Query 033045
Match_columns 128
No_of_seqs 68 out of 70
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 09:08:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033045.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033045hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00030 S21p ribosomal prote 99.7 1.1E-17 2.3E-22 110.8 6.5 53 39-92 2-55 (58)
2 PRK00270 rpsU 30S ribosomal pr 99.7 7.1E-17 1.5E-21 108.7 6.9 55 38-93 2-57 (64)
3 COG0828 RpsU Ribosomal protein 99.7 2.1E-16 4.6E-21 108.8 8.3 61 39-102 3-64 (67)
4 PF01165 Ribosomal_S21: Riboso 99.4 1.4E-16 3E-21 103.1 -9.4 55 38-93 1-56 (57)
5 PF09413 DUF2007: Domain of un 80.6 1.9 4E-05 27.3 2.6 19 38-56 46-64 (67)
6 TIGR00756 PPR pentatricopeptid 76.9 1.6 3.4E-05 22.6 1.2 21 42-63 11-31 (35)
7 PF13812 PPR_3: Pentatricopept 75.0 2.1 4.5E-05 22.7 1.4 21 42-63 12-32 (34)
8 cd04937 ACT_AKi-DapG-BS_2 ACT 73.0 1.9 4.2E-05 27.0 1.1 24 35-58 39-62 (64)
9 PF13840 ACT_7: ACT domain ; P 73.0 4.5 9.9E-05 26.0 2.8 22 35-56 44-65 (65)
10 PF00627 UBA: UBA/TS-N domain; 52.1 12 0.00026 21.7 1.7 13 42-54 25-37 (37)
11 PF01535 PPR: PPR repeat; Int 51.0 12 0.00026 19.1 1.5 20 42-62 11-30 (31)
12 TIGR03595 Obg_CgtA_exten Obg f 49.6 19 0.00041 24.1 2.6 28 43-70 25-52 (69)
13 cd04936 ACT_AKii-LysC-BS-like_ 48.7 19 0.00041 21.1 2.3 23 36-58 39-61 (63)
14 PF13041 PPR_2: PPR repeat fam 48.6 13 0.00027 21.9 1.5 13 43-55 15-27 (50)
15 COG1570 XseA Exonuclease VII, 43.4 10 0.00022 34.3 0.7 28 41-68 100-127 (440)
16 PF09269 DUF1967: Domain of un 42.8 15 0.00032 24.6 1.3 24 47-70 29-52 (69)
17 cd04923 ACT_AK-LysC-DapG-like_ 41.0 30 0.00065 20.2 2.3 24 35-58 38-61 (63)
18 PRK00286 xseA exodeoxyribonucl 38.3 16 0.00034 31.0 1.1 27 44-70 103-129 (438)
19 PF08690 GET2: GET complex sub 37.7 29 0.00062 29.5 2.5 29 78-106 5-33 (302)
20 cd04917 ACT_AKiii-LysC-EC_2 AC 37.6 33 0.00072 21.1 2.2 22 37-58 41-62 (64)
21 PF12854 PPR_1: PPR repeat 37.6 28 0.00061 19.8 1.8 14 43-56 19-32 (34)
22 PRK12772 bifunctional flagella 37.1 13 0.00028 34.0 0.4 25 75-99 267-291 (609)
23 cd04916 ACT_AKiii-YclM-BS_2 AC 36.5 36 0.00077 20.3 2.2 23 36-58 42-64 (66)
24 cd04892 ACT_AK-like_2 ACT doma 36.4 38 0.00082 19.3 2.2 23 36-58 41-63 (65)
25 TIGR01404 FlhB_rel_III type II 35.6 16 0.00034 31.2 0.6 25 75-99 5-29 (342)
26 TIGR00237 xseA exodeoxyribonuc 35.4 16 0.00035 31.6 0.7 27 43-69 96-122 (432)
27 cd04915 ACT_AK-Ectoine_2 ACT d 35.0 39 0.00084 21.6 2.3 22 37-58 43-64 (66)
28 PRK12332 tsf elongation factor 34.9 30 0.00066 27.6 2.1 15 43-57 29-43 (198)
29 PF06506 PrpR_N: Propionate ca 34.8 49 0.0011 24.6 3.1 25 38-62 10-34 (176)
30 PRK09377 tsf elongation factor 34.4 30 0.00064 29.3 2.1 15 43-57 30-44 (290)
31 TIGR00116 tsf translation elon 33.6 31 0.00068 29.2 2.1 15 43-57 29-43 (290)
32 cd00194 UBA Ubiquitin Associat 33.2 34 0.00075 19.3 1.6 13 42-54 24-36 (38)
33 cd04919 ACT_AK-Hom3_2 ACT doma 32.5 46 0.00099 20.1 2.2 23 36-58 42-64 (66)
34 PF07338 DUF1471: Protein of u 32.3 91 0.002 20.1 3.7 32 31-62 1-32 (56)
35 cd02684 MIT_2 MIT: domain cont 32.3 1.6E+02 0.0035 19.8 7.1 47 45-98 20-67 (75)
36 cd04920 ACT_AKiii-DAPDC_2 ACT 31.6 48 0.001 20.9 2.3 22 37-58 40-61 (63)
37 PF01312 Bac_export_2: FlhB Hr 31.5 16 0.00034 31.0 0.0 25 75-99 7-31 (343)
38 PRK06298 type III secretion sy 30.8 21 0.00045 30.8 0.6 25 75-99 6-30 (356)
39 PRK13109 flhB flagellar biosyn 30.5 20 0.00043 31.0 0.5 25 75-99 12-36 (358)
40 cd04922 ACT_AKi-HSDH-ThrA_2 AC 30.3 53 0.0011 19.5 2.2 23 36-58 42-64 (66)
41 cd04924 ACT_AK-Arch_2 ACT doma 29.9 52 0.0011 19.5 2.1 23 36-58 42-64 (66)
42 CHL00098 tsf elongation factor 29.8 41 0.0009 27.0 2.1 15 43-57 26-40 (200)
43 PRK05702 flhB flagellar biosyn 29.5 22 0.00049 30.6 0.6 25 75-99 11-35 (359)
44 TIGR00328 flhB flagellar biosy 29.3 22 0.00047 30.6 0.5 25 75-99 4-28 (347)
45 PRK09108 type III secretion sy 29.0 22 0.00048 30.6 0.5 25 75-99 7-31 (353)
46 PRK08156 type III secretion sy 28.8 24 0.00052 30.7 0.6 25 75-99 6-30 (361)
47 cd04918 ACT_AK1-AT_2 ACT domai 28.6 57 0.0012 20.5 2.2 22 37-58 42-63 (65)
48 PRK12721 secretion system appa 28.0 25 0.00055 30.2 0.7 25 75-99 6-30 (349)
49 PRK12468 flhB flagellar biosyn 27.9 25 0.00053 30.8 0.6 25 75-99 11-35 (386)
50 smart00165 UBA Ubiquitin assoc 26.7 51 0.0011 18.6 1.6 12 43-54 25-36 (37)
51 COG1377 FlhB Flagellar biosynt 25.7 30 0.00066 30.5 0.8 25 75-99 11-35 (363)
52 COG3763 Uncharacterized protei 25.6 38 0.00083 24.1 1.1 22 61-84 41-62 (71)
53 PRK01844 hypothetical protein; 23.7 44 0.00096 23.7 1.1 24 61-86 41-64 (72)
54 PRK00523 hypothetical protein; 23.6 45 0.00097 23.7 1.1 23 61-85 42-64 (72)
55 COG3603 Uncharacterized conser 23.4 65 0.0014 25.2 2.1 17 39-55 104-120 (128)
56 PF00486 Trans_reg_C: Transcri 23.1 43 0.00092 20.7 0.9 22 41-62 40-61 (77)
57 PF07721 TPR_4: Tetratricopept 22.8 57 0.0012 17.4 1.2 14 42-55 12-25 (26)
58 smart00668 CTLH C-terminal to 22.7 55 0.0012 19.4 1.3 16 41-56 11-26 (58)
59 PF07660 STN: Secretin and Ton 22.6 76 0.0016 18.9 1.9 25 30-54 8-32 (52)
60 PF09125 COX2-transmemb: Cytoc 22.5 1.1E+02 0.0023 19.7 2.5 19 108-126 12-30 (38)
61 PF03197 FRD2: Bacteriophage F 22.3 1.1E+02 0.0024 23.1 3.0 21 37-57 79-99 (102)
62 cd06337 PBP1_ABC_ligand_bindin 22.3 93 0.002 24.8 2.8 28 36-63 41-70 (357)
63 PF13176 TPR_7: Tetratricopept 22.1 1.1E+02 0.0024 17.1 2.5 14 43-56 11-24 (36)
64 PF13428 TPR_14: Tetratricopep 22.0 1E+02 0.0022 17.7 2.3 19 43-61 13-31 (44)
65 COG0264 Tsf Translation elonga 22.0 66 0.0014 27.9 2.1 15 43-57 30-44 (296)
66 PRK10564 maltose regulon perip 21.3 47 0.001 28.8 1.1 21 36-56 262-282 (303)
67 COG4080 SpoU rRNA Methylase fa 21.1 50 0.0011 26.3 1.1 26 30-56 46-74 (147)
68 PF13181 TPR_8: Tetratricopept 20.5 1E+02 0.0022 16.1 2.0 16 44-59 14-29 (34)
69 PRK08178 acetolactate synthase 20.4 1.2E+02 0.0027 22.1 2.9 50 4-56 21-71 (96)
70 PF02845 CUE: CUE domain; Int 20.2 84 0.0018 18.6 1.7 12 43-54 27-38 (42)
71 PF11823 DUF3343: Protein of u 20.1 1.3E+02 0.0027 19.6 2.7 21 36-56 41-61 (73)
72 PF14626 RNase_Zc3h12a_2: Zc3h 20.1 36 0.00079 26.3 0.1 9 72-80 100-108 (122)
No 1
>TIGR00030 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.
