 32 104-139 35-66 (219)
22 PF02563 Poly_export: Polysacc 45.8 9.9 0.00021 27.5 0.9 43 112-162 9-51 (82)
23 PF06071 YchF-GTPase_C: Protei 45.2 4.1 8.9E-05 31.0 -1.3 19 106-124 63-81 (84)
24 PRK15457 ethanolamine utilizat 44.9 30 0.00065 31.0 3.8 21 106-126 187-207 (233)
25 PF11213 DUF3006: Protein of u 43.2 56 0.0012 23.4 4.4 31 102-138 9-42 (71)
26 COG3264 Small-conductance mech 42.7 25 0.00055 36.6 3.5 45 119-177 652-696 (835)
27 TIGR01713 typeII_sec_gspC gene 39.1 50 0.0011 29.3 4.4 25 99-123 93-117 (259)
28 PF01050 MannoseP_isomer: Mann 39.0 47 0.001 27.3 3.9 21 105-125 95-115 (151)
29 PRK13501 transcriptional activ 38.9 75 0.0016 27.4 5.4 22 105-126 49-70 (290)
30 TIGR03214 ura-cupin putative a 37.1 46 0.00099 29.3 3.8 22 105-126 211-232 (260)
31 cd04092 mtEFG2_II_like mtEFG2_ 36.5 39 0.00085 24.0 2.8 22 115-136 60-81 (83)
32 cd06530 S26_SPase_I The S26 Ty 35.8 46 0.00099 23.4 3.0 12 116-127 14-25 (85)
33 PRK08983 fliN flagellar motor 35.4 1.2E+02 0.0026 24.5 5.7 62 99-168 49-115 (127)
34 PF11699 CENP-C_C: Mif2/CENP-C 34.5 54 0.0012 24.6 3.3 21 107-127 46-66 (85)
35 PRK10371 DNA-binding transcrip 33.7 54 0.0012 29.0 3.8 21 105-125 57-77 (302)
36 cd04088 EFG_mtEFG_II EFG_mtEFG 33.2 45 0.00098 23.5 2.6 21 116-136 61-81 (83)
37 PF05896 NQRA: Na(+)-transloca 32.9 69 0.0015 29.0 4.3 56 113-175 28-85 (257)
38 cd03691 BipA_TypA_II BipA_TypA 32.2 46 0.001 23.7 2.6 21 116-136 64-84 (86)
39 PF00717 Peptidase_S24: Peptid 31.9 45 0.00097 22.4 2.3 17 118-134 13-29 (70)
40 PRK10296 DNA-binding transcrip 31.8 66 0.0014 27.4 3.9 22 105-126 54-75 (278)
41 PRK06033 hypothetical protein; 31.8 92 0.002 23.2 4.2 40 129-168 27-71 (83)
42 PRK13500 transcriptional activ 31.2 1.1E+02 0.0023 27.0 5.2 22 105-126 79-100 (312)
43 TIGR03021 pilP_fam type IV pil 31.1 59 0.0013 25.9 3.2 24 99-122 77-101 (119)
44 TIGR00092 GTP-binding protein 30.2 30 0.00066 32.5 1.6 20 105-124 345-364 (368)
45 PRK11171 hypothetical protein; 29.9 71 0.0015 28.2 3.8 20 106-125 217-236 (266)
46 PF12961 DUF3850: Domain of Un 29.8 1E+02 0.0023 22.8 4.1 33 102-141 8-40 (72)
47 PF05899 Cupin_3: Protein of u 29.1 84 0.0018 22.3 3.5 16 110-125 42-57 (74)
48 KOG2925 Predicted translation 28.3 64 0.0014 27.5 3.1 50 86-137 21-82 (167)
49 PHA02885 putative interleukin 28.1 57 0.0012 26.4 2.6 28 111-138 61-93 (135)
50 TIGR02228 sigpep_I_arch signal 27.9 78 0.0017 26.1 3.5 32 107-138 36-69 (158)
51 PF09285 Elong-fact-P_C: Elong 27.5 1.1E+02 0.0023 21.6 3.7 26 112-139 22-47 (56)
52 TIGR02297 HpaA 4-hydroxyphenyl 27.3 76 0.0017 26.9 3.5 22 105-126 55-76 (287)
53 cd03689 RF3_II RF3_II: this su 27.0 64 0.0014 23.5 2.6 21 116-136 62-82 (85)
54 cd05794 S1_EF-P_repeat_2 S1_EF 26.5 1E+02 0.0022 21.7 3.4 26 112-139 22-47 (56)
55 TIGR02988 YaaA_near_RecF S4 do 26.1 47 0.001 22.4 1.6 12 113-124 47-58 (59)
56 smart00841 Elong-fact-P_C Elon 26.0 1E+02 0.0022 21.7 3.3 26 112-139 22-47 (56)
57 TIGR02480 fliN flagellar motor 25.9 2.1E+02 0.0046 20.5 5.1 58 103-168 10-72 (77)
58 COG0681 LepB Signal peptidase 25.6 81 0.0018 24.5 3.1 23 106-128 35-57 (166)
59 PF06130 PduL: Propanediol uti 25.4 79 0.0017 23.2 2.8 31 116-149 23-54 (71)
60 PF09956 DUF2190: Uncharacteri 25.3 2.1E+02 0.0044 22.3 5.3 32 113-145 3-34 (106)
61 PF10949 DUF2777: Protein of u 24.4 84 0.0018 27.2 3.2 22 106-127 67-88 (185)
62 TIGR01222 minC septum site-det 24.2 2.8E+02 0.0062 23.7 6.4 53 110-165 121-175 (217)
63 PRK09685 DNA-binding transcrip 24.0 1E+02 0.0022 26.4 3.7 22 105-126 82-103 (302)
64 PRK12784 hypothetical protein; 23.9 1.8E+02 0.0038 22.3 4.4 47 102-149 32-78 (84)
65 PRK14603 ruvA Holliday junctio 23.5 1.9E+02 0.0041 24.7 5.2 49 102-154 14-62 (197)
66 COG1974 LexA SOS-response tran 23.4 1.5E+02 0.0032 25.6 4.5 41 102-146 111-153 (201)
67 PRK09601 GTP-binding protein Y 23.4 57 0.0012 30.7 2.1 17 108-124 344-360 (364)
68 KOG1491 Predicted GTP-binding 23.1 52 0.0011 31.5 1.8 16 109-124 372-387 (391)
69 PRK13290 ectC L-ectoine syntha 23.0 1.1E+02 0.0024 24.2 3.5 18 109-126 71-89 (125)
70 PLN02765 pyruvate kinase 22.9 1.8E+02 0.0038 29.0 5.4 14 111-124 105-118 (526)
71 PRK04290 30S ribosomal protein 22.9 90 0.002 25.1 2.9 76 110-190 13-94 (115)
72 PRK13502 transcriptional activ 22.4 1.2E+02 0.0025 25.9 3.7 22 105-126 49-70 (282)
73 PF11948 DUF3465: Protein of u 22.1 2.8E+02 0.006 22.9 5.6 49 100-148 56-104 (131)
74 PF12969 DUF3857: Domain of Un 22.1 92 0.002 24.4 2.8 40 106-145 48-105 (177)
75 COG1917 Uncharacterized conser 21.9 1.1E+02 0.0023 23.4 3.1 20 107-126 77-96 (131)
76 PF14525 AraC_binding_2: AraC- 21.7 1.4E+02 0.003 22.7 3.7 21 105-125 66-86 (172)
77 PTZ00414 10 kDa heat shock pro 21.4 3.3E+02 0.0071 21.2 5.7 42 101-146 44-91 (100)
78 COG4766 EutQ Ethanolamine util 21.4 1.3E+02 0.0028 25.9 3.6 27 107-139 131-157 (176)
79 cd03690 Tet_II Tet_II: This su 21.2 88 0.0019 22.6 2.4 21 116-136 63-83 (85)
80 PRK11171 hypothetical protein; 21.1 1.3E+02 0.0029 26.4 3.9 22 105-126 94-115 (266)
81 PRK10572 DNA-binding transcrip 20.9 1.1E+02 0.0024 26.2 3.3 21 106-126 61-81 (290)
82 PF04347 FliO: Flagellar biosy 20.7 1.5E+02 0.0033 21.1 3.5 21 100-120 28-48 (84)
83 PRK14604 ruvA Holliday junctio 20.6 1.3E+02 0.0029 25.6 3.7 49 102-153 14-62 (195)
84 PRK04804 minC septum formation 20.6 3.8E+02 0.0083 23.1 6.5 52 111-165 124-177 (221)
85 PRK05698 fliN flagellar motor 20.3 1.9E+02 0.0042 24.2 4.5 61 100-168 78-143 (155)
86 smart00835 Cupin_1 Cupin. This 20.3 1.1E+02 0.0024 23.9 2.9 14 113-126 76-89 (146)
No 1
>CHL00075 rpl21 ribosomal protein L21
Probab=100.00 E-value=3.3e-42 Score=268.79 Aligned_cols=97 Identities=33% Similarity=0.498 Sum_probs=94.1
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEe
Q 028995 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKY 180 (200)
Q Consensus 101 ~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~ 180 (200)
+.|||||++|||||||++||+|.||+|+ +++|++|+|++|||+++++.+.+|.|||+||+|+|+|++|+||+||+||||
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 3699999999999999999999999995 899999999999999988889999999999999999999999999999999
Q ss_pred cCCCCcccccCCcCCccc
Q 028995 181 KKKKNYRRNIGHRQVKDL 198 (200)
Q Consensus 181 KrRK~yrRk~GHRQ~~T~ 198 (200)
||||+|||++||||+||+
T Consensus 80 krRK~yrrk~GHRQ~~T~ 97 (108)
T CHL00075 80 RPKKKTRKKQGHRQKLTR 97 (108)
T ss_pred CCCCCccCCCccCCCcEE
Confidence 999999999999999996
No 2
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.8e-42 Score=264.01 Aligned_cols=95 Identities=42% Similarity=0.673 Sum_probs=93.3
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEecC
Q 028995 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (200)
Q Consensus 103 mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~Kr 182 (200)
|||||++|||||+|++||+|+||+|. +++|++|+||+|||+++++.+.||.|||+||+|.|+|++|+|++||++|||||
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 99999999999999999999999995 89999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCcCCccc
Q 028995 183 KKNYRRNIGHRQVKDL 198 (200)
Q Consensus 183 RK~yrRk~GHRQ~~T~ 198 (200)
||+|+|++||||+||+
T Consensus 80 rK~~~rk~GHRQ~yT~ 95 (103)
T COG0261 80 RKNYRKKQGHRQPYTR 95 (103)
T ss_pred CcCcccccCcccceEE
Confidence 9999999999999996
No 3
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=100.00 E-value=2.6e-41 Score=261.37 Aligned_cols=95 Identities=44% Similarity=0.685 Sum_probs=93.3
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEecC
