Query psy17134
Match_columns 89
No_of_seqs 73 out of 75
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 22:45:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17134.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17134hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0821|consensus 99.9 1.5E-24 3.3E-29 170.0 5.6 67 3-69 257-324 (326)
2 PRK00274 ksgA 16S ribosomal RN 96.5 0.0027 5.8E-08 48.0 3.4 43 5-49 228-270 (272)
3 TIGR00755 ksgA dimethyladenosi 95.2 0.026 5.6E-07 41.9 3.8 39 5-46 214-252 (253)
4 PF00398 RrnaAD: Ribosomal RNA 94.9 0.037 8.1E-07 41.5 3.8 42 5-49 221-262 (262)
5 COG0030 KsgA Dimethyladenosine 94.4 0.051 1.1E-06 42.5 3.6 32 18-49 225-256 (259)
6 PF06831 H2TH: Formamidopyrimi 93.6 0.21 4.5E-06 32.9 4.9 38 16-53 43-80 (92)
7 PTZ00338 dimethyladenosine tra 93.6 0.12 2.6E-06 40.3 4.2 34 15-49 255-288 (294)
8 COG0099 RpsM Ribosomal protein 90.5 0.31 6.7E-06 34.8 3.0 34 15-48 28-61 (121)
9 PRK14896 ksgA 16S ribosomal RN 90.3 0.46 1E-05 35.6 4.0 29 20-48 226-255 (258)
10 PRK01103 formamidopyrimidine/5 89.8 0.71 1.5E-05 35.4 4.7 39 16-54 175-213 (274)
11 TIGR03631 bact_S13 30S ribosom 89.7 0.57 1.2E-05 32.3 3.8 33 15-47 26-58 (113)
12 CHL00137 rps13 ribosomal prote 89.7 0.6 1.3E-05 32.8 3.9 34 15-48 28-61 (122)
13 PF00416 Ribosomal_S13: Riboso 89.0 0.83 1.8E-05 30.7 4.1 35 15-49 26-60 (107)
14 PRK14810 formamidopyrimidine-D 88.9 0.94 2E-05 34.9 4.9 39 16-54 174-212 (272)
15 PF05833 FbpA: Fibronectin-bin 88.6 0.52 1.1E-05 37.6 3.4 51 5-55 193-243 (455)
16 PRK05179 rpsM 30S ribosomal pr 88.3 0.81 1.7E-05 32.0 3.8 34 15-48 28-61 (122)
17 PTZ00134 40S ribosomal protein 87.7 0.93 2E-05 33.2 3.9 34 15-48 41-74 (154)
18 PF09645 F-112: F-112 protein; 86.0 0.51 1.1E-05 33.1 1.7 39 32-70 30-68 (110)
19 TIGR03629 arch_S13P archaeal r 85.7 1.2 2.6E-05 32.1 3.6 45 15-59 32-76 (144)
20 PRK04053 rps13p 30S ribosomal 85.3 1.5 3.2E-05 31.8 3.9 48 15-63 36-84 (149)
21 PRK10445 endonuclease VIII; Pr 85.3 2 4.3E-05 32.9 4.8 37 17-53 172-208 (263)
22 PRK13945 formamidopyrimidine-D 85.2 2 4.3E-05 33.2 4.8 37 17-53 185-221 (282)
23 PRK14811 formamidopyrimidine-D 85.2 2 4.4E-05 33.0 4.8 38 17-54 164-201 (269)
24 PF09713 A_thal_3526: Plant pr 83.5 0.66 1.4E-05 28.8 1.3 37 15-63 17-54 (54)
25 TIGR00577 fpg formamidopyrimid 82.5 2.7 5.9E-05 32.3 4.5 40 17-56 176-215 (272)
26 PRK04184 DNA topoisomerase VI 81.8 2 4.4E-05 36.8 3.9 41 15-55 272-312 (535)
27 COG0266 Nei Formamidopyrimidin 65.5 14 0.0003 29.4 4.6 49 17-65 176-224 (273)
28 TIGR01052 top6b DNA topoisomer 64.9 9.1 0.0002 32.5 3.7 41 15-55 263-306 (488)
29 KOG3311|consensus 61.8 7.1 0.00015 28.9 2.3 34 15-48 39-72 (152)
30 PF03486 HI0933_like: HI0933-l 59.9 15 0.00032 30.0 4.0 42 5-49 297-339 (409)
31 TIGR01589 A_thal_3526 uncharac 58.9 6.3 0.00014 24.8 1.4 33 15-59 20-52 (57)
32 PF07035 Mic1: Colon cancer-as 55.5 11 0.00025 27.6 2.5 38 13-52 60-97 (167)
33 TIGR00275 flavoprotein, HI0933 54.7 13 0.00029 29.4 2.9 35 15-49 297-331 (400)
34 PF13499 EF-hand_7: EF-hand do 51.4 35 0.00076 19.6 3.7 28 14-44 39-66 (66)
35 cd04754 Commd6 COMM_Domain con 50.8 16 0.00036 24.7 2.4 23 29-51 60-82 (86)
36 COG1389 DNA topoisomerase VI, 49.4 19 0.00041 31.4 3.1 44 15-68 272-319 (538)
37 COG0394 Wzb Protein-tyrosine-p 48.7 21 0.00045 25.0 2.8 48 9-56 41-97 (139)
38 PF01451 LMWPc: Low molecular 46.9 34 0.00075 22.7 3.6 52 4-56 37-97 (138)
39 PF02236 Viral_DNA_bi: Viral D 44.2 45 0.00098 22.3 3.8 39 15-55 11-52 (86)
40 PF13305 WHG: WHG domain; PDB: 44.1 11 0.00025 22.2 0.8 25 41-65 1-25 (81)