Probab=99.72 E-value=1.1e-17 Score=110.84 Aligned_cols=53 Identities=34% Similarity=0.483 Sum_probs=46.9
Q ss_pred EEEEecCC-HHHHHHHHHHHHhhhhHHHHHHHHHhhccCCcHHHHHHHHHHHHHH
Q 033045 39 RVKVFNGN-LEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKI 92 (128)
Q Consensus 39 ~V~VrDnN-vEqALrvLKrKMq~eGifRemK~r~~~yeKPSEKR~raRk~~err~ 92 (128)
+|.|.||+ +|+||+.+|++++++||++||+.|+ |||||||+|.++..++.+++
T Consensus 2 ~V~V~~~e~ie~alrrfkr~~~~~gil~e~r~r~-~yeKPs~krkrk~~~a~rr~ 55 (58)
T TIGR00030 2 TVKVKEGESIDSALRRFKRKLEKEGILRELKKRR-YYEKPSERRRRKEKAAAKRI 55 (58)
T ss_pred eeEeCCCCcHHHHHHHHHHHHHHcchHHHHHHHH-hhcCHHHHHHHHHHHHHHHH
Confidence 59999999 9999999999999999999999995 99999999976665555544
No 2
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=99.69 E-value=7.1e-17 Score=108.68 Aligned_cols=55 Identities=31% Similarity=0.441 Sum_probs=47.6
Q ss_pred eEEEEecCC-HHHHHHHHHHHHhhhhHHHHHHHHHhhccCCcHHHHHHHHHHHHHHh
Q 033045 38 IRVKVFNGN-LEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIR 93 (128)
Q Consensus 38 I~V~VrDnN-vEqALrvLKrKMq~eGifRemK~r~~~yeKPSEKR~raRk~~err~R 93 (128)
+.|.|.||| +|+||+.+|++++++||++|++.++ |||||||+|.++..++.++.+
T Consensus 2 ~~V~V~~~e~ie~Alrrfkr~~~k~gil~e~r~r~-~yekPs~krkrk~~~a~rr~~ 57 (64)
T PRK00270 2 PQVKVRENESIDKALRRFKRKVEKAGILRELRRRE-FYEKPSEKRKRKKAAARKRRR 57 (64)
T ss_pred CeeEeCCCChHHHHHHHHHHHHHHcchHHHHHHHH-hhcCHHHHHHHHHHHHHHHHH
Confidence 469999999 9999999999999999999999985 999999999766555555543
No 3
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=2.1e-16 Score=108.85 Aligned_cols=61 Identities=36% Similarity=0.437 Sum_probs=55.0
Q ss_pred EEEEecCC-HHHHHHHHHHHHhhhhHHHHHHHHHhhccCCcHHHHHHHHHHHHHHhhHHHHHHHH
Q 033045 39 RVKVFNGN-LEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIRSQDLARKLK 102 (128)
Q Consensus 39 ~V~VrDnN-vEqALrvLKrKMq~eGifRemK~r~~~yeKPSEKR~raRk~~err~Rs~elarKLk 102 (128)
+|.|++|| +|+||+.+|++++.+||++|++.|. ||||||+++ ++++++++.|..+.+.+.+
T Consensus 3 ~v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r~-~yEkPs~kr--krK~a~a~kr~~k~~~k~~ 64 (67)
T COG0828 3 QVKVRENEPLDKALRRFKRKVEKEGILREMKERE-FYEKPSEKR--KRKKAAARKRKFKRLRKEQ 64 (67)
T ss_pred eeeecCCChHHHHHHHHHHHHHHHHHHHHHHHHH-hccCchHHH--HHHHHHHHHHHHHHHHHHh
Confidence 59999999 9999999999999999999999995 999999999 6888888888887776654
No 4
>PF01165 Ribosomal_S21: Ribosomal protein S21; InterPro: IPR001911 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome [], and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2VHO_U 3J18_U 2AVY_U 3OFO_U 3OFP_U 2WWL_U 3J0X_X 3IZV_Y 3ORA_U 3IZW_Y ....
Probab=99.44 E-value=1.4e-16 Score=103.06 Aligned_cols=55 Identities=33% Similarity=0.433 Sum_probs=45.3
Q ss_pred eEEEEecCC-HHHHHHHHHHHHhhhhHHHHHHHHHhhccCCcHHHHHHHHHHHHHHh
Q 033045 38 IRVKVFNGN-LEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIR 93 (128)
Q Consensus 38 I~V~VrDnN-vEqALrvLKrKMq~eGifRemK~r~~~yeKPSEKR~raRk~~err~R 93 (128)
|.|.|.||+ +|+||+.|+++|+++||.++++.++ |||||||+|.++++++.+++.
T Consensus 1 v~V~V~~~~~~e~Alrr~~r~~~~~gi~~~~r~r~-~yekps~kRkrk~~~~~rr~~ 56 (57)
T PF01165_consen 1 VTVKVRDGEDVERALRRFKRKVRRNGILKELRKRR-FYEKPSEKRKRKRSERWRRRF 56 (57)
T ss_dssp ---EEESSSSSSSSSGTTCCTSSTTHHHTTTSSSB--SSSCCCCTTHCCCCCTHHHH
T ss_pred CeeecCCCCCHHHHHHHHHHHHHHcChHHHHHHHH-hcCCHHHHHHHHHHHHHHHHh
Confidence 569999887 9999999999999999999999985 999999999877766666543
No 5
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=80.62 E-value=1.9 Score=27.34 Aligned_cols=19 Identities=21% Similarity=0.270 Sum_probs=17.3
Q ss_pred eEEEEecCCHHHHHHHHHH
Q 033045 38 IRVKVFNGNLEQALSWMQR 56 (128)
Q Consensus 38 I~V~VrDnNvEqALrvLKr 56 (128)
++|.|.+.|+|+|..+|+.
