Query 033754
Match_columns 112
No_of_seqs 106 out of 460
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:55:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033754.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033754hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00030 S21p ribosomal prote 99.9 1.6E-21 3.4E-26 126.6 6.5 56 38-94 1-57 (58)
2 PRK00270 rpsU 30S ribosomal pr 99.8 4E-20 8.6E-25 122.1 7.1 57 38-95 2-59 (64)
3 COG0828 RpsU Ribosomal protein 99.8 1.2E-18 2.7E-23 116.8 7.8 56 38-94 2-58 (67)
4 PF01165 Ribosomal_S21: Riboso 99.6 3.4E-19 7.4E-24 113.8 -9.4 56 38-94 1-57 (57)
5 TIGR03595 Obg_CgtA_exten Obg f 70.8 5.1 0.00011 26.3 2.8 25 46-70 28-52 (69)
6 PF09269 DUF1967: Domain of un 68.7 3.6 7.9E-05 26.9 1.7 25 46-70 28-52 (69)
7 cd04937 ACT_AKi-DapG-BS_2 ACT 67.5 3.1 6.7E-05 25.8 1.1 47 12-58 12-62 (64)
8 PF00472 RF-1: RF-1 domain; I 60.9 14 0.00031 26.1 3.7 51 11-62 18-74 (113)
9 PRK09256 hypothetical protein; 55.7 52 0.0011 24.5 6.0 49 36-88 68-121 (138)
10 TIGR00756 PPR pentatricopeptid 55.4 11 0.00024 19.1 1.8 21 42-63 11-31 (35)
11 PF07660 STN: Secretin and Ton 45.8 15 0.00032 21.7 1.5 26 29-54 7-32 (52)
12 PRK00286 xseA exodeoxyribonucl 40.6 18 0.0004 30.4 1.8 26 45-70 104-129 (438)
13 COG1570 XseA Exonuclease VII, 40.3 13 0.00029 32.8 0.9 47 24-70 83-129 (440)
14 PF03799 FtsQ: Cell division p 36.9 57 0.0012 21.3 3.4 32 30-61 72-103 (117)
15 PF13812 PPR_3: Pentatricopept 36.7 37 0.0008 17.4 2.0 21 42-63 12-32 (34)
16 COG0370 FeoB Fe2+ transport sy 34.5 16 0.00035 33.8 0.5 34 12-45 9-43 (653)
17 PF13840 ACT_7: ACT domain ; P 34.4 42 0.00091 21.1 2.3 22 35-56 44-65 (65)
18 TIGR03884 sel_bind_Methan sele 33.0 67 0.0014 22.1 3.3 32 31-62 5-42 (74)
19 PF09413 DUF2007: Domain of un 32.5 52 0.0011 20.3 2.5 18 38-55 46-63 (67)
20 PF12854 PPR_1: PPR repeat 32.4 40 0.00087 18.6 1.8 15 42-56 18-32 (34)
21 PF01535 PPR: PPR repeat; Int 32.0 43 0.00093 16.7 1.8 18 42-59 11-28 (31)
22 PF14559 TPR_19: Tetratricopep 31.5 33 0.00071 20.3 1.4 20 43-62 3-22 (68)
23 TIGR00237 xseA exodeoxyribonuc 30.6 24 0.00052 30.2 1.0 26 45-70 98-123 (432)
24 PF02421 FeoB_N: Ferrous iron 30.0 10 0.00022 28.4 -1.2 28 19-46 14-41 (156)
25 PF13041 PPR_2: PPR repeat fam 29.8 52 0.0011 18.9 2.1 21 42-63 14-34 (50)
26 smart00804 TAP_C C-terminal do 28.3 45 0.00097 21.8 1.7 24 43-66 36-60 (63)
27 cd04917 ACT_AKiii-LysC-EC_2 AC 28.2 51 0.0011 20.0 1.9 22 37-58 41-62 (64)
28 PF11393 IcmL: Macrophage kill 28.1 64 0.0014 22.5 2.6 27 48-75 52-78 (108)
29 cd04915 ACT_AK-Ectoine_2 ACT d 27.6 55 0.0012 20.5 2.0 22 37-58 43-64 (66)
30 COG1433 Uncharacterized conser 27.5 54 0.0012 24.0 2.2 32 25-56 74-106 (121)
31 PF02579 Nitro_FeMo-Co: Dinitr 27.2 77 0.0017 20.1 2.7 26 30-55 67-93 (94)
32 cd04936 ACT_AKii-LysC-BS-like_ 26.1 59 0.0013 18.7 1.9 23 36-58 39-61 (63)
33 PF12221 HflK_N: Bacterial mem 25.9 64 0.0014 19.7 2.0 15 46-60 22-36 (42)
34 PRK13780 phosphocarrier protei 25.4 1.1E+02 0.0025 20.6 3.4 32 32-63 55-86 (88)
35 PF13428 TPR_14: Tetratricopep 25.2 78 0.0017 17.9 2.2 20 43-62 13-32 (44)
36 TIGR03072 release_prfH putativ 25.1 2E+02 0.0044 22.7 5.2 50 12-61 113-167 (200)
37 cd04920 ACT_AKiii-DAPDC_2 ACT 23.4 71 0.0015 19.7 2.0 23 36-58 39-61 (63)
38 PF13181 TPR_8: Tetratricopept 23.1 1E+02 0.0023 15.8 2.3 17 44-60 14-30 (34)
39 PF02996 Prefoldin: Prefoldin 22.4 1.2E+02 0.0026 20.5 3.1 31 30-60 53-88 (120)
40 PF04108 APG17: Autophagy prot 22.3 1.5E+02 0.0032 25.3 4.2 44 61-105 349-392 (412)
41 TIGR02663 nifX nitrogen fixati 22.2 80 0.0017 21.9 2.2 33 30-62 77-111 (119)
42 cd04918 ACT_AK1-AT_2 ACT domai 21.8 78 0.0017 19.5 1.9 22 37-58 42-63 (65)
43 PF00486 Trans_reg_C: Transcri 21.6 46 0.00099 20.4 0.8 22 41-62 40-61 (77)
44 cd08003 WGR_PARP2_like WGR dom 21.2 90 0.002 21.9 2.3 29 46-77 63-92 (103)
45 TIGR00019 prfA peptide chain r 21.0 2.5E+02 0.0053 24.2 5.3 51 12-62 228-283 (360)
46 TIGR00293 prefoldin, archaeal 21.0 1.6E+02 0.0034 20.4 3.5 31 30-60 62-97 (126)
47 PF00625 Guanylate_kin: Guanyl 20.9 1.3E+02 0.0028 21.8 3.2 24 38-61 160-183 (183)
48 cd00584 Prefoldin_alpha Prefol 20.7 1.5E+02 0.0033 20.5 3.4 31 30-60 63-98 (129)
49 smart00862 Trans_reg_C Transcr 20.3 35 0.00077 20.8 0.1 20 43-62 43-62 (78)
50 PF11172 DUF2959: Protein of u 20.3 4.6E+02 0.01 21.1 7.0 52 41-92 56-126 (201)
51 PRK05783 hypothetical protein; 20.1 1.7E+02 0.0037 20.1 3.5 35 26-60 32-66 (84)
No 1
>TIGR00030 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.