41 PF02662 FlpD: Methyl-viologen 41.5 49 0.0011 22.7 3.8 42 12-53 76-119 (124)
42 PHA00687 hypothetical protein 41.0 85 0.0018 19.5 4.3 49 5-59 7-55 (56)
43 COG2519 GCD14 tRNA(1-methylade 40.2 14 0.00031 29.2 1.0 68 1-73 71-138 (256)
44 PF08518 GIT_SHD: Spa2 homolog 39.8 48 0.001 18.4 2.8 20 34-53 7-27 (31)
45 PF04994 TfoX_C: TfoX C-termin 39.3 1E+02 0.0023 19.8 5.4 47 1-57 1-49 (81)
46 PF08848 DUF1818: Domain of un 36.4 32 0.00069 24.4 2.2 28 31-58 27-54 (117)
47 KOG0700|consensus 34.7 22 0.00047 29.8 1.3 27 30-56 237-263 (390)
48 COG1908 FrhD Coenzyme F420-red 34.7 82 0.0018 22.9 4.1 47 13-59 78-126 (132)
49 PRK10974 glycerol-3-phosphate 34.2 67 0.0015 25.1 3.9 29 19-49 154-182 (438)
50 PF06732 Pescadillo_N: Pescadi 33.2 24 0.00052 28.3 1.3 15 31-45 20-34 (281)
51 PRK10126 tyrosine phosphatase; 31.3 53 0.0012 22.6 2.6 52 4-56 36-96 (147)
52 cd08541 SAM_PNT-FLI-1 Sterile 30.9 29 0.00063 23.4 1.2 47 15-61 30-91 (91)
53 KOG0034|consensus 30.9 65 0.0014 23.9 3.2 31 11-44 142-173 (187)
54 PF09448 MmlI: Methylmuconolac 30.7 37 0.00081 23.8 1.8 34 31-64 9-42 (112)
55 PF14483 Cut8_M: Cut8 dimerisa 30.0 41 0.00089 19.2 1.6 18 42-59 14-31 (38)
56 PF11237 DUF3038: Protein of u 29.6 1.4E+02 0.0031 22.3 4.8 45 4-53 35-82 (171)
57 PF05381 Peptidase_C21: Tymovi 29.0 20 0.00044 25.0 0.2 28 27-54 36-63 (104)
58 KOG3877|consensus 28.9 44 0.00094 28.0 2.1 63 18-88 232-298 (393)
59 cd00051 EFh EF-hand, calcium b 28.8 93 0.002 16.0 3.2 26 15-43 36-61 (63)
60 PF08743 Nse4_C: Nse4 C-termin 28.4 47 0.001 21.6 1.9 28 21-48 57-84 (93)
61 PRK11391 etp phosphotyrosine-p 28.4 78 0.0017 21.9 3.1 42 15-56 47-96 (144)
62 PF10955 DUF2757: Protein of u 28.3 28 0.0006 23.0 0.7 23 40-62 51-73 (76)
63 PF08704 GCD14: tRNA methyltra 28.0 29 0.00063 26.7 0.9 63 1-68 17-79 (247)
64 PRK13530 arsenate reductase; P 27.8 65 0.0014 22.0 2.6 42 15-56 46-94 (133)
65 smart00555 GIT Helical motif i 27.8 1.1E+02 0.0023 16.8 3.0 21 34-54 7-28 (31)
66 PF02229 PC4: Transcriptional 27.7 31 0.00066 20.8 0.8 19 28-46 37-55 (56)
67 PF02909 TetR_C: Tetracyclin r 27.6 75 0.0016 20.5 2.7 26 38-63 10-35 (139)
68 TIGR03851 chitin_NgcE carbohyd 27.4 1E+02 0.0022 24.1 3.9 27 18-49 169-195 (450)
69 PF14841 FliG_M: FliG middle d 27.3 38 0.00081 21.4 1.2 25 5-29 32-57 (79)
70 KOG0372|consensus 27.2 29 0.00062 28.3 0.8 36 2-40 206-241 (303)
71 PF09075 STb_secrete: Heat-sta 27.2 28 0.00061 21.0 0.6 14 40-53 6-19 (48)
72 PHA00542 putative Cro-like pro 27.0 62 0.0013 20.5 2.2 35 19-53 36-77 (82)
73 PF09420 Nop16: Ribosome bioge 26.3 53 0.0012 23.4 2.0 35 14-48 122-163 (164)
74 PF04190 DUF410: Protein of un 25.7 23 0.0005 27.0 0.0 38 15-60 193-230 (260)
75 PF13174 TPR_6: Tetratricopept 25.1 95 0.0021 14.9 2.9 19 38-56 14-32 (33)
76 cd02518 GT2_SpsF SpsF is a gly 24.9 68 0.0015 22.9 2.3 26 36-61 191-231 (233)
77 PF14807 AP4E_app_platf: Adapt 24.9 48 0.001 22.7 1.5 18 31-48 1-18 (104)
78 COG1164 Oligoendopeptidase F [ 23.6 88 0.0019 27.0 3.1 35 18-52 562-597 (598)
79 smart00226 LMWPc Low molecular 23.5 1.1E+02 0.0024 20.3 3.1 53 4-56 33-92 (140)
80 PF05939 Phage_min_tail: Phage 23.0 39 0.00086 22.7 0.8 49 23-71 34-82 (109)
81 PHA02135 hypothetical protein 22.8 61 0.0013 23.1 1.7 16 42-57 76-91 (122)
82 PF08344 TRP_2: Transient rece 22.5 30 0.00066 21.9 0.1 29 17-46 30-58 (63)
83 PF02828 L27: L27 domain; Int 22.4 72 0.0016 18.7 1.7 39 15-53 7-48 (56)
84 PF10964 DUF2766: Protein of u 22.2 47 0.001 22.1 1.0 25 7-31 31-62 (79)
85 PF13232 Complex1_LYR_1: Compl 22.1 71 0.0015 18.8 1.7 21 43-63 3-23 (61)