T Consensus 46 ~~v~V~~~d~~~A~~il~~ 64 (67)
T PF09413_consen 46 VEVYVPEEDYERAREILEE 64 (67)
T ss_dssp EEEEEEGGGHHHHHHHHHH
T ss_pred eEEEECHHHHHHHHHHHHH
Confidence 8899999999999999863
No 6
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=76.89 E-value=1.6 Score=22.65 Aligned_cols=21 Identities=33% Similarity=0.526 Sum_probs=15.8
Q ss_pred EecCCHHHHHHHHHHHHhhhhH
Q 033045 42 VFNGNLEQALSWMQRKMQSSGI 63 (128)
Q Consensus 42 VrDnNvEqALrvLKrKMq~eGi 63 (128)
++.|++++|+.++.+ |.++|+
T Consensus 11 ~~~~~~~~a~~~~~~-M~~~g~ 31 (35)
T TIGR00756 11 CKAGRVEEALELFKE-MLERGI 31 (35)
T ss_pred HHCCCHHHHHHHHHH-HHHcCC
Confidence 457899999998864 666654
No 7
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=74.95 E-value=2.1 Score=22.70 Aligned_cols=21 Identities=24% Similarity=0.480 Sum_probs=15.4
Q ss_pred EecCCHHHHHHHHHHHHhhhhH
Q 033045 42 VFNGNLEQALSWMQRKMQSSGI 63 (128)
Q Consensus 42 VrDnNvEqALrvLKrKMq~eGi 63 (128)
+..|++|.|+.++.. |++.||
T Consensus 12 ~~~g~~~~a~~~~~~-M~~~gv 32 (34)
T PF13812_consen 12 AKAGDPDAALQLFDE-MKEQGV 32 (34)
T ss_pred HHCCCHHHHHHHHHH-HHHhCC
Confidence 457899999988865 655654
No 8
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=72.99 E-value=1.9 Score=27.02 Aligned_cols=24 Identities=13% Similarity=0.213 Sum_probs=20.2
Q ss_pred ccceEEEEecCCHHHHHHHHHHHH
Q 033045 35 WRGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 35 ~rgI~V~VrDnNvEqALrvLKrKM 58 (128)
...|.+.|.++|.++|++.|.+-+
T Consensus 39 e~~is~~v~~~~~~~av~~Lh~~f 62 (64)
T cd04937 39 HTTISCLVSEDDVKEAVNALHEAF 62 (64)
T ss_pred ccEEEEEEcHHHHHHHHHHHHHHh
Confidence 446778999999999999998754
No 9
>PF13840 ACT_7: ACT domain ; PDB: 3S1T_A 1ZHV_A 3AB4_K 3AB2_O 2DTJ_A 3AAW_A 2RE1_B 3MAH_A 1ZVP_D.
Probab=72.97 E-value=4.5 Score=26.04 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=19.1
Q ss_pred ccceEEEEecCCHHHHHHHHHH
Q 033045 35 WRGIRVKVFNGNLEQALSWMQR 56 (128)
Q Consensus 35 ~rgI~V~VrDnNvEqALrvLKr 56 (128)
...+.+.|.+.++|+|+++|++
T Consensus 44 ~~~~~ilV~~~~~~~A~~~L~~ 65 (65)
T PF13840_consen 44 EISISILVKEEDLEKAVEALHE 65 (65)
T ss_dssp SSEEEEEEEGGGHHHHHHHHHH
T ss_pred eeeEEEEEeHHHHHHHHHHhcC
Confidence 3567899999999999999975
No 10
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=52.07 E-value=12 Score=21.74 Aligned_cols=13 Identities=46% Similarity=1.078 Sum_probs=10.4
Q ss_pred EecCCHHHHHHHH
Q 033045 42 VFNGNLEQALSWM 54 (128)
Q Consensus 42 VrDnNvEqALrvL 54 (128)
-.+||+|.|+..|
T Consensus 25 ~~~~nve~A~~~L 37 (37)
T PF00627_consen 25 ACNGNVERAVDWL 37 (37)
T ss_dssp HTTTSHHHHHHHH
T ss_pred HcCCCHHHHHHhC
Confidence 3578999999876
No 11
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=51.01 E-value=12 Score=19.14 Aligned_cols=20 Identities=30% Similarity=0.488 Sum_probs=14.6
Q ss_pred EecCCHHHHHHHHHHHHhhhh
Q 033045 42 VFNGNLEQALSWMQRKMQSSG 62 (128)
Q Consensus 42 VrDnNvEqALrvLKrKMq~eG 62 (128)
...|++|+|+++++ +|.+.|
T Consensus 11 ~~~~~~~~a~~~~~-~M~~~g 30 (31)
T PF01535_consen 11 CKMGQFEEALEVFD-EMRERG 30 (31)
T ss_pred HccchHHHHHHHHH-HHhHCc
Confidence 45689999999885 455555
No 12
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=49.64 E-value=19 Score=24.12 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=23.9
Q ss_pred ecCCHHHHHHHHHHHHhhhhHHHHHHHH
Q 033045 43 FNGNLEQALSWMQRKMQSSGIERLIKRE 70 (128)
Q Consensus 43 rDnNvEqALrvLKrKMq~eGifRemK~r 70 (128)
.|=|-+.|++-+.++|++.||...|+..
T Consensus 25 ~~~~~~e~~~~f~~~L~~~Gv~~~L~~~ 52 (69)
T TIGR03595 25 TPFNNDENLRRFARKLKKLGVEDALRKA 52 (69)
T ss_pred cCCCCHHHHHHHHHHHHHCCHHHHHHHc
Confidence 3445678999999999999999999876
No 13
>cd04936 ACT_AKii-LysC-BS-like_2 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive AK isoenzymes. The B. subtilis strain 168 AKII is induced by methionine and repressed and inhibited by lysine. Although C. glutamicum is known to contain a single AK, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regu
Probab=48.73 E-value=19 Score=21.06 Aligned_cols=23 Identities=13% Similarity=0.146 Sum_probs=20.2
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKrKM 58 (128)
..+.+.|.+.|+++|+++|.+.+
T Consensus 39 ~~is~~v~~~d~~~~~~~l~~~~ 61 (63)
T cd04936 39 IKISCLIDEDDAEKAVRALHEAF 61 (63)
T ss_pred ceEEEEEeHHHHHHHHHHHHHHh
Confidence 55779999999999999998865
No 14
>PF13041 PPR_2: PPR repeat family
Probab=48.60 E-value=13 Score=21.94 Aligned_cols=13 Identities=31% Similarity=0.514 Sum_probs=10.2
Q ss_pred ecCCHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQ 55 (128)
Q Consensus 43 rDnNvEqALrvLK 55 (128)
+.|++|+|+++++
T Consensus 15 ~~~~~~~a~~l~~ 27 (50)
T PF13041_consen 15 KAGKFEEALKLFK 27 (50)
T ss_pred HCcCHHHHHHHHH
Confidence 4689999998764
No 15
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=43.40 E-value=10 Score=34.26 Aligned_cols=28 Identities=18% Similarity=0.156 Sum_probs=23.8
Q ss_pred EEecCCHHHHHHHHHHHHhhhhHHHHHH
Q 033045 41 KVFNGNLEQALSWMQRKMQSSGIERLIK 68 (128)
Q Consensus 41 ~VrDnNvEqALrvLKrKMq~eGifRemK 68 (128)
-.-.|++-+++.-||+|++.||+|.+=.
T Consensus 100 p~G~G~L~~~~E~lK~kL~aEGlFd~~~ 127 (440)
T COG1570 100 PAGLGALYLAFEQLKAKLAAEGLFDPER 127 (440)
T ss_pred cCChhHHHHHHHHHHHHHHhCCCcChhh
Confidence 3456899999999999999999996643
No 16
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=42.83 E-value=15 Score=24.56 Aligned_cols=24 Identities=29% Similarity=0.595 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHH
Q 033045 47 LEQALSWMQRKMQSSGIERLIKRE 70 (128)
Q Consensus 47 vEqALrvLKrKMq~eGifRemK~r 70 (128)
-+.|++-+.++|.+.||...|+..