Probab=99.85 E-value=1.6e-21 Score=126.59 Aligned_cols=56 Identities=36% Similarity=0.489 Sum_probs=52.9
Q ss_pred eEEEecCC-CHHHHHHHHHHhHhhhhhHHHHHhhhcccCCchHHHHHHHHHHHHHHHh
Q 033754 38 IRVKVFNG-NLEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIRS 94 (112)
Q Consensus 38 i~V~V~~g-~IE~ALRrfKRk~~keGIl~eiK~R~~~YeKPSekRrrk~~ea~rR~rk 94 (112)
++|.|+|| |||+||++||++|+++||+.|+|+| +||||||++|+++..+|.+++++
T Consensus 1 ~~V~V~~~e~ie~alrrfkr~~~~~gil~e~r~r-~~yeKPs~krkrk~~~a~rr~~k 57 (58)
T TIGR00030 1 PTVKVKEGESIDSALRRFKRKLEKEGILRELKKR-RYYEKPSERRRRKEKAAAKRIRK 57 (58)
T ss_pred CeeEeCCCCcHHHHHHHHHHHHHHcchHHHHHHH-HhhcCHHHHHHHHHHHHHHHHhc
Confidence 46889998 6999999999999999999999999 99999999999999999999875
No 2
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=99.82 E-value=4e-20 Score=122.05 Aligned_cols=57 Identities=30% Similarity=0.427 Sum_probs=53.7
Q ss_pred eEEEecCC-CHHHHHHHHHHhHhhhhhHHHHHhhhcccCCchHHHHHHHHHHHHHHHhH
Q 033754 38 IRVKVFNG-NLEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIRSQ 95 (112)
Q Consensus 38 i~V~V~~g-~IE~ALRrfKRk~~keGIl~eiK~R~~~YeKPSekRrrk~~ea~rR~rkq 95 (112)
+.|.|+|| |||.||++||++|+++||+.|+|++ +||||||++|+++..+|.++.++.
T Consensus 2 ~~V~V~~~e~ie~Alrrfkr~~~k~gil~e~r~r-~~yekPs~krkrk~~~a~rr~~k~ 59 (64)
T PRK00270 2 PQVKVRENESIDKALRRFKRKVEKAGILRELRRR-EFYEKPSEKRKRKKAAARKRRRKK 59 (64)
T ss_pred CeeEeCCCChHHHHHHHHHHHHHHcchHHHHHHH-HhhcCHHHHHHHHHHHHHHHHHHH
Confidence 57889998 6999999999999999999999999 999999999999999999998773
No 3
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=1.2e-18 Score=116.76 Aligned_cols=56 Identities=30% Similarity=0.348 Sum_probs=52.5
Q ss_pred eEEEecCC-CHHHHHHHHHHhHhhhhhHHHHHhhhcccCCchHHHHHHHHHHHHHHHh
Q 033754 38 IRVKVFNG-NLEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIRS 94 (112)
Q Consensus 38 i~V~V~~g-~IE~ALRrfKRk~~keGIl~eiK~R~~~YeKPSekRrrk~~ea~rR~rk 94 (112)
..|.|++| +||.||++||++++++||+.|++.+ +||||||++++++..+|.++..+
T Consensus 2 ~~v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r-~~yEkPs~krkrK~a~a~kr~~k 58 (67)
T COG0828 2 PQVKVRENEPLDKALRRFKRKVEKEGILREMKER-EFYEKPSEKRKRKKAAARKRKFK 58 (67)
T ss_pred CeeeecCCChHHHHHHHHHHHHHHHHHHHHHHHH-HhccCchHHHHHHHHHHHHHHHH
Confidence 46788888 5999999999999999999999999 99999999999999999998877
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=99.63 E-value=3.4e-19 Score=113.75 Aligned_cols=56 Identities=34% Similarity=0.452 Sum_probs=49.3
Q ss_pred eEEEecCC-CHHHHHHHHHHhHhhhhhHHHHHhhhcccCCchHHHHHHHHHHHHHHHh
Q 033754 38 IRVKVFNG-NLEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNLERKIRS 94 (112)
Q Consensus 38 i~V~V~~g-~IE~ALRrfKRk~~keGIl~eiK~R~~~YeKPSekRrrk~~ea~rR~rk 94 (112)
|+|.|.+| |+|.||++|+++|+++||+.|++.+ +||||||++|+++..++.+++++
T Consensus 1 v~V~V~~~~~~e~Alrr~~r~~~~~gi~~~~r~r-~~yekps~kRkrk~~~~~rr~~k 57 (57)
T PF01165_consen 1 VTVKVRDGEDVERALRRFKRKVRRNGILKELRKR-RFYEKPSEKRKRKRSERWRRRFK 57 (57)
T ss_dssp ---EEESSSSSSSSSGTTCCTSSTTHHHTTTSSS-B-SSSCCCCTTHCCCCCTHHHHH
T ss_pred CeeecCCCCCHHHHHHHHHHHHHHcChHHHHHHH-HhcCCHHHHHHHHHHHHHHHHhC
Confidence 67999888 7999999999999999999999999 99999999999999999988764
No 5
>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=70.83 E-value=5.1 Score=26.27 Aligned_cols=25 Identities=24% Similarity=0.517 Sum_probs=22.6
Q ss_pred CHHHHHHHHHHhHhhhhhHHHHHhh
Q 033754 46 NLEQALSWMQRKMQSSGIERLIKRE 70 (112)
Q Consensus 46 ~IE~ALRrfKRk~~keGIl~eiK~R 70 (112)
+-+.|+++|.+.|.+.||.+.|++.
T Consensus 28 ~~~e~~~~f~~~L~~~Gv~~~L~~~ 52 (69)
T TIGR03595 28 NNDENLRRFARKLKKLGVEDALRKA 52 (69)
T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHc
Confidence 6678999999999999999999874
No 6
>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=68.73 E-value=3.6 Score=26.94 Aligned_cols=25 Identities=28% Similarity=0.601 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHhHhhhhhHHHHHhh
Q 033754 46 NLEQALSWMQRKMQSSGIERLIKRE 70 (112)
Q Consensus 46 ~IE~ALRrfKRk~~keGIl~eiK~R 70 (112)
+-+.|+.+|.++|.+.||.++|++.