86 cd00818 IleRS_core catalytic c 21.6 1.9E+02 0.0041 22.7 4.4 34 18-51 56-89 (338)
87 PRK11308 dppF dipeptide transp 21.5 2E+02 0.0044 22.4 4.6 45 15-61 132-179 (327)
88 TIGR03850 bind_CPR_0540 carboh 21.5 1.5E+02 0.0033 22.8 3.8 26 19-49 168-193 (437)
89 PF03819 MazG: MazG nucleotide 21.3 93 0.002 19.0 2.2 18 41-58 57-74 (74)
90 PF11090 DUF2833: Protein of u 21.3 1E+02 0.0022 20.8 2.5 31 34-64 32-66 (86)
91 PF09068 EF-hand_2: EF hand; 21.3 2.9E+02 0.0063 19.1 5.1 43 15-58 41-84 (127)
92 PF11964 SpoIIAA-like: SpoIIAA 20.9 1.2E+02 0.0026 18.8 2.7 28 33-60 9-36 (109)
No 1
>KOG0821|consensus
Probab=99.90 E-value=1.5e-24 Score=169.99 Aligned_cols=67 Identities=36% Similarity=0.648 Sum_probs=65.0
Q ss_pred ccccccCChhhH-HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCCC
Q psy17134 3 LWAILLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDI 69 (89)
Q Consensus 3 ~g~~~LFP~~~R-elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~~ 69 (89)
||++||||+++| |+|+.||++|+||||+||+|||+|||++||++|++||.++|++++||||.+|+..
T Consensus 257 rGl~TL~PeE~r~E~~~~Ll~~~~idpT~r~~~L~iEQf~~LAE~Y~E~c~~~p~~~ay~~r~~kn~e 324 (326)
T KOG0821|consen 257 RGLRTLFPEEQRLESTGRLLELADIDPTLRPRQLSIEQFKSLAEVYREMCDEDPQLFAYNFRKSKNEE 324 (326)
T ss_pred ccccccCCHHHHHHHHHHHHHHhcCCCccCceeeeHHHHHHHHHHHHHHhccChhhhhhccccccccc
Confidence 899999999999 9999999999999999999999999999999999999999999999999998753
No 2
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=96.52 E-value=0.0027 Score=48.04 Aligned_cols=43 Identities=30% Similarity=0.333 Sum_probs=34.5
Q ss_pred ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
++.+|| ..+.+.++++.+|++|+.||-+||.++|.+|+.++..
T Consensus 228 l~~~~~--~~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 228 LKNLFG--SKEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHhhcc--chHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 344555 1245678899999999999999999999999988764
No 3
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=95.24 E-value=0.026 Score=41.94 Aligned_cols=39 Identities=23% Similarity=0.273 Sum_probs=30.5
Q ss_pred ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHH
Q psy17134 5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLA 46 (89)
Q Consensus 5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~a 46 (89)
+..+||. +.+..++..+++||+.||.+||++||.+|..+
T Consensus 214 l~~~~~~---~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 214 LKQLLKA---SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred Hhhhcch---hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 3445553 23456788899999999999999999999764
No 4
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=94.86 E-value=0.037 Score=41.54 Aligned_cols=42 Identities=29% Similarity=0.392 Sum_probs=33.5
Q ss_pred ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
++.++|. +-++.+++.|||+|+.|+-+||+++|.+|...+.+
T Consensus 221 L~~~~~~---~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~k 262 (262)
T PF00398_consen 221 LKSLFPG---EQLEELLEKAGIDPNARAEELSPEQFLKLFKYLNK 262 (262)
T ss_dssp TTCTHHH---HHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHHH
T ss_pred HhhhcCH---HHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhhC
Confidence 4445553 34567778899999999999999999999988764
No 5
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=94.39 E-value=0.051 Score=42.46 Aligned_cols=32 Identities=28% Similarity=0.384 Sum_probs=29.8
Q ss_pred HHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 18 ~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
.+++..+++||+.|+-+||+++|.+|+.+++.