Q 028995 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (200)
Q Consensus 103 mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~Kr 182 (200)
|||||++||+||||++||+|.||+|+ +++||+|+|++|||+++++.+.+|+|||++|+|+|+|++|+|++||++|||||
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 CCCcccccCCcCCccc
Q 028995 183 KKNYRRNIGHRQVKDL 198 (200)
Q Consensus 183 RK~yrRk~GHRQ~~T~ 198 (200)
||+|+|++||||+||+
T Consensus 80 RK~y~r~~GHRQ~~T~ 95 (103)
T PRK05573 80 RKNYRKKQGHRQPYTK 95 (103)
T ss_pred CCCccccCCccCCcEE
Confidence 9999999999999996
No 4
>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=1.1e-41 Score=260.02 Aligned_cols=95 Identities=47% Similarity=0.726 Sum_probs=92.8
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEecC
Q 028995 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (200)
Q Consensus 103 mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~Kr 182 (200)
|||||++||+||+|++||+|+||+| ++++||+|+|++||++++++++.+|+|||++|+|+|+|++|+|++|+++|||||
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 9999999999999999999999999 699999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCcCCccc
Q 028995 183 KKNYRRNIGHRQVKDL 198 (200)
Q Consensus 183 RK~yrRk~GHRQ~~T~ 198 (200)
||+|+|++||||+||+
T Consensus 80 RK~y~r~~GhRq~~T~ 95 (96)
T PF00829_consen 80 RKRYRRKQGHRQPYTR 95 (96)
T ss_dssp TTTEEEEEEEEEEEEE
T ss_pred ccccccCCccCCCeEE
Confidence 9999999999999996
No 5
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=100.00 E-value=1.2e-40 Score=257.14 Aligned_cols=94 Identities=39% Similarity=0.597 Sum_probs=92.2
Q ss_pred EEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEecCC
Q 028995 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKKK 183 (200)
Q Consensus 104 YAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~KrR 183 (200)
||||++|||||||++||+|.||+|+ +++||.|+|++|||+++++.+.+|+|+|+||+|+|+|++|+||+||++||||||
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 899999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccCCcCCccc
Q 028995 184 KNYRRNIGHRQVKDL 198 (200)
Q Consensus 184 K~yrRk~GHRQ~~T~ 198 (200)
|+|||++||||+||+
T Consensus 80 K~y~r~~GHRQ~~T~ 94 (101)
T TIGR00061 80 KHSRKKQGHRQPYTK 94 (101)
T ss_pred CCccCCCccCCCcEE
Confidence 999999999999996
No 6
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=100.00 E-value=6.1e-39 Score=276.52 Aligned_cols=95 Identities=37% Similarity=0.590 Sum_probs=93.1
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEecC
Q 028995 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKK 182 (200)
Q Consensus 103 mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~Kr 182 (200)
|||||++|||||||++||+|.||+|. .++||+|.|++|||+++++.+.||+|||+|++|+|+|++|+||+||+||||||
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 99999999999999999999999995 79999999999999998899999999999999999999999999999999999
Q ss_pred CCCcccccCCcCCccc
Q 028995 183 KKNYRRNIGHRQVKDL 198 (200)
Q Consensus 183 RK~yrRk~GHRQ~~T~ 198 (200)
||+|||++||||+||+
T Consensus 80 RK~yrrk~GHRQ~~T~ 95 (221)
T PRK12278 80 RQSSRRTKGHRQLLTL 95 (221)
T ss_pred CCCcccCCCcCCCcEE
Confidence 9999999999999996
No 7
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.8e-24 Score=176.42 Aligned_cols=101 Identities=54% Similarity=0.647 Sum_probs=98.2
Q ss_pred CCCCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEE
Q 028995 98 PKREEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIV 177 (200)
Q Consensus 98 ~~~~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~V 177 (200)
..+...||||.+||+||+|..||.|+.+++++.++||.|.|++|||+|+.+++.+|+|.|++++|.|.|++|++..|+++
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 EEecCCCCcccccCCcCCccc
Q 028995 178 FKYKKKKNYRRNIGHRQVKDL 198 (200)
Q Consensus 178 fK~KrRK~yrRk~GHRQ~~T~ 198 (200)
||+|++|.|||.+||||..|+
T Consensus 101 fk~k~~k~tr~~~~~~qe~t~ 121 (151)
T KOG1686|consen 101 FKSKQWKVTRRDLGHRQEATE 121 (151)
T ss_pred EEecchhhhhhhhcccCcccE
Confidence 999999999999999998875
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=88.37 E-value=0.95 Score=30.68 Aligned_cols=37 Identities=24% Similarity=0.475 Sum_probs=30.3
Q ss_pred CCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEE
Q 028995 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLV 144 (200)
Q Consensus 101 ~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlv 144 (200)
.+.||||.+. .|+++.|.+-.+.++|++|.|+..-..
T Consensus 4 ~~~~aiVlT~-------dGeF~~ik~~~~~~vG~eI~~~~~~~~ 40 (56)
T PF12791_consen 4 KKKYAIVLTP-------DGEFIKIKRKPGMEVGQEIEFDEKDII 40 (56)
T ss_pred cCCEEEEEcC-------CCcEEEEeCCCCCcccCEEEEechhhc
Confidence 4568888886 688999999888999999999875444
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=83.60 E-value=1.7 Score=31.48 Aligned_cols=40 Identities=23% Similarity=0.153 Sum_probs=28.3
Q ss_pred CCCCCeEEEEE-ECCEEEEEcCCCEEE--EcccCCCCCCCeEEeeeEEE
Q 028995 98 PKREEIFAVVM-IGSRQYIVFPGRFIY--TQRLKGANVNDKIILNKVLL 143 (200)
Q Consensus 98 ~~~~~mYAIIe-iGGKQYkV~~Gd~I~--VerL~~~e~Gd~I~l~~VLl 143 (200)
......+|||+ .+|.|+.+..||.|. =-+|. .|.-|.|++
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 999999999999975 33443 466677777
No 10
>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=74.38 E-value=5.1 Score=29.04 Aligned_cols=21 Identities=19% Similarity=0.453 Sum_probs=16.0
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ve 125 (200)
..+.++|++|.|.+||++.++
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 356899999999999999987
No 11
>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=73.50 E-value=4.4 Score=32.91 Aligned_cols=24 Identities=25% Similarity=0.286 Sum_probs=21.8
Q ss_pred CCCeEEEEEE-CCEEEEEcCCCEEE
Q 028995 100 REEIFAVVMI-GSRQYIVFPGRFIY 123 (200)
Q Consensus 100 ~~~mYAIIei-GGKQYkV~~Gd~I~ 123 (200)
...++|+|+. .|+=|+|..||+|=
T Consensus 88 ~~~~~ALv~~pdg~v~~V~~G~yiG 112 (149)
T PF04351_consen 88 GGQPWALVQDPDGKVYRVKVGDYIG 112 (149)
T ss_dssp TTEEEEEEEE-TTEEEEEETTEEET
T ss_pred CCEEEEEEEeCCCCEEEecCCCEec
Confidence 5679999999 99999999999983
No 12
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=70.88 E-value=6.4 Score=30.70 Aligned_cols=26 Identities=31% Similarity=0.445 Sum_probs=22.0
Q ss_pred CCCeEE------EEEECCEEEEEcCCCEEEEc
Q 028995 100 REEIFA------VVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 100 ~~~mYA------IIeiGGKQYkV~~Gd~I~Ve 125 (200)
+.++|. +|.++|+++.|.+||.++|+
T Consensus 57 ~dE~~~Vl~G~g~v~~~~~~~~v~~gd~~~iP 88 (127)
T COG0662 57 RDEHWYVLEGTGKVTIGGEEVEVKAGDSVYIP 88 (127)
T ss_pred cceEEEEEeeEEEEEECCEEEEecCCCEEEEC
Confidence 455664 46799999999999999998
No 13
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=68.71 E-value=8.2 Score=32.91 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=22.8
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEc
Q 028995 100 REEIFAVVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 100 ~~~mYAIIeiGGKQYkV~~Gd~I~Ve 125 (200)
....+|+|+..|+-|+|..|++|=.+
T Consensus 107 g~~~~A~i~~~~~v~~V~vG~YlGqN 132 (170)
T COG3168 107 GQGVSALIEAPGGVYRVRVGQYLGQN 132 (170)
T ss_pred CCceEEEEEcCCceEEEeeccEeecc
Confidence 46699999999999999999998544
No 14
>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=63.90 E-value=11 Score=25.15 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=17.3
Q ss_pred EEECCEEEEEcCCCEEEEcc
Q 028995 107 VMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 107 IeiGGKQYkV~~Gd~I~Ver 126 (200)
+.++|..|.+.+||.++++.