T Consensus 28 ~~~e~~~rf~~~L~~~Gv~~~L~~~ 52 (69)
T PF09269_consen 28 DDEESLRRFQRKLKKMGVEKALRKA 52 (69)
T ss_dssp -TGGGHHHHHHHHHHTTHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHc
Confidence 4457899999999999999999874
No 7
>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=67.49 E-value=3.1 Score=25.76 Aligned_cols=47 Identities=9% Similarity=0.087 Sum_probs=29.5
Q ss_pred ccCCCCcccccccccccccccc----cccceEEEecCCCHHHHHHHHHHhH
Q 033754 12 LTQPSQGLNLFSRNQCQRHQVQ----QWRGIRVKVFNGNLEQALSWMQRKM 58 (112)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~v~----q~~gi~V~V~~g~IE~ALRrfKRk~ 58 (112)
...|+-....|+.++-..-.+. .-..|.+.|.+++.++|++.+.+.+
T Consensus 12 ~~~~gi~~~if~aL~~~~I~v~~~~~Se~~is~~v~~~~~~~av~~Lh~~f 62 (64)
T cd04937 12 RGVPGVMAKIVGALSKEGIEILQTADSHTTISCLVSEDDVKEAVNALHEAF 62 (64)
T ss_pred cCCcCHHHHHHHHHHHCCCCEEEEEcCccEEEEEEcHHHHHHHHHHHHHHh
Confidence 3444445555555543322232 2336778888889999999998765
No 8
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=60.87 E-value=14 Score=26.08 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=37.2
Q ss_pred cccCCCCccccccccccccccccccc-ceEEEecCC-----CHHHHHHHHHHhHhhhh
Q 033754 11 YLTQPSQGLNLFSRNQCQRHQVQQWR-GIRVKVFNG-----NLEQALSWMQRKMQSSG 62 (112)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~v~q~~-gi~V~V~~g-----~IE~ALRrfKRk~~keG 62 (112)
++++.|.|-|-+|...-.-. +...| ||+|.+.+. |.+.||.+|.-++...-
T Consensus 18 ~~RssGpGGQ~VNk~~s~V~-l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~ 74 (113)
T PF00472_consen 18 FSRSSGPGGQNVNKTNSKVR-LRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAY 74 (113)
T ss_dssp EEESSSSSSCHHHSSSEEEE-EEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred EEecCCCCCCcccccCCEEE-EEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 46677777788877544422 33334 899999863 99999999999998765
No 9
>PRK09256 hypothetical protein; Provisional
Probab=55.75 E-value=52 Score=24.47 Aligned_cols=49 Identities=20% Similarity=0.093 Sum_probs=33.8
Q ss_pred cceEEEecCC-----CHHHHHHHHHHhHhhhhhHHHHHhhhcccCCchHHHHHHHHHH
Q 033754 36 RGIRVKVFNG-----NLEQALSWMQRKMQSSGIERLIKREQRHHIKNSEKRVLARKNL 88 (112)
Q Consensus 36 ~gi~V~V~~g-----~IE~ALRrfKRk~~keGIl~eiK~R~~~YeKPSekRrrk~~ea 88 (112)
..++|.+.+. |.+.||.+|..++...-... ++ +--.||+..-++++.+.
T Consensus 68 g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~~~p--~~--r~~tk~~~~~~~rRl~~ 121 (138)
T PRK09256 68 GVIVIKAQEFRSQERNREDALERLVALIREALKPP--KK--RRATKPTRGSKERRLES 121 (138)
T ss_pred CcEEEEECCcCCHHHHHHHHHHHHHHHHHHHhhcc--cc--ccCCcccHHHHHHHHHH
Confidence 3588888873 99999999999999876533 22 33577876554444443
No 10
>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=55.43 E-value=11 Score=19.09 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=15.7
Q ss_pred ecCCCHHHHHHHHHHhHhhhhh
Q 033754 42 VFNGNLEQALSWMQRKMQSSGI 63 (112)
Q Consensus 42 V~~g~IE~ALRrfKRk~~keGI 63 (112)
++.|++|+|+..|.... +.|+
T Consensus 11 ~~~~~~~~a~~~~~~M~-~~g~ 31 (35)
T TIGR00756 11 CKAGRVEEALELFKEML-ERGI 31 (35)
T ss_pred HHCCCHHHHHHHHHHHH-HcCC
Confidence 46789999999998754 4453
No 11
>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=45.79 E-value=15 Score=21.72 Aligned_cols=26 Identities=27% Similarity=0.322 Sum_probs=16.2
Q ss_pred ccccccccceEEEecCCCHHHHHHHH
Q 033754 29 RHQVQQWRGIRVKVFNGNLEQALSWM 54 (112)
Q Consensus 29 ~~~v~q~~gi~V~V~~g~IE~ALRrf 54 (112)
+..+...+.+.|.+++-++|+||..+
T Consensus 7 ~~~v~~~~~vsl~~~~~~~~~~L~~l 32 (52)
T PF07660_consen 7 DDDVNGKKKVSLDVKNMSLEEALDQL 32 (52)
T ss_dssp CCCCTT-BE--EE-EEE-HHHHHHHH
T ss_pred HHHhCCCcceeEEcCCcCHHHHHHHH
Confidence 35577778888988788999999764
No 12
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=40.57 E-value=18 Score=30.41 Aligned_cols=26 Identities=19% Similarity=0.394 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHhHhhhhhHHHHHhh
Q 033754 45 GNLEQALSWMQRKMQSSGIERLIKRE 70 (112)
Q Consensus 45 g~IE~ALRrfKRk~~keGIl~eiK~R 70 (112)
|++..++..+|++|+++|++..-+++
T Consensus 104 G~l~~~~~~lk~~L~~eGlfd~~~k~ 129 (438)
T PRK00286 104 GALAAAFEQLKEKLAAEGLFDPERKK 129 (438)
T ss_pred cHHHHHHHHHHHHHHHCCCCChhhcC
Confidence 69999999999999999999877665
No 13
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=40.31 E-value=13 Score=32.76 Aligned_cols=47 Identities=15% Similarity=0.025 Sum_probs=32.4
Q ss_pred cccccccccccccceEEEecCCCHHHHHHHHHHhHhhhhhHHHHHhh
Q 033754 24 RNQCQRHQVQQWRGIRVKVFNGNLEQALSWMQRKMQSSGIERLIKRE 70 (112)
Q Consensus 24 ~~~~~~~~v~q~~gi~V~V~~g~IE~ALRrfKRk~~keGIl~eiK~R 70 (112)
++|-+++.-|-.-.-......|++-.++-.+|++|..||++.+-+++
T Consensus 83 s~Y~~rG~YQi~~~~~~p~G~G~L~~~~E~lK~kL~aEGlFd~~~Kk 129 (440)