T Consensus 225 ~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 225 EEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred HHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 48999999999999999999999999998765
No 6
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=93.56 E-value=0.21 Score=32.91 Aligned_cols=38 Identities=24% Similarity=0.259 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134 16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~ 53 (89)
.+.|+|=.|+|+|......||-+++.+|+.+=++++++
T Consensus 43 y~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~vl~~ 80 (92)
T PF06831_consen 43 YADEILFRAGIHPERPASSLSEEELRRLHEAIKRVLRE 80 (92)
T ss_dssp HHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHH
Confidence 46788889999999999999999999999998888775
No 7
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=93.55 E-value=0.12 Score=40.29 Aligned_cols=34 Identities=21% Similarity=0.442 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
+.....|..++++ +.||-+||+++|.+|+.+..+
T Consensus 255 ~~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 255 EFIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 3445679999997 799999999999999998764
No 8
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=90.46 E-value=0.31 Score=34.82 Aligned_cols=34 Identities=18% Similarity=0.205 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
-.|.+++..|||||..|.-+||-+|+.+|-++-.
T Consensus 28 ~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~ 61 (121)
T COG0099 28 RRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61 (121)
T ss_pred HHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHH
Confidence 5688999999999999999999999999998876
No 9
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=90.28 E-value=0.46 Score=35.58 Aligned_cols=29 Identities=21% Similarity=0.148 Sum_probs=23.6
Q ss_pred HHHhc-CCCCCcccccccHHHHHHHHHHHH
Q psy17134 20 LLERA-CVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 20 Ll~~A-dVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
++..+ .++++.||.+||++||.+|+.++.
T Consensus 226 ~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~ 255 (258)
T PRK14896 226 VVEALPEELLNKRVFQLSPEEIAELANLLY 255 (258)
T ss_pred HHHHcCCCCcCCCCccCCHHHHHHHHHHHH
Confidence 34555 466899999999999999998764
No 10
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=89.77 E-value=0.71 Score=35.39 Aligned_cols=39 Identities=23% Similarity=0.140 Sum_probs=34.8
Q ss_pred HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134 16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM 54 (89)
Q Consensus 16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~ 54 (89)
.+.+.|=.|+|+|.++.-.||-+++.+|..+=++++++-
T Consensus 175 ya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~vl~~a 213 (274)
T PRK01103 175 YADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEA 213 (274)
T ss_pred HHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHHH
Confidence 467888899999999999999999999999988887764
No 11
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=89.71 E-value=0.57 Score=32.35 Aligned_cols=33 Identities=24% Similarity=0.272 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAY 47 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY 47 (89)
..|..++..+||||..+.-+||-+|+.+|..+=
T Consensus 26 ~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l 58 (113)
T TIGR03631 26 TRARKILEKAGIDPDKRVKDLTEEELNAIREEI 58 (113)
T ss_pred HHHHHHHHHhCcCcccccccCCHHHHHHHHHHH
Confidence 578899999999999999999999999999875
No 12
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=89.65 E-value=0.6 Score=32.75 Aligned_cols=34 Identities=18% Similarity=0.284 Sum_probs=31.4
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
..|..++..+||||..+.-+||-+|+.+|..+=.
T Consensus 28 ~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 61 (122)
T CHL00137 28 TSAKEILEKANIDPDIRTKDLTDEQISALREIIE 61 (122)
T ss_pred HHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHH
Confidence 5788999999999999999999999999998764
No 13
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=88.97 E-value=0.83 Score=30.75 Aligned_cols=35 Identities=9% Similarity=0.118 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
-.|..++..+||||..+--+||-+|+.+|..+-..
T Consensus 26 ~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~ 60 (107)
T PF00416_consen 26 RKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK 60 (107)
T ss_dssp HHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH
Confidence 56889999999999999999999999999987654
No 14
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=88.90 E-value=0.94 Score=34.87 Aligned_cols=39 Identities=21% Similarity=0.178 Sum_probs=34.3
Q ss_pred HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134 16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM 54 (89)
Q Consensus 16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~ 54 (89)
.+.++|=+|+|+|.++.-.||-+++.+|.++-+.++++-
T Consensus 174 ya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~vl~~a 212 (272)
T PRK14810 174 YADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREA 212 (272)
T ss_pred HHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHHHHHHH
Confidence 467788889999999999999999999999888777663
No 15
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=88.61 E-value=0.52 Score=37.59 Aligned_cols=51 Identities=22% Similarity=0.204 Sum_probs=39.1
Q ss_pred ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCC
Q psy17134 5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMP 55 (89)
Q Consensus 5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P 55 (89)
+...|+--...++.+++.+|+||+...+-+|+-+++..|+.++..++.+-.
T Consensus 193 L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~~l~~~l~ 243 (455)
T PF05833_consen 193 LSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIRELLNELE 243 (455)
T ss_dssp HHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHHHHHHHHT
T ss_pred HHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHHHhhhhcc
Confidence 334455222389999999999999999999999999999999999998654
No 16
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=88.32 E-value=0.81 Score=32.04 Aligned_cols=34 Identities=21% Similarity=0.210 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
..|..++..+||||+.+.-+||-+|+.+|..+=.