T Consensus 29 ~~e~~~rf~~~L~~~Gv~~~L~~~ 52 (69)
T PF09269_consen 29 DEESLRRFQRKLKKMGVEKALRKA 52 (69)
T ss_dssp TGGGHHHHHHHHHHTTHHHHHHTT
T ss_pred CHHHHHHHHHHHHHCCHHHHHHHc
Confidence 457899999999999999999865
No 17
>cd04923 ACT_AK-LysC-DapG-like_2 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the second and fourth, of four, ACT domains present in cyanobacteria AK. Also included are the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (B. subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=41.02 E-value=30 Score=20.20 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=20.4
Q ss_pred ccceEEEEecCCHHHHHHHHHHHH
Q 033045 35 WRGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 35 ~rgI~V~VrDnNvEqALrvLKrKM 58 (128)
...+.+.|.+.|+++|+++|.+.+
T Consensus 38 ~~~is~~v~~~~~~~~~~~l~~~l 61 (63)
T cd04923 38 EIKISCLVDEDDAEKAVRALHEAF 61 (63)
T ss_pred CCeEEEEEeHHHHHHHHHHHHHHh
Confidence 355789999999999999998765
No 18
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=38.29 E-value=16 Score=31.03 Aligned_cols=27 Identities=19% Similarity=0.345 Sum_probs=23.1
Q ss_pred cCCHHHHHHHHHHHHhhhhHHHHHHHH
Q 033045 44 NGNLEQALSWMQRKMQSSGIERLIKRE 70 (128)
Q Consensus 44 DnNvEqALrvLKrKMq~eGifRemK~r 70 (128)
-|++.+++.-||+|+..||+|..-+.+
T Consensus 103 ~G~l~~~~~~lk~~L~~eGlfd~~~k~ 129 (438)
T PRK00286 103 IGALAAAFEQLKEKLAAEGLFDPERKK 129 (438)
T ss_pred ccHHHHHHHHHHHHHHHCCCCChhhcC
Confidence 399999999999999999999765433
No 19
>PF08690 GET2: GET complex subunit GET2; InterPro: IPR014802 This family corresponds to the GET complex subunit GET2. The GET complex is involved in the retrieval of ER resident proteins from the Golgi []. ; PDB: 3SJD_D 3ZS9_C.
Probab=37.74 E-value=29 Score=29.46 Aligned_cols=29 Identities=34% Similarity=0.425 Sum_probs=20.7
Q ss_pred cHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 033045 78 SEKRVLARKNLERKIRSQDLARKLKAILV 106 (128)
Q Consensus 78 SEKR~raRk~~err~Rs~elarKLk~Ili 106 (128)
+|||.+.|+.+|+++..=.-..+|..|+-
T Consensus 5 aEkrRLrRERReAKi~~GgaSaRLnKITg 33 (302)
T PF08690_consen 5 AEKRRLRRERREAKIKAGGASARLNKITG 33 (302)
T ss_dssp HHHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCcHHHHHHHhc
Confidence 58888888777777754444567888875
No 20
>cd04917 ACT_AKiii-LysC-EC_2 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The second ACT domain (ACT2), this CD, is not involved in the binding of heterotrophic effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=37.63 E-value=33 Score=21.12 Aligned_cols=22 Identities=5% Similarity=0.206 Sum_probs=18.5
Q ss_pred ceEEEEecCCHHHHHHHHHHHH
Q 033045 37 GIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 37 gI~V~VrDnNvEqALrvLKrKM 58 (128)
-|.+.|.+.|.++|++.|.+.+
T Consensus 41 ~is~~V~~~~~~~a~~~Lh~~f 62 (64)
T cd04917 41 NLCFLVKEEDKDEVVQRLHSRL 62 (64)
T ss_pred EEEEEEeHHHHHHHHHHHHHHH
Confidence 4667999999999999998754
No 21
>PF12854 PPR_1: PPR repeat
Probab=37.60 E-value=28 Score=19.77 Aligned_cols=14 Identities=14% Similarity=0.389 Sum_probs=11.5
Q ss_pred ecCCHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQR 56 (128)
Q Consensus 43 rDnNvEqALrvLKr 56 (128)
+.|++|.|++++.+
T Consensus 19 k~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 19 KAGRVDEAFELFDE 32 (34)
T ss_pred HCCCHHHHHHHHHh
Confidence 56999999998853
No 22
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=37.06 E-value=13 Score=34.00 Aligned_cols=25 Identities=16% Similarity=0.174 Sum_probs=20.4
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.++.++.=+.-+|+|+..
T Consensus 267 E~pT~krl~~ARekGqV~kS~El~~ 291 (609)
T PRK12772 267 EEATPKKKSDARKKGQIAKSKELAL 291 (609)
T ss_pred CCCChhHHHHHHhcCCCCchHHHHH
Confidence 9999999776666667889999764
No 23
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=36.46 E-value=36 Score=20.30 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=19.9
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKrKM 58 (128)
..+.+.|.+.|++.|+.+|.+.+
T Consensus 42 ~~isf~v~~~d~~~~~~~lh~~~ 64 (66)
T cd04916 42 ISIMIGVHNEDADKAVKAIYEEF 64 (66)
T ss_pred cEEEEEEeHHHHHHHHHHHHHHH
Confidence 55779999999999999998765
No 24
>cd04892 ACT_AK-like_2 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the second of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). The exception in this group, is the inclusion of the first ACT domain of the bifunctional aspartokinase - homoserine dehydrogenase-like enzyme group (ACT_AKi-HSDH-ThrA-like_1) which includes the monofunctional, threonine-sensitive, aspartokinase found in Methanococcus jannaschii and other related archaeal species. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. AK is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of AK with different repressors an
Probab=36.42 E-value=38 Score=19.27 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=19.8
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKrKM 58 (128)
..+.+.|.+.|++.+++.|.+.+
T Consensus 41 ~~i~~~v~~~~~~~~~~~l~~~~ 63 (65)
T cd04892 41 VNISFVVDEDDADKAVKALHEEF 63 (65)
T ss_pred eeEEEEEeHHHHHHHHHHHHHHH
Confidence 55778999999999999998765
No 25
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=35.56 E-value=16 Score=31.23 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=20.3
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=+.-+|+|+..
T Consensus 5 E~pT~kKL~dARekGqV~kS~el~~ 29 (342)
T TIGR01404 5 EKPTPKKLRDARKKGQVAKSKDLTS 29 (342)
T ss_pred CCCChhHHHHHHHcCCCcccHhHHH
Confidence 8999999766666667889999765
No 26
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=35.42 E-value=16 Score=31.63 Aligned_cols=27 Identities=19% Similarity=0.207 Sum_probs=22.9
Q ss_pred ecCCHHHHHHHHHHHHhhhhHHHHHHH
Q 033045 43 FNGNLEQALSWMQRKMQSSGIERLIKR 69 (128)
Q Consensus 43 rDnNvEqALrvLKrKMq~eGifRemK~ 69 (128)
.-|++..++.-||+|+..||+|..=+.