T COG1570 83 SLYEPRGDYQIVAESMEPAGLGALYLAFEQLKAKLAAEGLFDPERKK 129 (440)
T ss_pred EEEcCCCceEEEEecCCcCChhHHHHHHHHHHHHHHhCCCcChhhcC
Confidence 34444444443322223344469999999999999999999987765
No 14
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=36.90 E-value=57 Score=21.28 Aligned_cols=32 Identities=16% Similarity=0.199 Sum_probs=25.5
Q ss_pred cccccccceEEEecCCCHHHHHHHHHHhHhhh
Q 033754 30 HQVQQWRGIRVKVFNGNLEQALSWMQRKMQSS 61 (112)
Q Consensus 30 ~~v~q~~gi~V~V~~g~IE~ALRrfKRk~~ke 61 (112)
=+++-..|++|.+...+++..|.+|...+.+-
T Consensus 72 ~~l~l~dg~~V~lg~~~~~~kl~~~~~i~~~~ 103 (117)
T PF03799_consen 72 WTLYLDDGVEVKLGRSDLAEKLQRLVKILPQL 103 (117)
T ss_dssp EEEE-SSS-EEEEESSTHHHHHHHHHHHHHCC
T ss_pred EEEEECCCcEEEEcCcCHHHHHHHHHHHHHHH
Confidence 34777789999999999999999999888754
No 15
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=36.74 E-value=37 Score=17.40 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=15.6
Q ss_pred ecCCCHHHHHHHHHHhHhhhhh
Q 033754 42 VFNGNLEQALSWMQRKMQSSGI 63 (112)
Q Consensus 42 V~~g~IE~ALRrfKRk~~keGI 63 (112)
++.|++|.|+..|....+ .||
T Consensus 12 ~~~g~~~~a~~~~~~M~~-~gv 32 (34)
T PF13812_consen 12 AKAGDPDAALQLFDEMKE-QGV 32 (34)
T ss_pred HHCCCHHHHHHHHHHHHH-hCC
Confidence 356899999999987544 564
No 16
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=34.46 E-value=16 Score=33.79 Aligned_cols=34 Identities=24% Similarity=0.477 Sum_probs=27.0
Q ss_pred ccCCCC-cccccccccccccccccccceEEEecCC
Q 033754 12 LTQPSQ-GLNLFSRNQCQRHQVQQWRGIRVKVFNG 45 (112)
Q Consensus 12 ~~~~~~-~~~~~~~~~~~~~~v~q~~gi~V~V~~g 45 (112)
+-.|.. ---+||-+.|..-.|-+|||+||.-++|
T Consensus 9 vGNPNvGKTtlFN~LTG~~q~VgNwpGvTVEkkeg 43 (653)
T COG0370 9 VGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEG 43 (653)
T ss_pred ecCCCccHHHHHHHHhccCceecCCCCeeEEEEEE
Confidence 334444 3468999999999999999999997776
No 17
>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=34.36 E-value=42 Score=21.09 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=18.6
Q ss_pred ccceEEEecCCCHHHHHHHHHH
Q 033754 35 WRGIRVKVFNGNLEQALSWMQR 56 (112)
Q Consensus 35 ~~gi~V~V~~g~IE~ALRrfKR 56 (112)
...+.+.|++.++|+|++.|++
T Consensus 44 ~~~~~ilV~~~~~~~A~~~L~~ 65 (65)
T PF13840_consen 44 EISISILVKEEDLEKAVEALHE 65 (65)
T ss_dssp SSEEEEEEEGGGHHHHHHHHHH
T ss_pred eeeEEEEEeHHHHHHHHHHhcC
Confidence 4578899999999999998864
No 18
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=33.02 E-value=67 Score=22.11 Aligned_cols=32 Identities=13% Similarity=0.367 Sum_probs=20.8
Q ss_pred ccccccceEEE-----ecCC-CHHHHHHHHHHhHhhhh
Q 033754 31 QVQQWRGIRVK-----VFNG-NLEQALSWMQRKMQSSG 62 (112)
Q Consensus 31 ~v~q~~gi~V~-----V~~g-~IE~ALRrfKRk~~keG 62 (112)
|..+-||+.+. ...+ |+|+|+.+|...-++-|
T Consensus 5 T~~~i~G~ei~yl~iv~~~~~d~d~Al~eM~e~A~~lG 42 (74)
T TIGR03884 5 TADEIPGLQLYYLGIVSTESDNVDEIVENLREKVKAKG 42 (74)
T ss_pred ecccCCCeEEEEEEEEEEecCCHHHHHHHHHHHHHHcC
Confidence 44555666543 2234 99999999987765543
No 19
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=32.51 E-value=52 Score=20.30 Aligned_cols=18 Identities=22% Similarity=0.278 Sum_probs=16.2
Q ss_pred eEEEecCCCHHHHHHHHH
Q 033754 38 IRVKVFNGNLEQALSWMQ 55 (112)
Q Consensus 38 i~V~V~~g~IE~ALRrfK 55 (112)
+.|.|.+.++|+|...+.
T Consensus 46 ~~v~V~~~d~~~A~~il~ 63 (67)
T PF09413_consen 46 VEVYVPEEDYERAREILE 63 (67)
T ss_dssp EEEEEEGGGHHHHHHHHH
T ss_pred eEEEECHHHHHHHHHHHH
Confidence 899999999999988765
No 20
>PF12854 PPR_1: PPR repeat
Probab=32.40 E-value=40 Score=18.63 Aligned_cols=15 Identities=13% Similarity=0.364 Sum_probs=12.6
Q ss_pred ecCCCHHHHHHHHHH
Q 033754 42 VFNGNLEQALSWMQR 56 (112)
Q Consensus 42 V~~g~IE~ALRrfKR 56 (112)
.+.|.+|.|++.|.+
T Consensus 18 Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 18 CKAGRVDEAFELFDE 32 (34)
T ss_pred HHCCCHHHHHHHHHh
Confidence 467899999999875
No 21
>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=31.95 E-value=43 Score=16.67 Aligned_cols=18 Identities=22% Similarity=0.272 Sum_probs=14.1
Q ss_pred ecCCCHHHHHHHHHHhHh
Q 033754 42 VFNGNLEQALSWMQRKMQ 59 (112)
Q Consensus 42 V~~g~IE~ALRrfKRk~~ 59 (112)
.+.|++|+|+..|++..+
T Consensus 11 ~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 11 CKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HccchHHHHHHHHHHHhH
Confidence 356799999999987654
No 22
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=31.48 E-value=33 Score=20.27 Aligned_cols=20 Identities=15% Similarity=0.446 Sum_probs=15.3
Q ss_pred cCCCHHHHHHHHHHhHhhhh
Q 033754 43 FNGNLEQALSWMQRKMQSSG 62 (112)
Q Consensus 43 ~~g~IE~ALRrfKRk~~keG 62 (112)
..|+++.|+..|++-++.+.