T Consensus 28 ~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~ 61 (122)
T PRK05179 28 TRAKEILAAAGIDPDTRVKDLTDEELDKIREEID 61 (122)
T ss_pred HHHHHHHHHhCcCcccccccCCHHHHHHHHHHHH
Confidence 5788999999999999999999999999998765
No 17
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=87.68 E-value=0.93 Score=33.16 Aligned_cols=34 Identities=15% Similarity=0.189 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
..|..+++.+||||+.|.-+||-+|+.+|..+=.
T Consensus 41 ~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 41 RFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred HHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence 5788999999999999999999999999988764
No 18
>PF09645 F-112: F-112 protein; InterPro: IPR018601 This entry is represented by Sulfolobus virus-like particle SSV1, p11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2VQC_A.
Probab=86.03 E-value=0.51 Score=33.15 Aligned_cols=39 Identities=15% Similarity=0.224 Sum_probs=25.2
Q ss_pred cccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCCCC
Q psy17134 32 PYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIE 70 (89)
Q Consensus 32 p~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~~~ 70 (89)
-|+.|.+---.+-.+-+.||++||+.-.|++|+.|-.-+
T Consensus 30 qfeIS~s~Ay~I~~~lr~iCe~hq~eC~~~~k~rKtv~~ 68 (110)
T PF09645_consen 30 QFEISYSRAYNIQRVLRKICEQHQDECEVQKKNRKTVFK 68 (110)
T ss_dssp HH---HHHHHHHHHHHHHHHHH-TTTEEEEE-SS-EEEE
T ss_pred HhccchhhhhHHHHHHHHHHHhCcchhhhhhccchHHHH
Confidence 345555555566677789999999999999999875543
No 19
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=85.69 E-value=1.2 Score=32.09 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccc
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYE 59 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~ 59 (89)
..|..+++.+||||+.+.-+||-+|+.+|..+=...-...|+.+.
T Consensus 32 ~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~ 76 (144)
T TIGR03629 32 RFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLL 76 (144)
T ss_pred HHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHh
Confidence 578899999999999999999999999999887663334565443
No 20
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=85.30 E-value=1.5 Score=31.84 Aligned_cols=48 Identities=19% Similarity=0.179 Sum_probs=36.9
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH-HHHhCCCccccccC
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD-MCEEMPGLYEYTLE 63 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~-~c~~~P~L~~YdyR 63 (89)
..|..+++.+||||..+.-+||-+|+.+|..+=.+ .-...|..+ ||.|
T Consensus 36 ~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~-~Nr~ 84 (149)
T PRK04053 36 RTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM-LNRR 84 (149)
T ss_pred HHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh-hccc
Confidence 56889999999999999999999999999987643 223445443 5533
No 21
>PRK10445 endonuclease VIII; Provisional
Probab=85.26 E-value=2 Score=32.93 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=34.1
Q ss_pred HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134 17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~ 53 (89)
+.|.|=.|+|+|.++.-.||-+++.+|..+=++++..
T Consensus 172 adEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~ 208 (263)
T PRK10445 172 RVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRL 208 (263)
T ss_pred HHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHH
Confidence 5778889999999999999999999999999988877
No 22
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=85.18 E-value=2 Score=33.23 Aligned_cols=37 Identities=16% Similarity=0.145 Sum_probs=34.2
Q ss_pred HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134 17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~ 53 (89)
+.|.|=.|+|+|..+.-.||-+++.+|..+=++++..
T Consensus 185 a~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~vl~~ 221 (282)
T PRK13945 185 ADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKT 221 (282)
T ss_pred HHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHH
Confidence 5678889999999999999999999999999998887
No 23
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=85.17 E-value=2 Score=33.05 Aligned_cols=38 Identities=24% Similarity=0.225 Sum_probs=34.1
Q ss_pred HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134 17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM 54 (89)
Q Consensus 17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~ 54 (89)
+.|.|=.|+|+|.++.-.||-+++.+|..+=++++..-
T Consensus 164 adEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~a 201 (269)
T PRK14811 164 ADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEA 201 (269)
T ss_pred HHHHHHHcCCCccCCcccCCHHHHHHHHHHHHHHHHHH
Confidence 57788899999999999999999999999888887763
No 24
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=83.51 E-value=0.66 Score=28.85 Aligned_cols=37 Identities=22% Similarity=0.481 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccc-cccC
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYE-YTLE 63 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~-YdyR 63 (89)
|....|.+.|+|+|.... .+++++-+++|+.|. |..|
T Consensus 17 E~v~~L~~~a~I~P~~T~------------~VW~~Le~eN~eFF~aY~~r 54 (54)
T PF09713_consen 17 ECVRALQKQANIEPVFTS------------TVWQKLEKENPEFFKAYYTR 54 (54)
T ss_pred HHHHHHHHHcCCChHHHH------------HHHHHHHHHCHHHHHHhhcC
Confidence 778888899999997653 489999999999885 5443
No 25
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.46 E-value=2.7 Score=32.30 Aligned_cols=40 Identities=20% Similarity=0.161 Sum_probs=35.5
Q ss_pred HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCC
Q psy17134 17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPG 56 (89)
Q Consensus 17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~ 56 (89)
+.|.|=.|+|+|.++.-.||-+++.+|..+=++.++.-=.