T Consensus 32 ~~~~~~~~~l~~Gd~~~i~~ 51 (71)
T PF07883_consen 32 LTVDGERVELKPGDAIYIPP 51 (71)
T ss_dssp EEETTEEEEEETTEEEEEET
T ss_pred EEEccEEeEccCCEEEEECC
Confidence 44899999999999999874
No 15
>PRK06788 flagellar motor switch protein; Validated
Probab=62.45 E-value=30 Score=27.81 Aligned_cols=63 Identities=16% Similarity=0.147 Sum_probs=35.5
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeee------EEEEecCCceEeccceecCcEEEEEEEeecC
Q 028995 100 REEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK------VLLVGTKTTTYIGKPVVTNAAVHAVVEEQGL 171 (200)
Q Consensus 100 ~~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~------VLlvg~~~~t~vG~P~v~~a~V~AtVveh~k 171 (200)
...+=..+++|..+..+. | -| +.++||.|.|++ .+.++ +-....|.|.+.+-+.-..|.+-..
T Consensus 33 ~v~V~v~aeLG~t~ltl~--D-----lL-~L~vGDVI~Ldk~~~dpv~v~Vn-g~~~f~G~~Gv~~~~~AVrItei~~ 101 (119)
T PRK06788 33 DISIELGVKLGKASITLG--D-----VK-QLKVGDVLEVEKNLGHKVDVYLS-NMKVGIGEAIVMDEKFGIIISEIEA 101 (119)
T ss_pred cCceEEEEEEecceecHH--H-----Hh-CCCCCCEEEeCCcCCCCEEEEEC-CEEEEEEEEEEECCEEEEEEEEecC
Confidence 466777888887776543 1 12 244555555541 22333 3344557777777666666666444
No 16
>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=59.68 E-value=25 Score=34.43 Aligned_cols=38 Identities=24% Similarity=0.199 Sum_probs=30.9
Q ss_pred EEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEE
Q 028995 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLV 144 (200)
Q Consensus 104 YAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlv 144 (200)
-|.|-+||+.|+|...-.|.+..| .+|+.|.|++=+.+
T Consensus 60 ~~~v~~~g~~~~~~~~~~~~~~~l---~~g~~v~l~e~~~~ 97 (512)
T TIGR03689 60 TAEVFTAGRRMRVTVSPNVNAAEL---VPGQTVRLNEALQV 97 (512)
T ss_pred eEEEEeCCceEEEEeCCCCCHHHC---CCCCEEEECCccee
Confidence 377888999999998888888776 59999999866554
No 17
>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=59.28 E-value=4.4 Score=30.90 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=18.1
Q ss_pred EEEEEECCEEEEEcCCCEEEE
Q 028995 104 FAVVMIGSRQYIVFPGRFIYT 124 (200)
Q Consensus 104 YAIIeiGGKQYkV~~Gd~I~V 124 (200)
-..+++-||.|.|+.||++.+
T Consensus 61 ~Gkir~eGK~Yiv~DGDi~~f 81 (83)
T cd04867 61 AGKYRQEGKDYVVQDGDIIFF 81 (83)
T ss_pred cChhhhhCCceEeeCCeEEEE
Confidence 346788999999999999976
No 18
>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=56.87 E-value=20 Score=29.89 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.1
Q ss_pred EEECCEEEEEcCCCEEEEcccCCCCCCCeEEee
Q 028995 107 VMIGSRQYIVFPGRFIYTQRLKGANVNDKIILN 139 (200)
Q Consensus 107 IeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~ 139 (200)
|.+.|+-|...+||+|+++ .|++|.|.
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 4589999999999999886 46788884
No 19
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=56.00 E-value=17 Score=29.77 Aligned_cols=21 Identities=19% Similarity=0.349 Sum_probs=18.6
Q ss_pred EEEECCEEEEEcCCCEEEEcc
Q 028995 106 VVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~Ver 126 (200)
.+.++|+.|.+.+||.++++-
T Consensus 140 ~~~~~~~~~~l~~Gd~~~~~~ 160 (185)
T PRK09943 140 VLTINGQDYHLVAGQSYAINT 160 (185)
T ss_pred EEEECCEEEEecCCCEEEEcC
Confidence 467999999999999999983
No 20
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=52.19 E-value=6.5 Score=32.96 Aligned_cols=57 Identities=35% Similarity=0.402 Sum_probs=46.5
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEc---ccCCCCCCCeEEeeeEEEEecCCceEecccee
Q 028995 100 REEIFAVVMIGSRQYIVFPGRFIYTQ---RLKGANVNDKIILNKVLLVGTKTTTYIGKPVV 157 (200)
Q Consensus 100 ~~~mYAIIeiGGKQYkV~~Gd~I~Ve---rL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v 157 (200)
....++++...-||++++.-|..... +| ...-+.-|++.++++++..+++.+|.|.+
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 46678899999999999988877665 33 24568889999999999999999998863
No 21
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=47.32 E-value=65 Score=28.48 Aligned_cols=32 Identities=19% Similarity=0.301 Sum_probs=25.9
Q ss_pred EEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEee
Q 028995 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILN 139 (200)
Q Consensus 104 YAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~ 139 (200)
-|-|-+||-.|-+++||+|-|- -+-|..|.++
T Consensus 35 sA~Iyiggl~~~LtEgDil~VF----SqyGe~vdin 66 (219)
T KOG0126|consen 35 SAYIYIGGLPYELTEGDILCVF----SQYGEIVDIN 66 (219)
T ss_pred ceEEEECCCcccccCCcEEEEe----eccCceEEEE
Confidence 4889999999999999999984 2567777544
No 22
>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=45.78 E-value=9.9 Score=27.52 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=19.7
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEE
Q 028995 112 RQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAV 162 (200)
Q Consensus 112 KQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V 162 (200)
..|++.+||.|.|.-... -.|+.-..|+.++.+ --|++-.+.|
T Consensus 9 ~~y~l~pGD~l~i~v~~~------~~l~~~~~V~~dG~I--~lP~iG~v~v 51 (82)
T PF02563_consen 9 PEYRLGPGDVLRISVFGW------PELSGEYTVDPDGTI--SLPLIGPVKV 51 (82)
T ss_dssp ------TT-EEEEEETT-------HHHCCSEE--TTSEE--EETTTEEEE-
T ss_pred CCCEECCCCEEEEEEecC------CCcccceEECCCCcE--eecccceEEE
Confidence 579999999999986532 125556677766654 3365554443
No 23
>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=45.18 E-value=4.1 Score=31.05 Aligned_cols=19 Identities=26% Similarity=0.408 Sum_probs=13.3
Q ss_pred EEEECCEEEEEcCCCEEEE
Q 028995 106 VVMIGSRQYIVFPGRFIYT 124 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~V 124 (200)
.+++-||.|.|+.||+|.+
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 24
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=44.87 E-value=30 Score=30.96 Aligned_cols=21 Identities=14% Similarity=0.229 Sum_probs=18.1
Q ss_pred EEEECCEEEEEcCCCEEEEcc
Q 028995 106 VVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~Ver 126 (200)
.+.++|+.|.+.+||++++++
T Consensus 187 ~l~IdG~t~~l~pGDvlfIPk 207 (233)
T PRK15457 187 HVRHEGETMIAKAGDVMFIPK 207 (233)
T ss_pred EEEECCEEEEeCCCcEEEECC
Confidence 367899999999999999874
No 25
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=43.18 E-value=56 Score=23.37 Aligned_cols=31 Identities=26% Similarity=0.358 Sum_probs=21.6
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEc--cc-CCCCCCCeEEe
Q 028995 102 EIFAVVMIGSRQYIVFPGRFIYTQ--RL-KGANVNDKIIL 138 (200)
Q Consensus 102 ~mYAIIeiGGKQYkV~~Gd~I~Ve--rL-~~~e~Gd~I~l 138 (200)
+-|||+++++.+ +.+.|+ .| .++.+||.|.+
T Consensus 9 ~~~AVl~~~~~~------~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 9 GDYAVLELEDGE------KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CCEEEEEECCCe------EEEEEEHHHCCCCCCcccEEEE
Confidence 569999998876 344555 34 35778997766
No 26
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=42.75 E-value=25 Score=36.60 Aligned_cols=45 Identities=29% Similarity=0.340 Sum_probs=35.7
Q ss_pred CCEEEEcccCCCCCCCeEEeeeEEEEecCCceEeccceecCcEEEEEEEeecCCCeEEE
Q 028995 119 GRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIV 177 (200)
Q Consensus 119 Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~V 177 (200)
|=+|.+||- +++||.|++..+ .| +|....|.||.++.+.++.|+|
T Consensus 652 GlIiL~Erp--vkvGD~It~g~~----------~G--~V~~I~vRAT~I~~fd~~~vIV 696 (835)
T COG3264 652 GLIILFERP--VKVGDTVTIGTV----------SG--TVRKISVRATTIRTFDRKEVIV 696 (835)
T ss_pred hhhhheecC--cccCCEEEECCc----------eE--EEEEEEeeEEEEEeCCCCeEEe
Confidence 445667774 789999988653 13 6888999999999999999887
No 27
>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=39.06 E-value=50 Score=29.31 Aligned_cols=25 Identities=20% Similarity=0.073 Sum_probs=21.6
Q ss_pred CCCCeEEEEEECCEEEEEcCCCEEE
Q 028995 99 KREEIFAVVMIGSRQYIVFPGRFIY 123 (200)
Q Consensus 99 ~~~~mYAIIeiGGKQYkV~~Gd~I~ 123 (200)
+...-+|||+.+|+|.....||.|.