T Consensus 96 G~G~l~~~~~~lk~~L~~eGlfd~~~k 122 (432)
T TIGR00237 96 GEGLLQLAYEQLKEKLAAEGLFDQEYK 122 (432)
T ss_pred ChHHHHHHHHHHHHHHHHCCCCCchhc
Confidence 358999999999999999999965433
No 27
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=35.04 E-value=39 Score=21.60 Aligned_cols=22 Identities=9% Similarity=0.237 Sum_probs=18.9
Q ss_pred ceEEEEecCCHHHHHHHHHHHH
Q 033045 37 GIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 37 gI~V~VrDnNvEqALrvLKrKM 58 (128)
-|.+.|.+.|.++|++.|.+.+
T Consensus 43 ~is~~V~~~~~~~av~~Lh~~f 64 (66)
T cd04915 43 DVQFVVDRDDYDNAIKALHAAL 64 (66)
T ss_pred EEEEEEEHHHHHHHHHHHHHHH
Confidence 5778999999999999997754
No 28
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=34.93 E-value=30 Score=27.63 Aligned_cols=15 Identities=40% Similarity=1.015 Sum_probs=13.4
Q ss_pred ecCCHHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQRK 57 (128)
Q Consensus 43 rDnNvEqALrvLKrK 57 (128)
-|||+|+|+.+|++|
T Consensus 29 ~~gd~~~A~~~lr~~ 43 (198)
T PRK12332 29 ANGDMEKAIEWLREK 43 (198)
T ss_pred cCCCHHHHHHHHHHh
Confidence 469999999999986
No 29
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=34.77 E-value=49 Score=24.63 Aligned_cols=25 Identities=24% Similarity=0.441 Sum_probs=19.0
Q ss_pred eEEEEecCCHHHHHHHHHHHHhhhh
Q 033045 38 IRVKVFNGNLEQALSWMQRKMQSSG 62 (128)
Q Consensus 38 I~V~VrDnNvEqALrvLKrKMq~eG 62 (128)
+.|.|.++++|.|+...++.+..+|
T Consensus 10 ~~i~v~~~~~e~~v~~a~~~~~~~g 34 (176)
T PF06506_consen 10 AEIDVIEASLEEAVEEARQLLESEG 34 (176)
T ss_dssp SEEEEEE--HHHHHHHHHHHHTTTT
T ss_pred ceEEEEEecHHHHHHHHHHhhHhcC
Confidence 7799999999999999999844343
No 30
>PRK09377 tsf elongation factor Ts; Provisional
Probab=34.42 E-value=30 Score=29.32 Aligned_cols=15 Identities=33% Similarity=1.030 Sum_probs=13.3
Q ss_pred ecCCHHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQRK 57 (128)
Q Consensus 43 rDnNvEqALrvLKrK 57 (128)
-|||+|+|+.+|++|
T Consensus 30 ~~gD~ekAi~~Lrk~ 44 (290)
T PRK09377 30 ADGDIEKAIEWLRKK 44 (290)
T ss_pred cCCCHHHHHHHHHHh
Confidence 479999999999975
No 31
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=33.60 E-value=31 Score=29.19 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=13.6
Q ss_pred ecCCHHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQRK 57 (128)
Q Consensus 43 rDnNvEqALrvLKrK 57 (128)
-|||+|+|+.+|++|
T Consensus 29 ~~gDiekAi~~LRkk 43 (290)
T TIGR00116 29 ANGDFEKAIKNLRES 43 (290)
T ss_pred cCCCHHHHHHHHHHh
Confidence 479999999999986
No 32
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=33.24 E-value=34 Score=19.32 Aligned_cols=13 Identities=38% Similarity=0.877 Sum_probs=10.3
Q ss_pred EecCCHHHHHHHH
Q 033045 42 VFNGNLEQALSWM 54 (128)
Q Consensus 42 VrDnNvEqALrvL 54 (128)
--+||+|.|+..|
T Consensus 24 ~~~~d~~~A~~~L 36 (38)
T cd00194 24 ATNNNVERAVEWL 36 (38)
T ss_pred HhCCCHHHHHHHH
Confidence 3469999998776
No 33
>cd04919 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=32.54 E-value=46 Score=20.07 Aligned_cols=23 Identities=13% Similarity=0.171 Sum_probs=19.3
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKrKM 58 (128)
.-+.+.|.++|.++|++.|.+-+
T Consensus 42 ~~isf~v~~~~~~~a~~~lh~~~ 64 (66)
T cd04919 42 INISCVIDEKDAVKALNIIHTNL 64 (66)
T ss_pred ceEEEEEeHHHHHHHHHHHHHHH
Confidence 45778999999999999988754
No 34
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=32.35 E-value=91 Score=20.14 Aligned_cols=32 Identities=25% Similarity=0.244 Sum_probs=27.2
Q ss_pred chhcccceEEEEecCCHHHHHHHHHHHHhhhh
Q 033045 31 QVQQWRGIRVKVFNGNLEQALSWMQRKMQSSG 62 (128)
Q Consensus 31 qvQq~rgI~V~VrDnNvEqALrvLKrKMq~eG 62 (128)
|+|.--.|.|....++++.+-..|.+|=..+|
T Consensus 1 ~l~~iG~Isvs~~~~s~~d~~~~la~kAd~~G 32 (56)
T PF07338_consen 1 QLQKIGTISVSGNFGSPDDAEEALAKKADEKG 32 (56)
T ss_dssp TCEEEEEEEEEEECSSHHHHHHHHHHHHHHTT
T ss_pred CCeEEEEEEEccccCCHHHHHHHHHHHHHHcC
Confidence 35667778899998999999999999987776
No 35
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=32.30 E-value=1.6e+02 Score=19.83 Aligned_cols=47 Identities=23% Similarity=0.363 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHHHhhccCCcHHH-HHHHHHHHHHHhhHHHH
Q 033045 45 GNLEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKR-VLARKNLERKIRSQDLA 98 (128)
Q Consensus 45 nNvEqALrvLKrKMq~eGifRemK~r~~~yeKPSEKR-~raRk~~err~Rs~ela 98 (128)
||.+.|+.... +||...|..- .|||+.++| ....+-.+-.-|+++|-
T Consensus 20 g~y~eA~~lY~-----~ale~~~~~~--k~e~~~~~k~~lr~k~~eyl~RAE~LK 67 (75)
T cd02684 20 GDAAAALSLYC-----SALQYFVPAL--HYETDAQRKEALRQKVLQYVSRAEELK 67 (75)
T ss_pred ccHHHHHHHHH-----HHHHHHHHHH--hhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 78888887664 6888778766 379887776 33444455555544443
No 36
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.57 E-value=48 Score=20.90 Aligned_cols=22 Identities=5% Similarity=0.069 Sum_probs=18.5
Q ss_pred ceEEEEecCCHHHHHHHHHHHH
Q 033045 37 GIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 37 gI~V~VrDnNvEqALrvLKrKM 58 (128)
-|.+.|.+.|.++|++.|-+.+
T Consensus 40 ~is~vv~~~d~~~av~~LH~~f 61 (63)
T cd04920 40 NLTFVVDEDQADGLCARLHFQL 61 (63)
T ss_pred eEEEEEeHHHHHHHHHHHHHHH
Confidence 5668899999999999987653
No 37
>PF01312 Bac_export_2: FlhB HrpN YscU SpaS Family; InterPro: IPR006135 Salmonella, and related proteobacteria, secrete large amounts of proteins into the culture media. The major secreted proteins are either flagellar proteins or virulence factors [], secreted through the flagellar or virulence export structures respectively. Both secretion systems penetrate the inner and outer membranes and their components bear substantial sequence similarity. Both the flagellar and needle like pilus look fairly similar to each other []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. It is believed that the family of type III flagellar and pilus inner membrane proteins are used as structural moieties in a complex with several other subunits []. One such set of inner membrane proteins, labeled "S" here for nomenclature purposes, includes the Salmonella and Shigella SpaS, the Yersinia YscU, Rhizobium Y4YO, and the Erwinia HrcU genes, Salmonella FlhB and Escherichia coli EscU [, , , ]. Many of the proteins, in this entry, undergo autocatalytic cleavage promoted by cyclization of a conserved asparagine. These proteins belong to the MEROPS peptidase family N6. ; GO: 0009306 protein secretion, 0016020 membrane; PDB: 3C03_C 3BZT_A 3BZV_B 3BZP_A 3BZX_B 3BZL_B 3C00_A 3BZR_A 3BZY_A 3BZO_A ....
Probab=31.49 E-value=16 Score=31.04 Aligned_cols=25 Identities=16% Similarity=0.223 Sum_probs=0.0
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
|+||+||.++.++.=..-+|+|+..
T Consensus 7 E~pT~kkl~~ARekGqV~kS~el~~ 31 (343)
T PF01312_consen 7 EKPTPKKLRDAREKGQVPKSKELTS 31 (343)
T ss_dssp -------------------------
T ss_pred CCCChhHHHHHHhcCCCCchHHHHH
Confidence 9999999877777778899999874
No 38
>PRK06298 type III secretion system protein; Validated
Probab=30.76 E-value=21 Score=30.82 Aligned_cols=25 Identities=24% Similarity=0.292 Sum_probs=20.7
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
|+||+||.+...+.=+.-+|+|+..