T Consensus 176 adEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~vL~~ai~ 215 (272)
T TIGR00577 176 ADEVLFRAGIHPERLANSLSKEECELLHRAIKEVLRKAIE 215 (272)
T ss_pred HHHHHHHcCCCcchhhccCCHHHHHHHHHHHHHHHHHHHH
Confidence 5678889999999999999999999999999988876444
No 26
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=81.78 E-value=2 Score=36.79 Aligned_cols=41 Identities=22% Similarity=0.382 Sum_probs=36.8
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCC
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMP 55 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P 55 (89)
..|.++++.||+||..+|-.||-++..+|.+|.+++..-.|
T Consensus 272 ~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~p 312 (535)
T PRK04184 272 KTADEILEKAGLDPNKKPKELTREELERLVEAFKKYKFMAP 312 (535)
T ss_pred HHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhccCcCC
Confidence 77899999999999999999999999999999998754444
No 27
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=65.54 E-value=14 Score=29.41 Aligned_cols=49 Identities=22% Similarity=0.194 Sum_probs=40.3
Q ss_pred HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccccccCCC
Q psy17134 17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65 (89)
Q Consensus 17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~ 65 (89)
+.|.|=+|+|+|.+.+-.||..++..|+++=+.+..+-=....+..|.-
T Consensus 176 a~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~vl~~ai~~gGtt~r~~ 224 (273)
T COG0266 176 ADEILFRAGIHPARPAGDLSLAQLALLHEAIKDVLADAIERGGTTLRDF 224 (273)
T ss_pred HHHHHHHcCCCcccCccccCHHHHHHHHHHHHHHHHHHHHhCCCcccce
Confidence 5678889999999999999999999999999988877555555555544
No 28
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=64.85 E-value=9.1 Score=32.55 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCCC---CCcccccccHHHHHHHHHHHHHHHHhCC
Q psy17134 15 QLVVSLLERACVK---PVLRPYQLSVQEFGQICLAYRDMCEEMP 55 (89)
Q Consensus 15 elt~~Ll~~AdVD---PtlRp~qLsv~ef~~Lc~aY~~~c~~~P 55 (89)
..|.++++.||++ |..+|-.||-++..+|.+|.+++.-..|
T Consensus 263 ~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~P 306 (488)
T TIGR01052 263 KKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKEMKFMAP 306 (488)
T ss_pred HHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHhcCCCCC
Confidence 7789999999999 9999999999999999999887543333
No 29
>KOG3311|consensus
Probab=61.79 E-value=7.1 Score=28.90 Aligned_cols=34 Identities=12% Similarity=0.075 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
-.|....+++|||++.|.=+||-+|+.++...-.
T Consensus 39 ~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~ 72 (152)
T KOG3311|consen 39 RYAEIVCKKADLDLTKRAGELTEEQILRILQILN 72 (152)
T ss_pred hhhhhhhhhcCcchhhhhccccHHHHHHHHHHhc
Confidence 5788899999999999999999999999998766
No 30
>PF03486 HI0933_like: HI0933-like protein; InterPro: IPR004792 This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases.; PDB: 2I0Z_A 3V76_A 2GQF_A.
Probab=59.89 E-value=15 Score=29.99 Aligned_cols=42 Identities=29% Similarity=0.387 Sum_probs=34.1
Q ss_pred ccccCChhhHHHHHHHHHhcCC-CCCcccccccHHHHHHHHHHHHH
Q psy17134 5 AILLFPKRKRQLVVSLLERACV-KPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 5 ~~~LFP~~~Relt~~Ll~~AdV-DPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
+..++|+ .++..+++.+++ ||..+.-+||-++..+|+..-+.
T Consensus 297 l~~~lp~---rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 297 LKGLLPK---RLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp HTTTS-H---HHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred HHHHhHH---HHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 3445552 799999999999 99999999999999999988654
No 31
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=58.88 E-value=6.3 Score=24.80 Aligned_cols=33 Identities=18% Similarity=0.346 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccc
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYE 59 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~ 59 (89)
|...-|++.|+|+|.-... |.+++-+++|+.|.
T Consensus 20 E~v~~L~~~a~I~P~~T~~------------VW~~LekeN~eFF~ 52 (57)
T TIGR01589 20 ETVSFLFENAGISPKFTRF------------VWYLLEKENADFFR 52 (57)
T ss_pred HHHHHHHHHcCCCchhHHH------------HHHHHHHHHHHHHH
Confidence 7788899999999976543 78888889988875
No 32
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=55.50 E-value=11 Score=27.62 Aligned_cols=38 Identities=26% Similarity=0.426 Sum_probs=34.4
Q ss_pred hHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHH
Q psy17134 13 KRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCE 52 (89)
Q Consensus 13 ~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~ 52 (89)
...+|..|+.....+|.. .||+++=++||..+|.++|+
T Consensus 60 Sk~lA~~LLs~~~~~~~~--~Ql~lDMLkRL~~~~~~iie 97 (167)
T PF07035_consen 60 SKPLACQLLSLGNQYPPA--YQLGLDMLKRLGTAYEEIIE 97 (167)
T ss_pred cHHHHHHHHHhHccChHH--HHHHHHHHHHhhhhHHHHHH
Confidence 348999999999999885 89999999999999999996
No 33
>TIGR00275 flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
Probab=54.72 E-value=13 Score=29.36 Aligned_cols=35 Identities=29% Similarity=0.378 Sum_probs=31.4
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
.++..+++.++|||..+--+||-.+..+|+..-+.