T Consensus 93 ~~~~s~AiI~~~~~q~~y~iGd~i~ 117 (259)
T TIGR01713 93 DRIRSIAIIEEGSEQVSLGINESFE 117 (259)
T ss_pred CCcceEEEEEeCCeEEEEeCCCCcC
Confidence 3456789999999999999999974
No 28
>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=38.97 E-value=47 Score=27.27 Aligned_cols=21 Identities=19% Similarity=0.396 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ve 125 (200)
|.|.++|+.+.|.+||.++++
T Consensus 95 a~v~~~~~~~~~~~g~sv~Ip 115 (151)
T PF01050_consen 95 AEVTLDDEEFTLKEGDSVYIP 115 (151)
T ss_pred EEEEECCEEEEEcCCCEEEEC
Confidence 557899999999999999998
No 29
>PRK13501 transcriptional activator RhaR; Provisional
Probab=38.93 E-value=75 Score=27.36 Aligned_cols=22 Identities=18% Similarity=0.393 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+.+.++|+.|.+++||.+.|+.
T Consensus 49 ~~~~i~~~~~~l~~g~~~~I~p 70 (290)
T PRK13501 49 GLHVLNDHPYRITCGDVFYIQA 70 (290)
T ss_pred eEEEECCeeeeecCCeEEEEcC
Confidence 4567899999999999999973
No 30
>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=37.09 E-value=46 Score=29.31 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=18.9
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+++.++|+-|.|++||+|.++-
T Consensus 211 G~~~~~g~~~~V~~GD~i~i~~ 232 (260)
T TIGR03214 211 GVYNLDNNWVPVEAGDYIWMGA 232 (260)
T ss_pred EEEEECCEEEEecCCCEEEECC
Confidence 4567999999999999999873
No 31
>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=36.46 E-value=39 Score=23.98 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=14.4
Q ss_pred EEcCCCEEEEcccCCCCCCCeE
Q 028995 115 IVFPGRFIYTQRLKGANVNDKI 136 (200)
Q Consensus 115 kV~~Gd~I~VerL~~~e~Gd~I 136 (200)
.+..||++.+..++++..||+|
T Consensus 60 ~~~aGdI~~i~gl~~~~~Gdtl 81 (83)
T cd04092 60 SLSAGNIGVITGLKQTRTGDTL 81 (83)
T ss_pred eeCCCCEEEEECCCCcccCCEE
Confidence 3566777777666666667665
No 32
>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=35.78 E-value=46 Score=23.43 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=7.0
Q ss_pred EcCCCEEEEccc
Q 028995 116 VFPGRFIYTQRL 127 (200)
Q Consensus 116 V~~Gd~I~VerL 127 (200)
+..||+|.+++.
T Consensus 14 i~~gd~v~v~~~ 25 (85)
T cd06530 14 LQPGDLVLVNKL 25 (85)
T ss_pred ccCCCEEEEEEe
Confidence 455666666654
No 33
>PRK08983 fliN flagellar motor switch protein; Validated
Probab=35.42 E-value=1.2e+02 Score=24.53 Aligned_cols=62 Identities=15% Similarity=0.097 Sum_probs=35.1
Q ss_pred CCCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeee-----EEEEecCCceEeccceecCcEEEEEEEe
Q 028995 99 KREEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (200)
Q Consensus 99 ~~~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~-----VLlvg~~~~t~vG~P~v~~a~V~AtVve 168 (200)
....+=..+++|..+..+. .|-+.++||.|.|++ |-+.-++-....|.+.+-+-+.=..|.+
T Consensus 49 ~~v~V~v~v~LG~t~ltl~--------dlL~L~~GDVI~Ld~~~ddpv~v~Vng~~~f~G~~G~~~~k~AVrI~~ 115 (127)
T PRK08983 49 LDIPVTISMEVGRSFISIR--------NLLQLNQGSVVELDRVAGEPLDVMVNGTLIAHGEVVVVNDKFGIRLTD 115 (127)
T ss_pred ccCeeEEEEEEecCcccHH--------HHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 3466777778887765543 222456777777665 3333333445567777766554444444
No 34
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=34.46 E-value=54 Score=24.62 Aligned_cols=21 Identities=24% Similarity=0.265 Sum_probs=17.2
Q ss_pred EEECCEEEEEcCCCEEEEccc
Q 028995 107 VMIGSRQYIVFPGRFIYTQRL 127 (200)
Q Consensus 107 IeiGGKQYkV~~Gd~I~VerL 127 (200)
|.+++.+|.|.+|+..+||+-
T Consensus 46 Vti~~~~f~v~~G~~F~VP~g 66 (85)
T PF11699_consen 46 VTIHETSFVVTKGGSFQVPRG 66 (85)
T ss_dssp EEETTEEEEEETT-EEEE-TT
T ss_pred EEEcCcEEEEeCCCEEEECCC
Confidence 678999999999999999964
No 35
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=33.74 E-value=54 Score=28.96 Aligned_cols=21 Identities=10% Similarity=0.107 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ve 125 (200)
+.+.++|++|.+.+||.+.++
T Consensus 57 ~~~~i~g~~~~l~~Gd~ili~ 77 (302)
T PRK10371 57 VEYLINNEKVQINQGHITLFW 77 (302)
T ss_pred EEEEECCEEEEEcCCcEEEEe
Confidence 468899999999999999997
No 36
>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=33.16 E-value=45 Score=23.48 Aligned_cols=21 Identities=19% Similarity=0.164 Sum_probs=12.2
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 028995 116 VFPGRFIYTQRLKGANVNDKI 136 (200)
Q Consensus 116 V~~Gd~I~VerL~~~e~Gd~I 136 (200)
+..||++.+..++++.+||++
T Consensus 61 ~~aGdI~~i~g~~~~~~Gdtl 81 (83)
T cd04088 61 AGAGDIGAVAGLKDTATGDTL 81 (83)
T ss_pred eCCCCEEEEECCCCCccCCEe
Confidence 455666666655555566554
No 37
>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=32.90 E-value=69 Score=28.96 Aligned_cols=56 Identities=13% Similarity=0.183 Sum_probs=37.0
Q ss_pred EEEEcCCCEEEE-cccCCCCCCCeEEeeeEEEEecCC-ceEeccceecCcEEEEEEEeecCCCeE
Q 028995 113 QYIVFPGRFIYT-QRLKGANVNDKIILNKVLLVGTKT-TTYIGKPVVTNAAVHAVVEEQGLNPKV 175 (200)
Q Consensus 113 QYkV~~Gd~I~V-erL~~~e~Gd~I~l~~VLlvg~~~-~t~vG~P~v~~a~V~AtVveh~kg~Ki 175 (200)
.|-|...|++-+ ++|. +++||.|.....|+.+.++ .+. |. +-|.++|.+--||.|-
T Consensus 28 ~~al~~~Df~g~~Pkm~-VkeGD~Vk~Gq~LF~dK~~p~v~----ft--sPvsG~V~~I~RG~rR 85 (257)
T PF05896_consen 28 TVALLPDDFPGMKPKML-VKEGDRVKAGQPLFEDKKNPGVK----FT--SPVSGTVKAINRGERR 85 (257)
T ss_pred EEEEcCcccCCCCccEE-eccCCEEeCCCeeEeeCCCCCcE----Ee--cCCCeEEEEEecCCCc
Confidence 344455666553 4674 8999999999999997543 232 32 2366777777777763
No 38
>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=32.23 E-value=46 Score=23.66 Aligned_cols=21 Identities=14% Similarity=0.303 Sum_probs=13.8
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 028995 116 VFPGRFIYTQRLKGANVNDKI 136 (200)
Q Consensus 116 V~~Gd~I~VerL~~~e~Gd~I 136 (200)
+..||++.+..++++.+||.+
T Consensus 64 ~~aG~I~~i~gl~~~~~Gdtl 84 (86)
T cd03691 64 AEAGDIVAIAGIEDITIGDTI 84 (86)
T ss_pred ECCCCEEEEECCCCCccccee
Confidence 466777777666666666655
No 39
>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=31.94 E-value=45 Score=22.38 Aligned_cols=17 Identities=12% Similarity=0.202 Sum_probs=6.0
Q ss_pred CCCEEEEcccCCCCCCC
Q 028995 118 PGRFIYTQRLKGANVND 134 (200)
Q Consensus 118 ~Gd~I~VerL~~~e~Gd 134 (200)
.||+|.|++......||
T Consensus 13 ~Gd~v~v~~~~~~~~gd 29 (70)
T PF00717_consen 13 DGDIVLVDPSSEPKDGD 29 (70)
T ss_dssp TTEEEEEEETS---TTS
T ss_pred CCCEEEEEEcCCCccCe
Confidence 34444444433333444
No 40
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=31.81 E-value=66 Score=27.39 Aligned_cols=22 Identities=14% Similarity=0.295 Sum_probs=18.9
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+.+.++|+.|.+.+||.+.|+.