T Consensus 3 ~~~~~~~A~~~~~~~l~~~p 22 (68)
T PF14559_consen 3 KQGDYDEAIELLEKALQRNP 22 (68)
T ss_dssp HTTHHHHHHHHHHHHHHHTT
T ss_pred hccCHHHHHHHHHHHHHHCC
Confidence 46788888888888877644
No 23
>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=30.58 E-value=24 Score=30.22 Aligned_cols=26 Identities=19% Similarity=0.285 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHHhHhhhhhHHHHHhh
Q 033754 45 GNLEQALSWMQRKMQSSGIERLIKRE 70 (112)
Q Consensus 45 g~IE~ALRrfKRk~~keGIl~eiK~R 70 (112)
|++..++..+|++|+++|++..=+++
T Consensus 98 G~l~~~~~~lk~~L~~eGlfd~~~k~ 123 (432)
T TIGR00237 98 GLLQLAYEQLKEKLAAEGLFDQEYKK 123 (432)
T ss_pred HHHHHHHHHHHHHHHHCCCCCchhcC
Confidence 59999999999999999999876654
No 24
>PF02421 FeoB_N: Ferrous iron transport protein B; InterPro: IPR011619 Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [].; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0016021 integral to membrane; PDB: 3TAH_B 3B1X_A 3SS8_A 3B1W_C 3B1V_A 3LX5_A 3B1Y_A 3LX8_A 3B1Z_A 3K53_B ....
Probab=29.98 E-value=10 Score=28.40 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=23.5
Q ss_pred ccccccccccccccccccceEEEecCCC
Q 033754 19 LNLFSRNQCQRHQVQQWRGIRVKVFNGN 46 (112)
Q Consensus 19 ~~~~~~~~~~~~~v~q~~gi~V~V~~g~ 46 (112)
-.|||.+.|....|-+|||+||....|.
T Consensus 14 StLfN~Ltg~~~~v~n~pG~Tv~~~~g~ 41 (156)
T PF02421_consen 14 STLFNALTGAKQKVGNWPGTTVEKKEGI 41 (156)
T ss_dssp HHHHHHHHTTSEEEEESTTSSSEEEEEE
T ss_pred HHHHHHHHCCCceecCCCCCCeeeeeEE
Confidence 4589999999999999999999866553
No 25
>PF13041 PPR_2: PPR repeat family
Probab=29.76 E-value=52 Score=18.91 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=15.9
Q ss_pred ecCCCHHHHHHHHHHhHhhhhh
Q 033754 42 VFNGNLEQALSWMQRKMQSSGI 63 (112)
Q Consensus 42 V~~g~IE~ALRrfKRk~~keGI 63 (112)
.+.|++|+|++.|+... +.|+
T Consensus 14 ~~~~~~~~a~~l~~~M~-~~g~ 34 (50)
T PF13041_consen 14 CKAGKFEEALKLFKEMK-KRGI 34 (50)
T ss_pred HHCcCHHHHHHHHHHHH-HcCC
Confidence 35789999999998776 3343
No 26
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=28.32 E-value=45 Score=21.76 Aligned_cols=24 Identities=21% Similarity=0.133 Sum_probs=17.8
Q ss_pred cCC-CHHHHHHHHHHhHhhhhhHHH
Q 033754 43 FNG-NLEQALSWMQRKMQSSGIERL 66 (112)
Q Consensus 43 ~~g-~IE~ALRrfKRk~~keGIl~e 66 (112)
.+| |+|.|+..|...-....|-.|
T Consensus 36 ~~~Wd~~~Al~~F~~lk~~~~IP~e 60 (63)
T smart00804 36 DNNWDYERALKNFTELKSEGSIPPE 60 (63)
T ss_pred HcCCCHHHHHHHHHHHHhcCCCChh
Confidence 456 999999999987665555443
No 27
>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=28.25 E-value=51 Score=19.96 Aligned_cols=22 Identities=5% Similarity=0.206 Sum_probs=17.9
Q ss_pred ceEEEecCCCHHHHHHHHHHhH
Q 033754 37 GIRVKVFNGNLEQALSWMQRKM 58 (112)
Q Consensus 37 gi~V~V~~g~IE~ALRrfKRk~ 58 (112)
.+.+.|.+.+.+.|++.+.+.+
T Consensus 41 ~is~~V~~~~~~~a~~~Lh~~f 62 (64)
T cd04917 41 NLCFLVKEEDKDEVVQRLHSRL 62 (64)
T ss_pred EEEEEEeHHHHHHHHHHHHHHH
Confidence 5667888889999999988764
No 28
>PF11393 IcmL: Macrophage killing protein with similarity to conjugation protein; InterPro: IPR021055 IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane []. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing [].
Probab=28.10 E-value=64 Score=22.51 Aligned_cols=27 Identities=30% Similarity=0.463 Sum_probs=22.3
Q ss_pred HHHHHHHHHhHhhhhhHHHHHhhhcccC
Q 033754 48 EQALSWMQRKMQSSGIERLIKREQRHHI 75 (112)
Q Consensus 48 E~ALRrfKRk~~keGIl~eiK~R~~~Ye 75 (112)
+.+...|..-|+++|+|+.+|.+ +...
T Consensus 52 ~~g~~~f~~aL~~Sg~l~~ik~~-~l~~ 78 (108)
T PF11393_consen 52 DEGWNSFQKALQKSGILDAIKDK-RLNL 78 (108)
T ss_pred HHHHHHHHHHHHHCCCHHHHHhc-ceEE
Confidence 45677899999999999999998 6543
No 29
>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=27.59 E-value=55 Score=20.47 Aligned_cols=22 Identities=9% Similarity=0.237 Sum_probs=18.6
Q ss_pred ceEEEecCCCHHHHHHHHHHhH
Q 033754 37 GIRVKVFNGNLEQALSWMQRKM 58 (112)
Q Consensus 37 gi~V~V~~g~IE~ALRrfKRk~ 58 (112)
.|.+.|.+.+.++|++.+...+
T Consensus 43 ~is~~V~~~~~~~av~~Lh~~f 64 (66)
T cd04915 43 DVQFVVDRDDYDNAIKALHAAL 64 (66)
T ss_pred EEEEEEEHHHHHHHHHHHHHHH
Confidence 5778888889999999988765
No 30
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=27.53 E-value=54 Score=23.96 Aligned_cols=32 Identities=22% Similarity=0.196 Sum_probs=24.6
Q ss_pred ccccccccccccceEEEecCC-CHHHHHHHHHH
Q 033754 25 NQCQRHQVQQWRGIRVKVFNG-NLEQALSWMQR 56 (112)
Q Consensus 25 ~~~~~~~v~q~~gi~V~V~~g-~IE~ALRrfKR 56 (112)
.+-..-.+.+..||.|.+-++ ++|.|++.|..