T Consensus 297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 297 RLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred HHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 58889999999999999999999999999987553
No 34
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=51.39 E-value=35 Score=19.57 Aligned_cols=28 Identities=11% Similarity=0.169 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCCCCcccccccHHHHHHHH
Q psy17134 14 RQLVVSLLERACVKPVLRPYQLSVQEFGQIC 44 (89)
Q Consensus 14 Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc 44 (89)
++.+..+|+.+|.| +.=.+|.+||..++
T Consensus 39 ~~~~~~~~~~~D~d---~dG~i~~~Ef~~~~ 66 (66)
T PF13499_consen 39 DEMIDQIFREFDTD---GDGRISFDEFLNFM 66 (66)
T ss_dssp HHHHHHHHHHHTTT---SSSSEEHHHHHHHH
T ss_pred HHHHHHHHHHhCCC---CcCCCcHHHHhccC
Confidence 38889999999998 55689999998764
No 35
>cd04754 Commd6 COMM_Domain containing protein 6. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=50.75 E-value=16 Score=24.68 Aligned_cols=23 Identities=17% Similarity=0.631 Sum_probs=19.8
Q ss_pred CcccccccHHHHHHHHHHHHHHH
Q psy17134 29 VLRPYQLSVQEFGQICLAYRDMC 51 (89)
Q Consensus 29 tlRp~qLsv~ef~~Lc~aY~~~c 51 (89)
+...++||++||.+++...+++-
T Consensus 60 ~~~~~EmTlpEFq~f~~~~~~~~ 82 (86)
T cd04754 60 VTKSFEMTIPEFQNFSRQFKEMA 82 (86)
T ss_pred cceEEEEcHHHHHHHHHHHHHHH
Confidence 44599999999999999988874
No 36
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=49.36 E-value=19 Score=31.40 Aligned_cols=44 Identities=25% Similarity=0.380 Sum_probs=37.8
Q ss_pred HHHHHHHHhcCCCCCccccccc----HHHHHHHHHHHHHHHHhCCCccccccCCCCCC
Q psy17134 15 QLVVSLLERACVKPVLRPYQLS----VQEFGQICLAYRDMCEEMPGLYEYTLEDTPGD 68 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLs----v~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~ 68 (89)
.-++++++.++.||...|-.|+ -++-.+|.+|+++ |+|+++...
T Consensus 272 ~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~----------~~fm~Pptd 319 (538)
T COG1389 272 KTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKK----------MKFMAPPTD 319 (538)
T ss_pred hhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHh----------CcccCCCcc
Confidence 5678999999999999999999 9999999999764 678877543
No 37
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=48.68 E-value=21 Score=25.04 Aligned_cols=48 Identities=23% Similarity=0.376 Sum_probs=40.9
Q ss_pred CChhhH-HHHHHHHHhcCCCCC-cccccccHHHHHH------HH-HHHHHHHHhCCC
Q psy17134 9 FPKRKR-QLVVSLLERACVKPV-LRPYQLSVQEFGQ------IC-LAYRDMCEEMPG 56 (89)
Q Consensus 9 FP~~~R-elt~~Ll~~AdVDPt-lRp~qLsv~ef~~------Lc-~aY~~~c~~~P~ 56 (89)
-|.... ..|.+.++..|||.+ .||-|++.++|.+ || .....+|...|.
T Consensus 41 ~~g~~~~~~a~~vl~e~Gid~~~~~~k~i~~~~~~~~DlIitmd~~~~~~~~~~~p~ 97 (139)
T COG0394 41 HPGEPPDPRAVEVLAEHGIDISGHRSKQLTEEDFDEFDLIITMDESNAADLCPLAPG 97 (139)
T ss_pred CCCCCCCHHHHHHHHHcCCCcCCccCccCchhhhhhCCEEEEeChHHHhhHhhcCcc
Confidence 454445 899999999999999 8999999999964 56 788899999887
No 38
>PF01451 LMWPc: Low molecular weight phosphotyrosine protein phosphatase; InterPro: IPR023485 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [, ]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 alpha-helices and 4 beta-strands forming a 3-layer alpha-beta-alpha sandwich architecture.; PDB: 3RH0_B 1JL3_B 2IPA_B 1Z2D_A 1Z2E_A 2CWD_D 2L18_A 2L17_A 2L19_A 1BVH_A ....