T Consensus 6 E~pT~kkl~~ARekGqV~kS~el~~ 30 (356)
T PRK06298 6 EKATPKRLRDARKKGQVAKSQDFPS 30 (356)
T ss_pred CCCChhHHHHHHHcCCCccchhHHH
Confidence 8999999776666667889999875
No 39
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=30.53 E-value=20 Score=30.96 Aligned_cols=25 Identities=12% Similarity=0.021 Sum_probs=20.5
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=..-+|+|+..
T Consensus 12 E~pT~kkl~~AR~kGqV~kS~el~~ 36 (358)
T PRK13109 12 EEATERKVRDAIEKGDIPVSREAPV 36 (358)
T ss_pred CCCChhHHHHHHhcCCCCChHhHHH
Confidence 9999999776666667889999764
No 40
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=30.32 E-value=53 Score=19.55 Aligned_cols=23 Identities=17% Similarity=0.283 Sum_probs=19.6
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKrKM 58 (128)
..+.+.|.++|.++|++.|.+.+
T Consensus 42 ~~is~~v~~~~~~~~~~~lh~~~ 64 (66)
T cd04922 42 RNISAVIDEDDATKALRAVHERF 64 (66)
T ss_pred cEEEEEEeHHHHHHHHHHHHHHH
Confidence 56778999999999999988754
No 41
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.86 E-value=52 Score=19.49 Aligned_cols=23 Identities=13% Similarity=0.034 Sum_probs=19.7
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKrKM 58 (128)
..+.+.|.+.|+++|++.|.+.+
T Consensus 42 ~~isf~i~~~~~~~~~~~Lh~~~ 64 (66)
T cd04924 42 YNISFVVAEDDGWAAVKAVHDEF 64 (66)
T ss_pred ceEEEEEeHHHHHHHHHHHHHHh
Confidence 45778999999999999998765
No 42
>CHL00098 tsf elongation factor Ts
Probab=29.80 E-value=41 Score=27.02 Aligned_cols=15 Identities=40% Similarity=0.660 Sum_probs=13.4
Q ss_pred ecCCHHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQRK 57 (128)
Q Consensus 43 rDnNvEqALrvLKrK 57 (128)
-|||+|.|+.+|++|
T Consensus 26 ~~gd~~~A~~~Lr~~ 40 (200)
T CHL00098 26 ANGDFEKALESLRQK 40 (200)
T ss_pred cCCCHHHHHHHHHHh
Confidence 469999999999986
No 43
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=29.48 E-value=22 Score=30.61 Aligned_cols=25 Identities=16% Similarity=0.202 Sum_probs=20.4
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=+.-+|+|+..
T Consensus 11 E~pT~kKL~dARkkGqV~kS~el~~ 35 (359)
T PRK05702 11 EEPTPKKLEKAREKGQVPRSRELNT 35 (359)
T ss_pred CCCChhHHHHHHHcCCCCchHHHHH
Confidence 8999999766666667889999864
No 44
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=29.32 E-value=22 Score=30.58 Aligned_cols=25 Identities=8% Similarity=0.129 Sum_probs=20.2
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=+.-+|+|+..
T Consensus 4 E~pT~kKl~dARkkGqV~kS~el~~ 28 (347)
T TIGR00328 4 EEPTPKKLRKAREEGNVPKSREVNS 28 (347)
T ss_pred CCCChhHHHHHHhcCCCCchHhHHH
Confidence 8999999766666667889999864
No 45
>PRK09108 type III secretion system protein HrcU; Validated
Probab=29.03 E-value=22 Score=30.57 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=20.2
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=+.-+|+|+..
T Consensus 7 E~pT~KKL~dARekGqV~kS~el~~ 31 (353)
T PRK09108 7 EEPTEKKLKDARKDGEVAKSPDLTA 31 (353)
T ss_pred CCCChhHHHHHHhcCCCCchHHHHH
Confidence 8999999776666667889999753
No 46
>PRK08156 type III secretion system protein SpaS; Validated
Probab=28.80 E-value=24 Score=30.69 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=20.4
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=..-+|+|+..
T Consensus 6 E~pT~kkL~dARekGqV~kS~el~~ 30 (361)
T PRK08156 6 EKPTKKKLRDSAKKGQSFKSKDLIT 30 (361)
T ss_pred CCCChhHHHHHHHcCCCCchHhHHH
Confidence 9999999766666667889999765
No 47
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.62 E-value=57 Score=20.46 Aligned_cols=22 Identities=14% Similarity=0.250 Sum_probs=18.6
Q ss_pred ceEEEEecCCHHHHHHHHHHHH
Q 033045 37 GIRVKVFNGNLEQALSWMQRKM 58 (128)
Q Consensus 37 gI~V~VrDnNvEqALrvLKrKM 58 (128)
-|.+.|.+.|.++|++.|.+.+
T Consensus 42 sis~~v~~~~~~~av~~Lh~~f 63 (65)
T cd04918 42 NISLIVNDSEAEGCVQALHKSF 63 (65)
T ss_pred eEEEEEeHHHHHHHHHHHHHHH
Confidence 4668899999999999997754
No 48
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=27.98 E-value=25 Score=30.17 Aligned_cols=25 Identities=16% Similarity=0.296 Sum_probs=20.3
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=..-+|+|+..
T Consensus 6 E~pT~kkl~dARkkGqV~kS~el~~ 30 (349)
T PRK12721 6 EKPTEKKLRDARKKGQVVKSVEITS 30 (349)
T ss_pred CCCChHHHHHHHHcCCCcchhhHHH
Confidence 8999999777666667889999764
No 49
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=27.91 E-value=25 Score=30.77 Aligned_cols=25 Identities=12% Similarity=0.174 Sum_probs=20.3
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
||||+||.+...+.=..-+|+|+..
T Consensus 11 E~pT~kkl~dARkkGqV~kS~el~~ 35 (386)
T PRK12468 11 EEPTASKLEKAREKGQIPRSRELTS 35 (386)
T ss_pred CCCChHHHHHHHhcCCCCchHHHHH
Confidence 8999999766666667889999875
No 50
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=26.70 E-value=51 Score=18.57 Aligned_cols=12 Identities=42% Similarity=0.753 Sum_probs=9.4
Q ss_pred ecCCHHHHHHHH
Q 033045 43 FNGNLEQALSWM 54 (128)
Q Consensus 43 rDnNvEqALrvL 54 (128)
-+||+|+|+..|
T Consensus 25 ~~~d~~~A~~~L 36 (37)
T smart00165 25 ANGNVERAAEYL 36 (37)
T ss_pred hCCCHHHHHHHH
Confidence 368999998765
No 51
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=25.72 E-value=30 Score=30.53 Aligned_cols=25 Identities=16% Similarity=0.223 Sum_probs=20.9
Q ss_pred cCCcHHHHHHHHHHHHHHhhHHHHH
Q 033045 75 IKNSEKRVLARKNLERKIRSQDLAR 99 (128)
Q Consensus 75 eKPSEKR~raRk~~err~Rs~elar 99 (128)
|||++||.+...+.=+.-+|+|+..
T Consensus 11 E~pT~kKl~dArekG~v~kS~el~~ 35 (363)
T COG1377 11 EKPTPKKLRDAREKGQVPKSRELTS 35 (363)
T ss_pred CCCChhhHHHHHHcCCCccchhHHH
Confidence 9999999777766667889999874
No 52
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.56 E-value=38 Score=24.07 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=14.0
Q ss_pred hhHHHHHHHHHhhccCCcHHHHHH
Q 033045 61 SGIERLIKREQRHHIKNSEKRVLA 84 (128)
Q Consensus 61 eGifRemK~r~~~yeKPSEKR~ra 84 (128)
|-..|.|=.- -=.||||+++..