T Consensus 54 ~~~~i~~~~~~l~~g~l~~i~p 75 (278)
T PRK10296 54 YYQEINGKRVLLERGDFVFIPL 75 (278)
T ss_pred EEEEECCEEEEECCCcEEEeCC
Confidence 4577899999999999999873
No 41
>PRK06033 hypothetical protein; Validated
Probab=31.76 E-value=92 Score=23.15 Aligned_cols=40 Identities=13% Similarity=0.173 Sum_probs=20.6
Q ss_pred CCCCCCeEEeee-----EEEEecCCceEeccceecCcEEEEEEEe
Q 028995 129 GANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (200)
Q Consensus 129 ~~e~Gd~I~l~~-----VLlvg~~~~t~vG~P~v~~a~V~AtVve 168 (200)
+.++||.|.|++ |-+.-++-..+.|.|...+.+.=.+|.+
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 355666666653 3333333445557777666554444443
No 42
>PRK13500 transcriptional activator RhaR; Provisional
Probab=31.22 E-value=1.1e+02 Score=27.04 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=19.1
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+.+.++|+.|.+.+||++.|+.
T Consensus 79 g~~~v~~~~~~l~~Gdl~~I~~ 100 (312)
T PRK13500 79 GLHVLNDRPYRITRGDLFYIHA 100 (312)
T ss_pred EEEEECCEEEeecCCeEEEECC
Confidence 4467889999999999999984
No 43
>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=31.15 E-value=59 Score=25.86 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=21.4
Q ss_pred CCCCeEEEEEE-CCEEEEEcCCCEE
Q 028995 99 KREEIFAVVMI-GSRQYIVFPGRFI 122 (200)
Q Consensus 99 ~~~~mYAIIei-GGKQYkV~~Gd~I 122 (200)
....+.|.++. ||++.-|..||.|
T Consensus 77 ~~~~l~A~l~l~~G~~~~v~~G~~l 101 (119)
T TIGR03021 77 RGGRLTATLRLPGGREVDVQVGDSL 101 (119)
T ss_pred cCCCeEEEEEeCCCcEEEecCCCcc
Confidence 35789999999 8999999999985
No 44
>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=30.19 E-value=30 Score=32.52 Aligned_cols=20 Identities=15% Similarity=0.448 Sum_probs=17.6
Q ss_pred EEEEECCEEEEEcCCCEEEE
Q 028995 105 AVVMIGSRQYIVFPGRFIYT 124 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~V 124 (200)
..++..||.|.|+.||+|.+
T Consensus 345 Gk~r~eGK~YivqDGDIi~f 364 (368)
T TIGR00092 345 GLMRLEGKYYVVDDGDVLFF 364 (368)
T ss_pred CchhhcCCeEEeeCCeEEEE
Confidence 45788999999999999976
No 45
>PRK11171 hypothetical protein; Provisional
Probab=29.88 E-value=71 Score=28.18 Aligned_cols=20 Identities=25% Similarity=0.335 Sum_probs=17.1
Q ss_pred EEEECCEEEEEcCCCEEEEc
Q 028995 106 VVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~Ve 125 (200)
++.++|+-|.|++||.|.++
T Consensus 217 ~~~~~~~~~~l~~GD~i~~~ 236 (266)
T PRK11171 217 VYRLNNDWVEVEAGDFIWMR 236 (266)
T ss_pred EEEECCEEEEeCCCCEEEEC
Confidence 45689999999999999886
No 46
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=29.78 E-value=1e+02 Score=22.81 Aligned_cols=33 Identities=21% Similarity=0.363 Sum_probs=24.8
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeE
Q 028995 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKV 141 (200)
Q Consensus 102 ~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~V 141 (200)
.-|.-|..|-|.|-+..+|. +.++||.+.|.+.
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 34555667778888888875 5789999988774
No 47
>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=29.13 E-value=84 Score=22.32 Aligned_cols=16 Identities=6% Similarity=0.104 Sum_probs=13.0
Q ss_pred CCEEEEEcCCCEEEEc
Q 028995 110 GSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 110 GGKQYkV~~Gd~I~Ve 125 (200)
+|.++.+.+||.++++
T Consensus 42 ~G~~~~~~aGD~~~~p 57 (74)
T PF05899_consen 42 DGETVTFKAGDAFFLP 57 (74)
T ss_dssp TTEEEEEETTEEEEE-
T ss_pred CCCEEEEcCCcEEEEC
Confidence 7888888889888876
No 48
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=28.31 E-value=64 Score=27.50 Aligned_cols=50 Identities=8% Similarity=0.211 Sum_probs=34.8
Q ss_pred chHHHHHhhccCCCCCCeEEEEEECCEEE------------EEcCCCEEEEcccCCCCCCCeEE
Q 028995 86 TTEVVESAAKEEPKREEIFAVVMIGSRQY------------IVFPGRFIYTQRLKGANVNDKII 137 (200)
Q Consensus 86 ~~~~~~~~~~~~~~~~~mYAIIeiGGKQY------------kV~~Gd~I~VerL~~~e~Gd~I~ 137 (200)
..|++..+-+ .+.++.+-|+...|.-| ||.-|+++.|+.+...+-|++|.
T Consensus 21 ~~q~IaqVvq--lrGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVk 82 (167)
T KOG2925|consen 21 ECQSIAQVVQ--LRGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVK 82 (167)
T ss_pred hhhhHHHHHh--cCCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccc
Confidence 4466555655 45778888888888766 56778888888875445577764
No 49
>PHA02885 putative interleukin binding protein; Provisional
Probab=28.15 E-value=57 Score=26.45 Aligned_cols=28 Identities=29% Similarity=0.592 Sum_probs=23.3
Q ss_pred CEEEEE-----cCCCEEEEcccCCCCCCCeEEe
Q 028995 111 SRQYIV-----FPGRFIYTQRLKGANVNDKIIL 138 (200)
Q Consensus 111 GKQYkV-----~~Gd~I~VerL~~~e~Gd~I~l 138 (200)
|.-||+ .+|++|+++.+.++.+|+..+|
T Consensus 61 gyiywi~pnntspgeyif~enl~g~~egqd~t~ 93 (135)
T PHA02885 61 GYIYWIGPNNTSPGEYIFIENLEGANEGQDNTF 93 (135)
T ss_pred ceEEEEeCCCCCCcceeeeecccccccCccchh
Confidence 556776 5789999999999999998776
No 50
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=27.90 E-value=78 Score=26.09 Aligned_cols=32 Identities=25% Similarity=0.279 Sum_probs=15.2
Q ss_pred EEECCEEEEEcCCCEEEEcc--cCCCCCCCeEEe
Q 028995 107 VMIGSRQYIVFPGRFIYTQR--LKGANVNDKIIL 138 (200)
Q Consensus 107 IeiGGKQYkV~~Gd~I~Ver--L~~~e~Gd~I~l 138 (200)
|..+.-.=-..+||.+.+++ ..+.+.||.|.|
T Consensus 36 V~g~SM~Ptl~~GD~vlv~~~~~~~~~~GDIVvf 69 (158)
T TIGR02228 36 VLSGSMEPTFNTGDLILVTGADPNDIQVGDVITY 69 (158)
T ss_pred EcCCCCcCCccCCCEEEEEecccCCCCCCCEEEE
Confidence 34333333345566666655 223445555544
No 51
>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=27.54 E-value=1.1e+02 Score=21.59 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=16.7
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEee
Q 028995 112 RQYIVFPGRFIYTQRLKGANVNDKIILN 139 (200)
Q Consensus 112 KQYkV~~Gd~I~VerL~~~e~Gd~I~l~ 139 (200)
|.=.++-|-.|.|+.+ .+.||.|.+|
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 5556677788999977 6899988665
No 52
>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=27.27 E-value=76 Score=26.92 Aligned_cols=22 Identities=14% Similarity=0.314 Sum_probs=19.1
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+.+.++|+.|.+.+||.+.++.