T Consensus 74 iG~~a~~~l~~~GIkv~~~~~~~V~e~i~~~~~ 106 (121)
T COG1433 74 IGPNAYNALKAAGIKVYVAPGGTVEEAIKAFLE 106 (121)
T ss_pred cCHHHHHHHHHcCcEEEecCCCCHHHHHHHHhc
Confidence 333445567788999998887 99999998864
No 31
>PF02579 Nitro_FeMo-Co: Dinitrogenase iron-molybdenum cofactor; InterPro: IPR003731 This entry represents several Nif (B, X and Y) proteins, which are involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing bacteria. The nitrogenase complex catalyses the reduction of atmospheric dinitrogen to ammonia, and is composed of an iron metalloprotein (dinitrogenase reductase; homodimer of NifH; IPR000392 from INTERPRO) and a Fe-Mo metalloprotein (dinitrogenase; heterotetramer of NifD and NifK; IPR000318 from INTERPRO). The pathway for the synthesis of the Fe-Mo cofactor involves several proteins, including NifB, NifE, NifH, NifN, NifQ, NifV and NifX. NifB appears to be an iron-sulphur source for FeMo-co biosynthesis, while NifX may be associated with the mature FeMo-co, in particular with the addition of homocitrate during the last step of biosynthesis []. The NifX protein shows sequence similarity with the C terminus of NifB [], as well as to the conserved protein MTH1175 from the archaeon Methanobacterium thermoautotrophicum, which displays a ribonuclease H-like motif of three layers, alpha/beta/alpha, with a single mixed beta-sheet [].; PDB: 2QTD_A 2KLA_A 1EO1_A 1P90_A 1RDU_A 2YX6_D 1O13_A 1T3V_A 2RE2_B 2WFB_A.
Probab=27.24 E-value=77 Score=20.12 Aligned_cols=26 Identities=27% Similarity=0.332 Sum_probs=19.6
Q ss_pred cccccccceEEEe-cCCCHHHHHHHHH
Q 033754 30 HQVQQWRGIRVKV-FNGNLEQALSWMQ 55 (112)
Q Consensus 30 ~~v~q~~gi~V~V-~~g~IE~ALRrfK 55 (112)
-......||.|.. ..+++|.||..|.
T Consensus 67 ~~~L~~~gI~v~~~~~~~i~~~l~~~~ 93 (94)
T PF02579_consen 67 FRALKEAGIKVYQGAGGDIEEALEAYL 93 (94)
T ss_dssp HHHHHHTTSEEEESTSSBHHHHHHHHH
T ss_pred HHHHHHCCCEEEEcCCCCHHHHHHHHh
Confidence 3445667899988 4569999999874
No 32
>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=26.14 E-value=59 Score=18.73 Aligned_cols=23 Identities=13% Similarity=0.146 Sum_probs=19.7
Q ss_pred cceEEEecCCCHHHHHHHHHHhH
Q 033754 36 RGIRVKVFNGNLEQALSWMQRKM 58 (112)
Q Consensus 36 ~gi~V~V~~g~IE~ALRrfKRk~ 58 (112)
..+.+.|.+.+++.|++.+.+.+
T Consensus 39 ~~is~~v~~~d~~~~~~~l~~~~ 61 (63)
T cd04936 39 IKISCLIDEDDAEKAVRALHEAF 61 (63)
T ss_pred ceEEEEEeHHHHHHHHHHHHHHh
Confidence 56888898889999999988765
No 33
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=25.90 E-value=64 Score=19.69 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=13.6
Q ss_pred CHHHHHHHHHHhHhh
Q 033754 46 NLEQALSWMQRKMQS 60 (112)
Q Consensus 46 ~IE~ALRrfKRk~~k 60 (112)
++|++++.|.+++..
T Consensus 22 DLdel~r~l~~kl~~ 36 (42)
T PF12221_consen 22 DLDELFRKLQDKLGG 36 (42)
T ss_pred CHHHHHHHHHHHHhc
Confidence 999999999999864
No 34
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=25.40 E-value=1.1e+02 Score=20.59 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=26.8
Q ss_pred cccccceEEEecCCCHHHHHHHHHHhHhhhhh
Q 033754 32 VQQWRGIRVKVFNGNLEQALSWMQRKMQSSGI 63 (112)
Q Consensus 32 v~q~~gi~V~V~~g~IE~ALRrfKRk~~keGI 63 (112)
+.++-.|+|.+...|=|.|+..+..-++++|+
T Consensus 55 ~~~G~~v~i~a~G~De~~Al~~l~~~l~~~~l 86 (88)
T PRK13780 55 VGQGADITISAEGADAADAIAAIEETMKKEGL 86 (88)
T ss_pred CCCCCEEEEEEeCcCHHHHHHHHHHHHHhccc
Confidence 67788888988555999999999999987764
No 35
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=25.23 E-value=78 Score=17.88 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=16.7
Q ss_pred cCCCHHHHHHHHHHhHhhhh
Q 033754 43 FNGNLEQALSWMQRKMQSSG 62 (112)
Q Consensus 43 ~~g~IE~ALRrfKRk~~keG 62 (112)
..|+.|+|.+.|.+-++.+.