T Consensus 41 e~~iR~M~~q--mGqKpSe~kI~Q 62 (71)
T COG3763 41 EEMIRMMMAQ--MGQKPSEKKINQ 62 (71)
T ss_pred HHHHHHHHHH--hCCCchHHHHHH
Confidence 4555665443 247999999743
No 53
>PRK01844 hypothetical protein; Provisional
Probab=23.69 E-value=44 Score=23.68 Aligned_cols=24 Identities=13% Similarity=0.138 Sum_probs=14.5
Q ss_pred hhHHHHHHHHHhhccCCcHHHHHHHH
Q 033045 61 SGIERLIKREQRHHIKNSEKRVLARK 86 (128)
Q Consensus 61 eGifRemK~r~~~yeKPSEKR~raRk 86 (128)
|-..|.|=.- -=.||||+++.+=-
T Consensus 41 e~mir~Mm~Q--MGqkPSekki~Q~m 64 (72)
T PRK01844 41 EQMLKMMMMQ--MGQKPSQKKINQMM 64 (72)
T ss_pred HHHHHHHHHH--hCCCccHHHHHHHH
Confidence 4455555322 24799999975543
No 54
>PRK00523 hypothetical protein; Provisional
Probab=23.62 E-value=45 Score=23.66 Aligned_cols=23 Identities=17% Similarity=0.114 Sum_probs=15.0
Q ss_pred hhHHHHHHHHHhhccCCcHHHHHHH
Q 033045 61 SGIERLIKREQRHHIKNSEKRVLAR 85 (128)
Q Consensus 61 eGifRemK~r~~~yeKPSEKR~raR 85 (128)
|-..|.|=.- -=.||||+++.+=
T Consensus 42 e~mir~M~~Q--MGqKPSekki~Q~ 64 (72)
T PRK00523 42 ENMIRAMYMQ--MGRKPSESQIKQV 64 (72)
T ss_pred HHHHHHHHHH--hCCCccHHHHHHH
Confidence 5666666333 2479999997543
No 55
>COG3603 Uncharacterized conserved protein [Function unknown]
Probab=23.41 E-value=65 Score=25.19 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=15.1
Q ss_pred EEEEecCCHHHHHHHHH
Q 033045 39 RVKVFNGNLEQALSWMQ 55 (128)
Q Consensus 39 ~V~VrDnNvEqALrvLK 55 (128)
.|.|+.+|+|+|.+.|+
T Consensus 104 hiLVr~~dLekAv~~L~ 120 (128)
T COG3603 104 HILVREEDLEKAVKALE 120 (128)
T ss_pred eEEEehhhHHHHHHHHH
Confidence 38899999999999886
No 56
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=23.14 E-value=43 Score=20.74 Aligned_cols=22 Identities=23% Similarity=0.536 Sum_probs=19.3
Q ss_pred EEecCCHHHHHHHHHHHHhhhh
Q 033045 41 KVFNGNLEQALSWMQRKMQSSG 62 (128)
Q Consensus 41 ~VrDnNvEqALrvLKrKMq~eG 62 (128)
.+-+++++..+.-|++|+...|
T Consensus 40 ~~~~~~l~~~I~rLR~kL~~~~ 61 (77)
T PF00486_consen 40 DVSDNSLDVHISRLRKKLEDAG 61 (77)
T ss_dssp TTCTHHHHHHHHHHHHHHHSST
T ss_pred ccchhhHHHHHHHHHHHHhhcC
Confidence 5678999999999999999864
No 57
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=22.81 E-value=57 Score=17.40 Aligned_cols=14 Identities=14% Similarity=0.337 Sum_probs=11.1
Q ss_pred EecCCHHHHHHHHH
Q 033045 42 VFNGNLEQALSWMQ 55 (128)
Q Consensus 42 VrDnNvEqALrvLK 55 (128)
...|+.|+|.+++.
T Consensus 12 ~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 12 LAQGDPDEAERLLR 25 (26)
T ss_pred HHcCCHHHHHHHHh
Confidence 34599999999875
No 58
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=22.68 E-value=55 Score=19.40 Aligned_cols=16 Identities=25% Similarity=0.831 Sum_probs=13.3
Q ss_pred EEecCCHHHHHHHHHH
Q 033045 41 KVFNGNLEQALSWMQR 56 (128)
Q Consensus 41 ~VrDnNvEqALrvLKr 56 (128)
.|.+||++.|+..+..
T Consensus 11 ~i~~g~~~~a~~~~~~ 26 (58)
T smart00668 11 LILKGDWDEALEWLSS 26 (58)
T ss_pred HHHcCCHHHHHHHHHH
Confidence 4678999999998854
No 59
>PF07660 STN: Secretin and TonB N terminus short domain; InterPro: IPR011662 This is a conserved region found at the N-terminal region of bacterial proteins involved in either protein secretion or the uptake of selective substrates, including: Bundle-forming pilus protein B, an outer-membrane protein absolutely required for pilus biogenesis, and for enteropathogenic Escherichia coli localized adherence and autoaggregation []. PilQ, which is required for type IV pilus biogenesis and competence and is thought to function both as a pore for exit of the pilus and as a channel for entry of haem and antimicrobial agents and uptake of transforming DNA []. PupB, a specific receptor for the siderophores ferric pseudobactin BN8 and ferric pseudobactin BN7, iron chelating molecules that allow the organism to extract iron from the environment, especially under iron-restricted conditions []. TonB, which couples the electrochemical potential of the cytoplasmic membrane to the active transport of iron-siderophores and vitamin B12 across the outer membrane []. ; GO: 0019867 outer membrane; PDB: 2D1U_A 1ZZV_A 2W75_B 2O5P_A 2W77_A 2W16_A 2W6U_B 2W6T_A 2W76_B 2W78_B ....
Probab=22.64 E-value=76 Score=18.88 Aligned_cols=25 Identities=28% Similarity=0.339 Sum_probs=15.7
Q ss_pred cchhcccceEEEEecCCHHHHHHHH
Q 033045 30 HQVQQWRGIRVKVFNGNLEQALSWM 54 (128)
Q Consensus 30 ~qvQq~rgI~V~VrDnNvEqALrvL 54 (128)
..+...+.+.|.+.|-.+|+||..|
T Consensus 8 ~~v~~~~~vsl~~~~~~~~~~L~~l 32 (52)
T PF07660_consen 8 DDVNGKKKVSLDVKNMSLEEALDQL 32 (52)
T ss_dssp CCCTT-BE--EE-EEE-HHHHHHHH
T ss_pred HHhCCCcceeEEcCCcCHHHHHHHH
Confidence 3466677888888999999999865
No 60
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=22.50 E-value=1.1e+02 Score=19.68 Aligned_cols=19 Identities=32% Similarity=0.391 Sum_probs=13.2
Q ss_pred HhhcccchhhHHHHHhHhc
Q 033045 108 KVRRDRSFGFAMVAFFFLL 126 (128)
Q Consensus 108 kiRg~~~~~~~~~~~~~~~ 126 (128)
==||=--||.+|+..|..+
T Consensus 12 YEr~Wi~F~l~mi~vFi~l 30 (38)
T PF09125_consen 12 YERGWIAFALAMILVFIAL 30 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHH
Confidence 3344446999999888654
No 61
>PF03197 FRD2: Bacteriophage FRD2 protein; InterPro: IPR004885 This is group of bacteriophage proteins has no known function.