T Consensus 55 ~~~~~~~~~~~l~~g~~~ii~~ 76 (287)
T TIGR02297 55 IALQLDEHEYSEYAPCFFLTPP 76 (287)
T ss_pred eEEEECCEEEEecCCeEEEeCC
Confidence 4577899999999999999983
No 53
>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=27.03 E-value=64 Score=23.50 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=14.3
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 028995 116 VFPGRFIYTQRLKGANVNDKI 136 (200)
Q Consensus 116 V~~Gd~I~VerL~~~e~Gd~I 136 (200)
+..||++.+-.++++..||++
T Consensus 62 a~aGdIv~v~gl~~~~~Gdtl 82 (85)
T cd03689 62 AYPGDIIGLVNPGNFQIGDTL 82 (85)
T ss_pred ECCCCEEEEECCCCccccCEe
Confidence 466777777777666677765
No 54
>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=26.52 E-value=1e+02 Score=21.71 Aligned_cols=26 Identities=12% Similarity=0.144 Sum_probs=17.9
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEee
Q 028995 112 RQYIVFPGRFIYTQRLKGANVNDKIILN 139 (200)
Q Consensus 112 KQYkV~~Gd~I~VerL~~~e~Gd~I~l~ 139 (200)
|.=.++-|-.|.|+.+ .+.||.|.+|
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 4555566667888876 5788887654
No 55
>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=26.07 E-value=47 Score=22.42 Aligned_cols=12 Identities=25% Similarity=0.456 Sum_probs=7.8
Q ss_pred EEEEcCCCEEEE
Q 028995 113 QYIVFPGRFIYT 124 (200)
Q Consensus 113 QYkV~~Gd~I~V 124 (200)
.|+|..||.|.|
T Consensus 47 ~~~l~~Gd~v~i 58 (59)
T TIGR02988 47 GKKLYPGDVIEI 58 (59)
T ss_pred CCCCCCCCEEEe
Confidence 556666776655
No 56
>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=25.97 E-value=1e+02 Score=21.68 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=18.0
Q ss_pred EEEEEcCCCEEEEcccCCCCCCCeEEee
Q 028995 112 RQYIVFPGRFIYTQRLKGANVNDKIILN 139 (200)
Q Consensus 112 KQYkV~~Gd~I~VerL~~~e~Gd~I~l~ 139 (200)
|.=.++-|-.|.|+.+ .+.||+|.+|
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 4445556677888876 5789887665
No 57
>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=25.87 E-value=2.1e+02 Score=20.46 Aligned_cols=58 Identities=17% Similarity=0.142 Sum_probs=27.3
Q ss_pred eEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeee-----EEEEecCCceEeccceecCcEEEEEEEe
Q 028995 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (200)
Q Consensus 103 mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~-----VLlvg~~~~t~vG~P~v~~a~V~AtVve 168 (200)
+=..+++|..+..+ ..|-+.++||.|.|++ |-+.-++-....|.+..-+-+.=.+|.+
T Consensus 10 v~l~~~Lg~~~itl--------~ell~L~~Gdvi~L~~~~~~~v~l~v~g~~~~~g~lg~~~~~~avrI~~ 72 (77)
T TIGR02480 10 VELTVELGRTRITL--------GDLLKLGEGSVIELDKLAGEPLDILVNGRLIARGEVVVVEDKFGIRITE 72 (77)
T ss_pred EEEEEEEeceEeEH--------HHHhcCCCCCEEEcCCCCCCcEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 33445555555433 2333456666666652 3332233334445565555444444444
No 58
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=25.59 E-value=81 Score=24.49 Aligned_cols=23 Identities=22% Similarity=0.249 Sum_probs=15.9
Q ss_pred EEEECCEEEEEcCCCEEEEcccC
Q 028995 106 VVMIGSRQYIVFPGRFIYTQRLK 128 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~VerL~ 128 (200)
.|..+.-+=-...||+|.|+++.
T Consensus 35 ~V~s~SM~Ptl~~GD~v~v~k~~ 57 (166)
T COG0681 35 VVPSGSMEPTLNVGDRVLVKKFS 57 (166)
T ss_pred EECCCccccccccCCEEEEEecc
Confidence 44455555556689999999864
No 59
>PF06130 PduL: Propanediol utilisation protein PduL; InterPro: IPR008300 Salmonella enterica subsp. enterica serovar Typhimurium degrades 1,2-propanediol by a pathway that requires coenzyme B12, adenosylcobalamin (AdoCbl). Proteins required for 1,2-propanediol degradation are encoded by the pdu operon []. PduL functions in this pathway, but its exact role is not yet determined. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilization (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and coregulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR010254 from INTERPRO and IPR009204 from INTERPRO for more details on the propanediol utilization pathway and the pdu operon.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=25.42 E-value=79 Score=23.18 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=24.2
Q ss_pred EcCCCEEEEcccCCCCCCCe-EEeeeEEEEecCCc
Q 028995 116 VFPGRFIYTQRLKGANVNDK-IILNKVLLVGTKTT 149 (200)
Q Consensus 116 V~~Gd~I~VerL~~~e~Gd~-I~l~~VLlvg~~~~ 149 (200)
+..||++.++. . ..|.+ ..|++|+..++..+
T Consensus 23 ~~dg~~v~ve~-~--~~g~r~~~~~~V~Vrv~~~~ 54 (71)
T PF06130_consen 23 GQDGQFVSVEV-T--VVGPRGGIFENVRVRVPERF 54 (71)
T ss_pred CCCCCEEEEEE-e--ccCCCcceeeeeEEEcCCCc
Confidence 38999999987 3 46777 89999998876543
No 60
>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=25.30 E-value=2.1e+02 Score=22.33 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=22.2
Q ss_pred EEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEe
Q 028995 113 QYIVFPGRFIYTQRLKGANVNDKIILNKVLLVG 145 (200)
Q Consensus 113 QYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg 145 (200)
.| |++|+.|.+.--.++..|+-|.+..++-|-
T Consensus 3 Ny-vq~G~~i~~ta~~~V~sG~~V~vG~~~GVA 34 (106)
T PF09956_consen 3 NY-VQDGDTIDVTAPAAVASGDVVVVGSLFGVA 34 (106)
T ss_pred cc-ccCCCEEEEecCcccccCCEEEECCEEEEE
Confidence 44 778888887654456778877777766654
No 61
>PF10949 DUF2777: Protein of unknown function (DUF2777); InterPro: IPR024488 This family of proteins with unknown function appears to be restricted to Bacillaceae.
Probab=24.44 E-value=84 Score=27.22 Aligned_cols=22 Identities=23% Similarity=0.235 Sum_probs=19.9
Q ss_pred EEEECCEEEEEcCCCEEEEccc
Q 028995 106 VVMIGSRQYIVFPGRFIYTQRL 127 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~VerL 127 (200)
+|..+|.+|.++.||.|.+++-
T Consensus 67 ~v~~~~e~~~L~~ge~IRi~K~ 88 (185)
T PF10949_consen 67 IVSIDGEQIPLSNGESIRIRKK 88 (185)
T ss_pred eEEeCCeEEecCCCCEEEEeec
Confidence 6799999999999999999863
No 62
>TIGR01222 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs.
Probab=24.16 E-value=2.8e+02 Score=23.66 Aligned_cols=53 Identities=17% Similarity=0.276 Sum_probs=33.9
Q ss_pred CCEEEEEcCCCEEEEcccCCCCCCCeEEee-eEEEEec-CCceEeccceecCcEEEEE
Q 028995 110 GSRQYIVFPGRFIYTQRLKGANVNDKIILN-KVLLVGT-KTTTYIGKPVVTNAAVHAV 165 (200)
Q Consensus 110 GGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~-~VLlvg~-~~~t~vG~P~v~~a~V~At 165 (200)
.|.|.....||+|.+- ++++|.+|.-+ .|..+|. ++...-|-.--++|.|-|.
T Consensus 121 SGQ~i~~~~gDliilG---~Vn~GAeViA~GnI~V~G~LrG~a~AG~~Gd~~A~I~a~ 175 (217)
T TIGR01222 121 SGQQIYAKHGDLIVLG---NVNAGAEVLADGNIHVYGKLRGRALAGANGDTSAVIFAL 175 (217)
T ss_pred CCCEEEecCCCEEEEC---CCCCCCEEEeCCCEEEEEEeccEEEcCCCCCCCcEEEec
Confidence 3556666668988775 46788887765 6666664 4555556665556666554
No 63
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=24.01 E-value=1e+02 Score=26.40 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=17.9
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+.+..+|+.|.|.+||.+.++.