T Consensus 13 ~~G~~~~A~~~~~~~l~~~P 32 (44)
T PF13428_consen 13 RLGQPDEAERLLRRALALDP 32 (44)
T ss_pred HcCCHHHHHHHHHHHHHHCc
Confidence 45899999999999988654
No 36
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=25.08 E-value=2e+02 Score=22.70 Aligned_cols=50 Identities=18% Similarity=0.179 Sum_probs=31.4
Q ss_pred ccCCCCcccccccccccccccccccceEEEecCC-----CHHHHHHHHHHhHhhh
Q 033754 12 LTQPSQGLNLFSRNQCQRHQVQQWRGIRVKVFNG-----NLEQALSWMQRKMQSS 61 (112)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~v~q~~gi~V~V~~g-----~IE~ALRrfKRk~~ke 61 (112)
+++.+.+-|-+|-..-.-....--.||+|.+.+. |-+.|+.+|+-++..-
T Consensus 113 ~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~l~~~ 167 (200)
T TIGR03072 113 LRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADL 167 (200)
T ss_pred EECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHH
Confidence 3344444455554432222223345899998874 8899999999988654
No 37
>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=23.43 E-value=71 Score=19.71 Aligned_cols=23 Identities=4% Similarity=0.034 Sum_probs=18.4
Q ss_pred cceEEEecCCCHHHHHHHHHHhH
Q 033754 36 RGIRVKVFNGNLEQALSWMQRKM 58 (112)
Q Consensus 36 ~gi~V~V~~g~IE~ALRrfKRk~ 58 (112)
..|++.|++.+.++|++.+-..+
T Consensus 39 ~~is~vv~~~d~~~av~~LH~~f 61 (63)
T cd04920 39 LNLTFVVDEDQADGLCARLHFQL 61 (63)
T ss_pred CeEEEEEeHHHHHHHHHHHHHHH
Confidence 35777888889999999987654
No 38
>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=23.06 E-value=1e+02 Score=15.77 Aligned_cols=17 Identities=24% Similarity=0.585 Sum_probs=14.0
Q ss_pred CCCHHHHHHHHHHhHhh
Q 033754 44 NGNLEQALSWMQRKMQS 60 (112)
Q Consensus 44 ~g~IE~ALRrfKRk~~k 60 (112)
-|++|.|+.-|++-++-
T Consensus 14 ~~~~~~A~~~~~~a~~~ 30 (34)
T PF13181_consen 14 LGDYEEALEYFEKALEL 30 (34)
T ss_dssp TTSHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhh
Confidence 47999999999987653
No 39
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=22.37 E-value=1.2e+02 Score=20.47 Aligned_cols=31 Identities=16% Similarity=0.425 Sum_probs=24.7
Q ss_pred cccccccceEEEecCC-----CHHHHHHHHHHhHhh
Q 033754 30 HQVQQWRGIRVKVFNG-----NLEQALSWMQRKMQS 60 (112)
Q Consensus 30 ~~v~q~~gi~V~V~~g-----~IE~ALRrfKRk~~k 60 (112)
+.|-.+..|.|.+..| ++|.|...+++++..
T Consensus 53 g~i~~~~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~ 88 (120)
T PF02996_consen 53 GKIPDTDKVLVSLGAGYYVEMSLEEAIEFLKKRIKE 88 (120)
T ss_dssp EE-SSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHH
T ss_pred EEeCCCCEEEEEeeCCeEEEecHHHHHHHHHHHHHH
Confidence 3466677788888887 999999999998765
No 40
>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy
Probab=22.34 E-value=1.5e+02 Score=25.31 Aligned_cols=44 Identities=14% Similarity=0.142 Sum_probs=35.5
Q ss_pred hhhHHHHHhhhcccCCchHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 033754 61 SGIERLIKREQRHHIKNSEKRVLARKNLERKIRSQDLARKLKAIL 105 (112)
Q Consensus 61 eGIl~eiK~R~~~YeKPSekRrrk~~ea~rR~rkqe~~rKi~~Im 105 (112)
.++|.|+-+| ++|.+--..--+...+.-.+++.+|..++-.|+-
T Consensus 349 ~~LL~Ev~RR-r~~~~k~~~i~~~~~eeL~~l~eeE~~~Re~F~~ 392 (412)
T PF04108_consen 349 DSLLLEVERR-RAVRDKMKKIIREANEELDKLREEEQRRREAFLK 392 (412)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3488999999 8887777777777788888888888888888863
No 41
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=22.24 E-value=80 Score=21.95 Aligned_cols=33 Identities=9% Similarity=0.023 Sum_probs=24.3
Q ss_pred cccccccceEEEe-cCC-CHHHHHHHHHHhHhhhh
Q 033754 30 HQVQQWRGIRVKV-FNG-NLEQALSWMQRKMQSSG 62 (112)
Q Consensus 30 ~~v~q~~gi~V~V-~~g-~IE~ALRrfKRk~~keG 62 (112)
-...+..||.+.. ..+ +||.||..|.+.|..+.
T Consensus 77 ~~~L~~~gI~~~~~~~~~~v~eal~~l~~~~~~~~ 111 (119)
T TIGR02663 77 AAKVVAAKIHPIKVNEPESISELLERLQKMLKGNP 111 (119)
T ss_pred HHHHHHcCCeeEecCCCccHHHHHHHHHHHHcCCC
Confidence 4456667888874 333 89999999998886543
No 42
>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=21.80 E-value=78 Score=19.48 Aligned_cols=22 Identities=14% Similarity=0.250 Sum_probs=18.3
Q ss_pred ceEEEecCCCHHHHHHHHHHhH
Q 033754 37 GIRVKVFNGNLEQALSWMQRKM 58 (112)
Q Consensus 37 gi~V~V~~g~IE~ALRrfKRk~ 58 (112)
.|.+.|++.+.+.|++.+.+.+
T Consensus 42 sis~~v~~~~~~~av~~Lh~~f 63 (65)
T cd04918 42 NISLIVNDSEAEGCVQALHKSF 63 (65)
T ss_pred eEEEEEeHHHHHHHHHHHHHHH
Confidence 5777888889999999988765
No 43
>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=21.57 E-value=46 Score=20.41 Aligned_cols=22 Identities=23% Similarity=0.536 Sum_probs=18.6
Q ss_pred EecCCCHHHHHHHHHHhHhhhh
Q 033754 41 KVFNGNLEQALSWMQRKMQSSG 62 (112)
Q Consensus 41 ~V~~g~IE~ALRrfKRk~~keG 62 (112)
.+.+++++..+.++++++...|
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 4456699999999999999865
No 44
>cd08003 WGR_PARP2_like WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of human PARP-2 and similar proteins. Similar to PARP-1, PARP-2 is ubiquitously expressed and it
Probab=21.22 E-value=90 Score=21.94 Aligned_cols=29 Identities=24% Similarity=0.258 Sum_probs=23.3
Q ss_pred CHHHHHHHHHHhH-hhhhhHHHHHhhhcccCCc
Q 033754 46 NLEQALSWMQRKM-QSSGIERLIKREQRHHIKN 77 (112)
Q Consensus 46 ~IE~ALRrfKRk~-~keGIl~eiK~R~~~YeKP 77 (112)
++|.|++.|++++ +++| .++..| .-|+|+
T Consensus 63 ~l~~A~~~F~k~F~~KTg--n~W~~R-~~f~k~ 92 (103)
T cd08003 63 DLEQAKSLFEKKFLDKTK--NEWEDR-ANFEKV 92 (103)
T ss_pred CHHHHHHHHHHHHHHHhC--Cchhhc-cCCCCC
Confidence 5999999999996 5688 467778 667764
No 45
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=21.05 E-value=2.5e+02 Score=24.19 Aligned_cols=51 Identities=12% Similarity=0.168 Sum_probs=32.7
Q ss_pred ccCCCCcccccccccccccccccccceEEEecCC-----CHHHHHHHHHHhHhhhh
Q 033754 12 LTQPSQGLNLFSRNQCQRHQVQQWRGIRVKVFNG-----NLEQALSWMQRKMQSSG 62 (112)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~v~q~~gi~V~V~~g-----~IE~ALRrfKRk~~keG 62 (112)
++++|.|-|-+|...-.-...---.||+|.+.+. |-+.|+++|+.+|...-
T Consensus 228 ~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~~L~~~L~~~~ 283 (360)
T TIGR00019 228 FRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAE 283 (360)
T ss_pred EECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555554433222223345899999875 78999999999887654
No 46
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=21.04 E-value=1.6e+02 Score=20.37 Aligned_cols=31 Identities=16% Similarity=0.440 Sum_probs=23.4
Q ss_pred cccccccceEEEecCC-----CHHHHHHHHHHhHhh
Q 033754 30 HQVQQWRGIRVKVFNG-----NLEQALSWMQRKMQS 60 (112)
Q Consensus 30 ~~v~q~~gi~V~V~~g-----~IE~ALRrfKRk~~k 60 (112)
+.|.....|.|.+..| ++|.|...|++++..