Probab=22.34 E-value=1.1e+02 Score=23.15 Aligned_cols=21 Identities=19% Similarity=0.341 Sum_probs=18.8
Q ss_pred ceEEEEecCCHHHHHHHHHHH
Q 033045 37 GIRVKVFNGNLEQALSWMQRK 57 (128)
Q Consensus 37 gI~V~VrDnNvEqALrvLKrK 57 (128)
.|.+.|-.||+++-+..||+-
T Consensus 79 ~IHciVde~NvdeIIeLl~kT 99 (102)
T PF03197_consen 79 KIHCIVDENNVDEIIELLQKT 99 (102)
T ss_pred EEEEEEccCCHHHHHHHHHHH
Confidence 488999999999999999874
No 62
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=22.31 E-value=93 Score=24.77 Aligned_cols=28 Identities=14% Similarity=0.087 Sum_probs=24.4
Q ss_pred cceEEEEecC--CHHHHHHHHHHHHhhhhH
Q 033045 36 RGIRVKVFNG--NLEQALSWMQRKMQSSGI 63 (128)
Q Consensus 36 rgI~V~VrDn--NvEqALrvLKrKMq~eGi 63 (128)
++|++.+.|+ |.++|+...++=+.++|+
T Consensus 41 ~~i~lv~~D~~~~p~~a~~~a~~li~~d~v 70 (357)
T cd06337 41 YEVEIIVRDSQSNPNRAGLVAQELILTDKV 70 (357)
T ss_pred eEEEEEEecCCCCHHHHHHHHHHHHhccCc
Confidence 4688999998 999999999998888765
No 63
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=22.15 E-value=1.1e+02 Score=17.06 Aligned_cols=14 Identities=21% Similarity=0.584 Sum_probs=11.2
Q ss_pred ecCCHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQR 56 (128)
Q Consensus 43 rDnNvEqALrvLKr 56 (128)
.-||.|+|+...++
T Consensus 11 ~~g~~~~Ai~~y~~ 24 (36)
T PF13176_consen 11 QQGDYEKAIEYYEQ 24 (36)
T ss_dssp HCT-HHHHHHHHHH
T ss_pred HcCCHHHHHHHHHH
Confidence 35899999999988
No 64
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=21.98 E-value=1e+02 Score=17.73 Aligned_cols=19 Identities=16% Similarity=0.204 Sum_probs=15.2
Q ss_pred ecCCHHHHHHHHHHHHhhh
Q 033045 43 FNGNLEQALSWMQRKMQSS 61 (128)
Q Consensus 43 rDnNvEqALrvLKrKMq~e 61 (128)
.-|+.|+|++++++=++..
T Consensus 13 ~~G~~~~A~~~~~~~l~~~ 31 (44)
T PF13428_consen 13 RLGQPDEAERLLRRALALD 31 (44)
T ss_pred HcCCHHHHHHHHHHHHHHC
Confidence 4599999999998876653
No 65
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=21.97 E-value=66 Score=27.91 Aligned_cols=15 Identities=40% Similarity=1.015 Sum_probs=13.4
Q ss_pred ecCCHHHHHHHHHHH
Q 033045 43 FNGNLEQALSWMQRK 57 (128)
Q Consensus 43 rDnNvEqALrvLKrK 57 (128)
-+||+|+|+.+|++|
T Consensus 30 ~~Gd~EkAie~LR~k 44 (296)
T COG0264 30 ANGDIEKAIEWLREK 44 (296)
T ss_pred cCCCHHHHHHHHHHh
Confidence 489999999999885
No 66
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=21.34 E-value=47 Score=28.77 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=17.2
Q ss_pred cceEEEEecCCHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQR 56 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKr 56 (128)
..|+=-|.+||+|+||+.|..
T Consensus 262 ~aI~~AVk~gDi~KAL~LldE 282 (303)
T PRK10564 262 QAIKQAVKKGDVDKALKLLDE 282 (303)
T ss_pred HHHHHHHHcCCHHHHHHHHHH
Confidence 456667999999999999853
No 67
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=21.13 E-value=50 Score=26.31 Aligned_cols=26 Identities=31% Similarity=0.374 Sum_probs=20.7
Q ss_pred cchhc---ccceEEEEecCCHHHHHHHHHH
Q 033045 30 HQVQQ---WRGIRVKVFNGNLEQALSWMQR 56 (128)
Q Consensus 30 ~qvQq---~rgI~V~VrDnNvEqALrvLKr 56 (128)
++++. ..|..|.|. +++|.|+.+|+-
T Consensus 46 p~~~kla~k~G~~vlvf-~dL~DAlevL~P 74 (147)
T COG4080 46 PEVLKLAFKLGKPVLVF-PDLDDALEVLRP 74 (147)
T ss_pred HHHHHHHHHhCCcEEEe-hhHHHHHHhcCC
Confidence 44554 678999999 899999999863
No 68
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=20.49 E-value=1e+02 Score=16.09 Aligned_cols=16 Identities=25% Similarity=0.665 Sum_probs=12.7
Q ss_pred cCCHHHHHHHHHHHHh
Q 033045 44 NGNLEQALSWMQRKMQ 59 (128)
Q Consensus 44 DnNvEqALrvLKrKMq 59 (128)
-||.|+|+..+++=++
T Consensus 14 ~~~~~~A~~~~~~a~~ 29 (34)
T PF13181_consen 14 LGDYEEALEYFEKALE 29 (34)
T ss_dssp TTSHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHh
Confidence 3899999999887544
No 69
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=20.41 E-value=1.2e+02 Score=22.12 Aligned_cols=50 Identities=18% Similarity=0.138 Sum_probs=29.8
Q ss_pred HHHhhhccccCCCCcccccccccccccchhcccceEEEEe-cCCHHHHHHHHHH
Q 033045 4 VGRQLAGYLTQPSQGLNLFSRNQCQRHQVQQWRGIRVKVF-NGNLEQALSWMQR 56 (128)
Q Consensus 4 iar~~~~l~~~~~~~~~~~~~~~~~~~qvQq~rgI~V~Vr-DnNvEqALrvLKr 56 (128)
+--+++|+|...+.|+...+...-+ .....-|.+.|. |..+||-.+-|.|
T Consensus 21 VL~RIaglFsRRgyNIeSLtvg~te---~~~iSRmtivv~~~~~i~Qi~kQL~K 71 (96)
T PRK08178 21 VMSHVCGLFARRAFNVEGILCLPIQ---DGDKSRIWLLVNDDQRLEQMISQIEK 71 (96)
T ss_pred HHHHHHHHHhcCCcCeeeEEEeecC---CCCceEEEEEEcCchHHHHHHHHHhC
Confidence 4567899999999887655443333 334344555554 4445565555554
No 70
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=20.20 E-value=84 Score=18.59 Aligned_cols=12 Identities=33% Similarity=0.545 Sum_probs=9.7
Q ss_pred ecCCHHHHHHHH
Q 033045 43 FNGNLEQALSWM 54 (128)
Q Consensus 43 rDnNvEqALrvL 54 (128)
.|||+|.|+..|
T Consensus 27 ~~~~ve~ai~~L 38 (42)
T PF02845_consen 27 NNGDVEAAIDAL 38 (42)
T ss_dssp TTTTHHHHHHHH
T ss_pred cCCCHHHHHHHH
Confidence 479999998765
No 71
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=20.08 E-value=1.3e+02 Score=19.63 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=17.9
Q ss_pred cceEEEEecCCHHHHHHHHHH
Q 033045 36 RGIRVKVFNGNLEQALSWMQR 56 (128)
Q Consensus 36 rgI~V~VrDnNvEqALrvLKr 56 (128)
=|+-+.+.++|.|.+..+|++
T Consensus 41 CG~al~~~~~d~~~i~~~l~~ 61 (73)
T PF11823_consen 41 CGLALRFEPEDLEKIKEILEE 61 (73)
T ss_pred CCEEEEEChhhHHHHHHHHHH
Confidence 356689999999999999986
No 72
>PF14626 RNase_Zc3h12a_2: Zc3h12a-like Ribonuclease NYN domain
Probab=20.06 E-value=36 Score=26.29 Aligned_cols=9 Identities=44% Similarity=0.349 Sum_probs=7.5
Q ss_pred hhccCCcHH
Q 033045 72 RHHIKNSEK 80 (128)
Q Consensus 72 ~~yeKPSEK 80 (128)
-+|+||||+
T Consensus 100 ~~y~k~ser 108 (122)
T PF14626_consen 100 IHYNKPSER 108 (122)
T ss_pred ccccCcccc
Confidence 479999996
Done!