T Consensus 82 ~~~~~~g~~~~l~~G~~~l~~~ 103 (302)
T PRK09685 82 AIIEQDDRQVQLAAGDITLIDA 103 (302)
T ss_pred EEEEECCeEEEEcCCCEEEEEC
Confidence 3467889999999999998863
No 64
>PRK12784 hypothetical protein; Provisional
Probab=23.89 E-value=1.8e+02 Score=22.33 Aligned_cols=47 Identities=11% Similarity=0.002 Sum_probs=37.4
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCc
Q 028995 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTT 149 (200)
Q Consensus 102 ~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~ 149 (200)
..|.|=..+|+--+|..|=-=++..++ +++||+|.-+.+|..=.+|-
T Consensus 32 kL~~I~~~dg~le~v~vGiSG~I~~v~-Ve~Gq~i~~dtlL~~~edDl 78 (84)
T PRK12784 32 KLMMIRKNNGELEKVAVGISGNIRLVN-VVVGQQIHTDTLLVRLEDDL 78 (84)
T ss_pred eeeEEeecCCcEEEEEEeeeeeEEEEE-eecCceecCCcEEEEEeece
Confidence 366777788888899999888888885 99999999988887654443
No 65
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.55 E-value=1.9e+02 Score=24.71 Aligned_cols=49 Identities=20% Similarity=0.083 Sum_probs=36.6
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEecc
Q 028995 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIGK 154 (200)
Q Consensus 102 ~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG~ 154 (200)
.-|+||+.+|-=|.|..-.... .. .+.|+.+.|---+.+..+...+.|-
T Consensus 14 ~~~vvi~~~GvGY~V~vs~~~~-~~---l~~g~~v~l~t~~~vrEd~~~LyGF 62 (197)
T PRK14603 14 EGSAVLLAGGVGLEVQCPAPTL-AR---LVEGQEAELHTRLVVREDALSLYGF 62 (197)
T ss_pred CCEEEEEECCEEEEEEcCHHHH-HH---cCCCCeEEEEEEEEEccCCceeeCc
Confidence 3589999999999987653321 12 3579999998888888877777773
No 66
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=23.45 E-value=1.5e+02 Score=25.65 Aligned_cols=41 Identities=17% Similarity=0.268 Sum_probs=27.7
Q ss_pred CeEEEEEECC--EEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEec
Q 028995 102 EIFAVVMIGS--RQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGT 146 (200)
Q Consensus 102 ~mYAIIeiGG--KQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~ 146 (200)
..|++--.|. .---+..||.|.|++-..++.||.| |.++++
T Consensus 111 ~~f~L~V~GdSM~~~gi~dGDlvvV~~~~~a~~GdiV----vA~i~g 153 (201)
T COG1974 111 ATFFLRVSGDSMIDAGILDGDLVVVDPTEDAENGDIV----VALIDG 153 (201)
T ss_pred ceEEEEecCCccccCcCCCCCEEEEcCCCCCCCCCEE----EEEcCC
Confidence 5666544442 2223448999999988888899987 666665
No 67
>PRK09601 GTP-binding protein YchF; Reviewed
Probab=23.39 E-value=57 Score=30.66 Aligned_cols=17 Identities=24% Similarity=0.407 Sum_probs=15.1
Q ss_pred EECCEEEEEcCCCEEEE
Q 028995 108 MIGSRQYIVFPGRFIYT 124 (200)
Q Consensus 108 eiGGKQYkV~~Gd~I~V 124 (200)
++-||.|.|+.||+|.+
T Consensus 344 rleGkdY~v~DGDIi~f 360 (364)
T PRK09601 344 RLEGKDYIVQDGDVMHF 360 (364)
T ss_pred eccCCceEecCCCEEEE
Confidence 46799999999999987
No 68
>KOG1491 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]
Probab=23.09 E-value=52 Score=31.51 Aligned_cols=16 Identities=31% Similarity=0.509 Sum_probs=14.3
Q ss_pred ECCEEEEEcCCCEEEE
Q 028995 109 IGSRQYIVFPGRFIYT 124 (200)
Q Consensus 109 iGGKQYkV~~Gd~I~V 124 (200)
.-||+|.|++||+|..
T Consensus 372 ~~Gk~yiVedGDIi~F 387 (391)
T KOG1491|consen 372 QVGKEYIVEDGDIIFF 387 (391)
T ss_pred hcCceeeecCCCEEEE
Confidence 7799999999999865
No 69
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=23.02 E-value=1.1e+02 Score=24.17 Aligned_cols=18 Identities=11% Similarity=0.207 Sum_probs=15.9
Q ss_pred E-CCEEEEEcCCCEEEEcc
Q 028995 109 I-GSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 109 i-GGKQYkV~~Gd~I~Ver 126 (200)
+ +|+.|.+.+||.++++.
T Consensus 71 i~~g~~~~L~aGD~i~~~~ 89 (125)
T PRK13290 71 LATGEVHPIRPGTMYALDK 89 (125)
T ss_pred cCCCEEEEeCCCeEEEECC
Confidence 6 49999999999999873
No 70
>PLN02765 pyruvate kinase
Probab=22.90 E-value=1.8e+02 Score=28.96 Aligned_cols=14 Identities=7% Similarity=0.088 Sum_probs=9.4
Q ss_pred CEEEEEcCCCEEEE
Q 028995 111 SRQYIVFPGRFIYT 124 (200)
Q Consensus 111 GKQYkV~~Gd~I~V 124 (200)
+..+.+++||.+.+
T Consensus 105 ~~~i~l~~G~~~~l 118 (526)
T PLN02765 105 EKPISLKAGNTVTL 118 (526)
T ss_pred CCcEecCCCCEEEE
Confidence 33477777887765
No 71
>PRK04290 30S ribosomal protein S6e; Validated
Probab=22.88 E-value=90 Score=25.08 Aligned_cols=76 Identities=17% Similarity=0.071 Sum_probs=41.0
Q ss_pred CCEEEEEcCCCEEEEcccCCCCCCCeEEeee------EEEEecCCceEeccceecCcEEEEEEEeecCCCeEEEEEecCC
Q 028995 110 GSRQYIVFPGRFIYTQRLKGANVNDKIILNK------VLLVGTKTTTYIGKPVVTNAAVHAVVEEQGLNPKVIVFKYKKK 183 (200)
Q Consensus 110 GGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~------VLlvg~~~~t~vG~P~v~~a~V~AtVveh~kg~Ki~VfK~KrR 183 (200)
-|+||.++..|.-... +-+...||+|.-+- +|-+-+++. .-|.|.-.++.-.+.+-=-..+. .-|+- +|
T Consensus 13 tG~~~~~ei~~~~~~~-f~gkriG~evdg~~lG~~Gy~l~ItGGsD-k~GfPM~~~v~~~~r~rlLl~~g--~gyrp-~r 87 (115)
T PRK04290 13 TGKAYQIEIDGAEANR-LIGKKIGDEIDGSIVGLDGYKLKITGGSD-KSGFPMRPDVPGPVRRRILLSGG--PGFRP-KE 87 (115)
T ss_pred CCeEEEEEeCcHHHhh-hhccccccEEccceeCCCCeEEEEecccC-CCCccccCCccCCceEEEEecCC--CCCCc-CC
Confidence 4899999887775333 44677888887654 444422221 23888777754333332212222 24544 34
Q ss_pred CCccccc
Q 028995 184 KNYRRNI 190 (200)
Q Consensus 184 K~yrRk~ 190 (200)
++-||++
T Consensus 88 ~GeRrRK 94 (115)
T PRK04290 88 KGERRRK 94 (115)
T ss_pred CCcEEEE
Confidence 5555543
No 72
>PRK13502 transcriptional activator RhaR; Provisional
Probab=22.38 E-value=1.2e+02 Score=25.88 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
..+.++|+.|.+.+||.+.++.
T Consensus 49 ~~~~i~~~~~~l~~g~l~li~~ 70 (282)
T PRK13502 49 GLHVLNERPYRITRGDLFYIRA 70 (282)
T ss_pred EEEEECCEEEeecCCcEEEECC
Confidence 4577889999999999999984
No 73
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=22.09 E-value=2.8e+02 Score=22.87 Aligned_cols=49 Identities=12% Similarity=0.057 Sum_probs=28.9
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCC
Q 028995 100 REEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKT 148 (200)
Q Consensus 100 ~~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~ 148 (200)
..--|-||++...|=..-.-++=..+++.++++||.|+|.=-...+..+
T Consensus 56 srHQ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 56 SRHQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred CcceEEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEEEECCCC
Confidence 3456777777653322222111112788888999999997666555443
No 74
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=22.06 E-value=92 Score=24.38 Aligned_cols=40 Identities=10% Similarity=-0.015 Sum_probs=19.0
Q ss_pred EEEECCEEEEEcCCCEEEEc------------------ccCCCCCCCeEEeeeEEEEe
Q 028995 106 VVMIGSRQYIVFPGRFIYTQ------------------RLKGANVNDKIILNKVLLVG 145 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~Ve------------------rL~~~e~Gd~I~l~~VLlvg 145 (200)
|+.-+|+..++...++-... .+.++++||.|++.-.+-..
T Consensus 48 v~~~dg~i~~~~~~~i~~~~~~~~~~~~~y~~~~~~~~~~p~v~~GdiIe~~y~~~~~ 105 (177)
T PF12969_consen 48 VIRPDGKIDKLDKSDIKDRSAESASEAPIYSDSRTKVFAFPDVRVGDIIEYSYTIKSK 105 (177)
T ss_dssp EE-TTS-EEE--GGGEEEE--GGGTT-GGGTT-EEEEEE--S--TT-EEEEEEEEEE-
T ss_pred EEcCCCeEEecChHHeEEeecccccccccccCcEEEEEEcCCCCCCcEEEEEEEEEec
Confidence 45566777777777543332 24567899999998665443
No 75
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=21.95 E-value=1.1e+02 Score=23.42 Aligned_cols=20 Identities=15% Similarity=0.147 Sum_probs=16.2
Q ss_pred EEECCEEEEEcCCCEEEEcc
Q 028995 107 VMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 107 IeiGGKQYkV~~Gd~I~Ver 126 (200)
+.++|.-|.+.+||+|.++.
T Consensus 77 ~~~~g~~~~l~~Gd~i~ip~ 96 (131)
T COG1917 77 VQLEGEKKELKAGDVIIIPP 96 (131)
T ss_pred EEecCCceEecCCCEEEECC
Confidence 45668888999999999884
No 76
>PF14525 AraC_binding_2: AraC-binding-like domain
Probab=21.69 E-value=1.4e+02 Score=22.71 Aligned_cols=21 Identities=24% Similarity=0.404 Sum_probs=17.7
Q ss_pred EEEEECCEEEEEcCCCEEEEc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQ 125 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ve 125 (200)
+.++.||+.+.+.+||.+.++
T Consensus 66 ~~~~~~g~~~~~~pg~~~l~d 86 (172)
T PF14525_consen 66 ARIEQGGREVELAPGDVVLLD 86 (172)
T ss_pred EEEEECCEEEEEcCCeEEEEc
Confidence 457889999999999988776
No 77
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=21.42 E-value=3.3e+02 Score=21.23 Aligned_cols=42 Identities=12% Similarity=0.105 Sum_probs=25.7
Q ss_pred CCeEEEEEECC-E---EEEEcCCCEEEEcccCCCCCCCeEEee--eEEEEec
Q 028995 101 EEIFAVVMIGS-R---QYIVFPGRFIYTQRLKGANVNDKIILN--KVLLVGT 146 (200)
Q Consensus 101 ~~mYAIIeiGG-K---QYkV~~Gd~I~VerL~~~e~Gd~I~l~--~VLlvg~ 146 (200)
+..--||.+|. + ..-|.+||.+..++. .|.+|.++ +-+++..