T Consensus 62 ~~v~~~~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~ 97 (126)
T TIGR00293 62 AKVKDTDKVLVSIGSGYYVEKDAEEAIEFLKKRIEE 97 (126)
T ss_pred EEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHH
Confidence 3455556677777665 999999999998876
No 47
>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2.7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....
Probab=20.85 E-value=1.3e+02 Score=21.76 Aligned_cols=24 Identities=17% Similarity=0.331 Sum_probs=19.1
Q ss_pred eEEEecCCCHHHHHHHHHHhHhhh
Q 033754 38 IRVKVFNGNLEQALSWMQRKMQSS 61 (112)
Q Consensus 38 i~V~V~~g~IE~ALRrfKRk~~ke 61 (112)
....+.|+++|.|+..++..++++
T Consensus 160 fd~vi~n~~le~~~~~l~~ii~~~ 183 (183)
T PF00625_consen 160 FDYVIVNDDLEEAVKELKEIIEQE 183 (183)
T ss_dssp SSEEEECSSHHHHHHHHHHHHHHH
T ss_pred CCEEEECcCHHHHHHHHHHHHHhC
Confidence 445555779999999999988764
No 48
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=20.66 E-value=1.5e+02 Score=20.53 Aligned_cols=31 Identities=23% Similarity=0.481 Sum_probs=24.5
Q ss_pred cccccccceEEEecCC-----CHHHHHHHHHHhHhh
Q 033754 30 HQVQQWRGIRVKVFNG-----NLEQALSWMQRKMQS 60 (112)
Q Consensus 30 ~~v~q~~gi~V~V~~g-----~IE~ALRrfKRk~~k 60 (112)
+.|.-+..|.|.+..| +++.|...|+++++.
T Consensus 63 ~~i~~~~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~ 98 (129)
T cd00584 63 AKVKDTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEE 98 (129)
T ss_pred EEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHH
Confidence 4566667788888776 899999999998764
No 49
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=20.32 E-value=35 Score=20.83 Aligned_cols=20 Identities=20% Similarity=0.479 Sum_probs=17.0
Q ss_pred cCCCHHHHHHHHHHhHhhhh
Q 033754 43 FNGNLEQALSWMQRKMQSSG 62 (112)
Q Consensus 43 ~~g~IE~ALRrfKRk~~keG 62 (112)
.+++++.++.++++++...|
T Consensus 43 ~~~~l~~~i~~LR~~l~~~~ 62 (78)
T smart00862 43 DDNTLDVHISRLRKKLEDDG 62 (78)
T ss_pred ccchHHHHHHHHHHHHhcCC
Confidence 45689999999999998755
No 50
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=20.27 E-value=4.6e+02 Score=21.07 Aligned_cols=52 Identities=17% Similarity=0.164 Sum_probs=38.4
Q ss_pred EecCCCHHHHHHHHHHhHhh-------------------hhhHHHHHhhhcccCCchHHHHHHHHHHHHHH
Q 033754 41 KVFNGNLEQALSWMQRKMQS-------------------SGIERLIKREQRHHIKNSEKRVLARKNLERKI 92 (112)
Q Consensus 41 ~V~~g~IE~ALRrfKRk~~k-------------------eGIl~eiK~R~~~YeKPSekRrrk~~ea~rR~ 92 (112)
.+.+|++|..+..|+..++. +-+|.||..--.-|..||-++.-..+-+.-+.
T Consensus 56 ~~~ggdLe~~Y~~ln~~ye~s~~~A~~V~~RI~~vE~Va~ALF~EWe~EL~~Y~~~sLR~~S~~kL~~tr~ 126 (201)
T PF11172_consen 56 NFDGGDLEDKYNALNDEYESSEDAAEEVSDRIDAVEDVADALFDEWEQELDQYSNASLRRASEQKLAETRR 126 (201)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHH
Confidence 34567999999999998875 35688888877899999988855444444333
No 51
>PRK05783 hypothetical protein; Provisional
Probab=20.10 E-value=1.7e+02 Score=20.12 Aligned_cols=35 Identities=11% Similarity=0.018 Sum_probs=29.3
Q ss_pred cccccccccccceEEEecCCCHHHHHHHHHHhHhh
Q 033754 26 QCQRHQVQQWRGIRVKVFNGNLEQALSWMQRKMQS 60 (112)
Q Consensus 26 ~~~~~~v~q~~gi~V~V~~g~IE~ALRrfKRk~~k 60 (112)
++.-..|.++.-+.+.+.++|-|.|.......|++
T Consensus 32 ~~~V~~VRvGK~iel~l~~~~~e~a~~~v~~mc~~ 66 (84)
T PRK05783 32 TGNIIEVRAGKYLVFKIEANSPEEAKELALKIARE 66 (84)
T ss_pred CCCcceEEeeEEEEEEEcCCCHHHHHHHHHHHHHh
Confidence 55567789999999999878999999888888765
Done!