T Consensus 44 p~~g~VvAVG~G~~~~~~~Vk~GD~Vl~~~y----~Gtevk~dg~ey~i~~e 91 (100)
T PTZ00414 44 VNEGTVVAVAAATKDWTPTVKVGDTVLLPEF----GGSSVKVEGEEFFLYNE 91 (100)
T ss_pred CceeEEEEECCCCccccceecCCCEEEEcCC----CCcEEEECCEEEEEEEh
Confidence 33334666663 2 466999999988765 36677664 3444443
No 78
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=21.40 E-value=1.3e+02 Score=25.88 Aligned_cols=27 Identities=26% Similarity=0.391 Sum_probs=20.4
Q ss_pred EEECCEEEEEcCCCEEEEcccCCCCCCCeEEee
Q 028995 107 VMIGSRQYIVFPGRFIYTQRLKGANVNDKIILN 139 (200)
Q Consensus 107 IeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~ 139 (200)
|.+.|+.-...+||+|++++ |+.|+|.
T Consensus 131 V~~~g~tv~a~aGDvifiPK------gssIefs 157 (176)
T COG4766 131 VRIDGRTVIAGAGDVIFIPK------GSSIEFS 157 (176)
T ss_pred EEEcCCeEecCCCcEEEecC------CCeEEEe
Confidence 67888888888899988874 4566663
No 79
>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=21.15 E-value=88 Score=22.59 Aligned_cols=21 Identities=33% Similarity=0.438 Sum_probs=11.5
Q ss_pred EcCCCEEEEcccCCCCCCCeE
Q 028995 116 VFPGRFIYTQRLKGANVNDKI 136 (200)
Q Consensus 116 V~~Gd~I~VerL~~~e~Gd~I 136 (200)
+..||++-+-.++++..||.|
T Consensus 63 ~~aGdI~ai~gl~~~~~Gdtl 83 (85)
T cd03690 63 VTAGDIAILTGLKGLRVGDVL 83 (85)
T ss_pred ECCCCEEEEECCCCCcCcccc
Confidence 445565555555555555543
No 80
>PRK11171 hypothetical protein; Provisional
Probab=21.07 E-value=1.3e+02 Score=26.43 Aligned_cols=22 Identities=9% Similarity=0.249 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEcCCCEEEEcc
Q 028995 105 AVVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 105 AIIeiGGKQYkV~~Gd~I~Ver 126 (200)
+.+.++|+.|.+.+||.++++.
T Consensus 94 l~v~~~g~~~~L~~GDsi~~p~ 115 (266)
T PRK11171 94 ITLTLEGKTHALSEGGYAYLPP 115 (266)
T ss_pred EEEEECCEEEEECCCCEEEECC
Confidence 4577899999999999999983
No 81
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=20.87 E-value=1.1e+02 Score=26.19 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=18.1
Q ss_pred EEEECCEEEEEcCCCEEEEcc
Q 028995 106 VVMIGSRQYIVFPGRFIYTQR 126 (200)
Q Consensus 106 IIeiGGKQYkV~~Gd~I~Ver 126 (200)
.+.++|+.|.+.+||.+.++.
T Consensus 61 ~~~~~~~~~~~~~g~~i~i~p 81 (290)
T PRK10572 61 VIFNGGRAFVCRPGDLLLFPP 81 (290)
T ss_pred EEecCCeeEecCCCCEEEECC
Confidence 367899999999999999874
No 82
>PF04347 FliO: Flagellar biosynthesis protein, FliO; InterPro: IPR022781 FliO is an essential component of the flagellum-specific protein export apparatus []. It is an integral membrane protein. Its precise molecular function is unknown. FliO is a short protein found in flagellar biosynthesis operons, and which contains a highly hydrophobic N-terminal sequence followed generally by two basic amino acids. This region is reminiscent of but distinct from the twin-arginine translocation signal sequence. Some instances of this gene have been names "FliZ" but phylogenetic tree building supports a single FliO family.; GO: 0043064 flagellum organization, 0016021 integral to membrane, 0019861 flagellum
Probab=20.67 E-value=1.5e+02 Score=21.07 Aligned_cols=21 Identities=14% Similarity=0.229 Sum_probs=16.6
Q ss_pred CCCeEEEEEECCEEEEEcCCC
Q 028995 100 REEIFAVVMIGSRQYIVFPGR 120 (200)
Q Consensus 100 ~~~mYAIIeiGGKQYkV~~Gd 120 (200)
....-.||++||++|.+-.++
T Consensus 28 ~~~~l~lV~v~~~~~Llgvt~ 48 (84)
T PF04347_consen 28 PKKSLVLVEVGGRYLLLGVTD 48 (84)
T ss_pred CCCEEEEEEECCEEEEEEECC
Confidence 456778999999999986554
No 83
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.61 E-value=1.3e+02 Score=25.63 Aligned_cols=49 Identities=18% Similarity=0.350 Sum_probs=36.8
Q ss_pred CeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeeeEEEEecCCceEec
Q 028995 102 EIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNKVLLVGTKTTTYIG 153 (200)
Q Consensus 102 ~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~VLlvg~~~~t~vG 153 (200)
.-|+||+.||--|.|..-..... .|. +.|+.+.|---+.+..+...+.|
T Consensus 14 ~~~viie~~GvGY~v~vs~~~~~-~l~--~~g~~v~l~t~~~vrEd~~~LyG 62 (195)
T PRK14604 14 NDHLIVETGGVGLLIYAPRSVLA-AIG--AIGDEVFLYTHLIVREDALTLYG 62 (195)
T ss_pred CCEEEEEECCEEEEEEeCHHHHH-Hhc--cCCCeEEEEEEEEEecCCceeeC
Confidence 45899999999999875533221 232 57999999888888887777776
No 84
>PRK04804 minC septum formation inhibitor; Reviewed
Probab=20.55 E-value=3.8e+02 Score=23.07 Aligned_cols=52 Identities=13% Similarity=0.208 Sum_probs=31.8
Q ss_pred CEEEEEcCCCEEEEcccCCCCCCCeEEee-eEEEEec-CCceEeccceecCcEEEEE
Q 028995 111 SRQYIVFPGRFIYTQRLKGANVNDKIILN-KVLLVGT-KTTTYIGKPVVTNAAVHAV 165 (200)
Q Consensus 111 GKQYkV~~Gd~I~VerL~~~e~Gd~I~l~-~VLlvg~-~~~t~vG~P~v~~a~V~At 165 (200)
|.|.....||+|.+- ++++|.+|.=+ .|..+|. ++...-|-.--++|.|-|.
T Consensus 124 GQ~I~a~~gdliIlG---dVn~GAEViA~GnI~V~G~LrG~a~AG~~Gd~~A~I~a~ 177 (221)
T PRK04804 124 GQQIYAKNGDLVILG---AVSNGAEVIADGSIHIYGTLRGRAIAGASGDKEAVIICH 177 (221)
T ss_pred CCEEEecCCCEEEEc---cCCCCCEEEeCCCEEEEEEeccEEEecCCCCCccEEEec
Confidence 344444568888775 46788887664 6666654 4555556555555665543
No 85
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=20.26 E-value=1.9e+02 Score=24.23 Aligned_cols=61 Identities=18% Similarity=0.141 Sum_probs=32.8
Q ss_pred CCCeEEEEEECCEEEEEcCCCEEEEcccCCCCCCCeEEeee-----EEEEecCCceEeccceecCcEEEEEEEe
Q 028995 100 REEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKIILNK-----VLLVGTKTTTYIGKPVVTNAAVHAVVEE 168 (200)
Q Consensus 100 ~~~mYAIIeiGGKQYkV~~Gd~I~VerL~~~e~Gd~I~l~~-----VLlvg~~~~t~vG~P~v~~a~V~AtVve 168 (200)
...+-..+++|..+..+. .|-+.++||.|.|++ |-++-++-....|.+.+-+-+.=..|.+
T Consensus 78 dvpV~lsveLG~t~itlr--------dLL~L~~GDVI~Ldk~~~epv~V~VnG~~~f~Ge~Gvvn~k~AVrIte 143 (155)
T PRK05698 78 DIPVSISMEVGSTDINIR--------NLLQLNQGSVIELDRLAGEPLDVLVNGTLIAHGEVVVVNEKFGIRLTD 143 (155)
T ss_pred cceeEEEEEEecCcccHH--------HHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 456777778887665443 222356666666655 3333233344556666666444444444
No 86
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=20.25 E-value=1.1e+02 Score=23.92 Aligned_cols=14 Identities=7% Similarity=0.050 Sum_probs=12.5
Q ss_pred EEEEcCCCEEEEcc
Q 028995 113 QYIVFPGRFIYTQR 126 (200)
Q Consensus 113 QYkV~~Gd~I~Ver 126 (200)
.|.+++||.+.++.
T Consensus 76 ~~~l~~GD~~~ip~ 89 (146)
T smart00835 76 DARLREGDVFVVPQ 89 (146)
T ss_pred EEEecCCCEEEECC
Confidence 89999999999974
Done!