Probab=46.87 E-value=34 Score=22.65 Aligned_cols=52 Identities=15% Similarity=0.279 Sum_probs=39.5
Q ss_pred cccccCChhhH-HHHHHHHHhcCCCCC-cccccccHHHHHH------HH-HHHHHHHHhCCC
Q psy17134 4 WAILLFPKRKR-QLVVSLLERACVKPV-LRPYQLSVQEFGQ------IC-LAYRDMCEEMPG 56 (89)
Q Consensus 4 g~~~LFP~~~R-elt~~Ll~~AdVDPt-lRp~qLsv~ef~~------Lc-~aY~~~c~~~P~ 56 (89)
|+... |...= ..|.+.|+..|||.. .+|-+|+-+.+.+ +| ..+..+|...|+
T Consensus 37 G~~~~-~~~~~~~~a~~~l~~~gid~~~~~s~~l~~~~~~~~D~Ii~m~~~~~~~~~~~~~~ 97 (138)
T PF01451_consen 37 GTEAW-PGEPVDPRAIAVLKEHGIDISGHRSRQLTEEDLDEADLIITMDDSHREELCPLFPG 97 (138)
T ss_dssp ESSST-TTSSSTHHHHHHHHHTTSSCTTSBBCBGGHHHHHHSSEEEESSHHHHHHHHHHHGT
T ss_pred eeccc-ccccccchHHHHHHHhCCCcccceeccccccccccCCEEEEccHHHhhhhhhhcch
Confidence 44444 43323 889999999999999 8999999988775 33 356688888888
No 39
>PF02236 Viral_DNA_bi: Viral DNA-binding protein, all alpha domain; InterPro: IPR003176 This domain represents the N-terminal domain of the viral DNA-binding protein, a multi functional protein involved in DNA replication and transcription control.; GO: 0003677 DNA binding, 0006260 DNA replication, 0006351 transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ADU_A 1ADV_B 2WB0_X 2WAZ_X 1ANV_A.
Probab=44.19 E-value=45 Score=22.28 Aligned_cols=39 Identities=23% Similarity=0.238 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCCCC---cccccccHHHHHHHHHHHHHHHHhCC
Q psy17134 15 QLVVSLLERACVKPV---LRPYQLSVQEFGQICLAYRDMCEEMP 55 (89)
Q Consensus 15 elt~~Ll~~AdVDPt---lRp~qLsv~ef~~Lc~aY~~~c~~~P 55 (89)
|++..|+..-+||.. +.|.+= +-|++||.+|-.--..++
T Consensus 11 e~~~~l~e~~kvd~~~~t~lPd~~--e~~~Ki~~~~l~~~k~~~ 52 (86)
T PF02236_consen 11 ELAHKLMEKYKVDWKGFTFLPDQG--ECFRKICQTWLNEEKRGL 52 (86)
T ss_dssp HHHHHHHHHTT--HHH--S-TT----HHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHhccccccCeECCCcH--HHHHHHHHHHHHhcCcCC
Confidence 888899999999976 566654 789999999966544443
No 40
>PF13305 WHG: WHG domain; PDB: 1ZK8_B 3ON2_B 3CJD_B.
Probab=44.07 E-value=11 Score=22.22 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHhCCCccccccCCC
Q psy17134 41 GQICLAYRDMCEEMPGLYEYTLEDT 65 (89)
Q Consensus 41 ~~Lc~aY~~~c~~~P~L~~YdyR~~ 65 (89)
++++.+|-..-.++|++|.-=|...
T Consensus 1 ra~~~aY~~Fa~~~p~~f~~mf~~~ 25 (81)
T PF13305_consen 1 RAMGRAYIRFAREHPELFRLMFMSD 25 (81)
T ss_dssp HHHHHHHHHHHHHSHHHHHHHHHSC
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4789999999999999998655444
No 41
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=41.47 E-value=49 Score=22.69 Aligned_cols=42 Identities=26% Similarity=0.356 Sum_probs=36.3
Q ss_pred hhH-HHHHHHHHhcCCCCC-cccccccHHHHHHHHHHHHHHHHh
Q psy17134 12 RKR-QLVVSLLERACVKPV-LRPYQLSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 12 ~~R-elt~~Ll~~AdVDPt-lRp~qLsv~ef~~Lc~aY~~~c~~ 53 (89)
..| +.+.++|+..||+|. ++=.++|..+..+++.+-.+|-++
T Consensus 76 ~~Rv~~~k~~L~~~Gi~~eRv~~~~~~~~~~~~fa~~~~~f~~~ 119 (124)
T PF02662_consen 76 EKRVERLKKLLEELGIEPERVRLYWISAPEGKRFAEIVNEFTER 119 (124)
T ss_pred HHHHHHHHHHHHHcCCChhHeEEEEeCcccHHHHHHHHHHHHHH
Confidence 457 999999999999965 677799999999999988888765
No 42
>PHA00687 hypothetical protein
Probab=41.01 E-value=85 Score=19.49 Aligned_cols=49 Identities=20% Similarity=0.339 Sum_probs=38.0
Q ss_pred ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccc
Q psy17134 5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYE 59 (89)
Q Consensus 5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~ 59 (89)
+.+-.|++ |..||+.|.--|.+|.--|. ..+.|-.|-...-..+|++|.
T Consensus 7 vqttlppe----amrllqqaaqtpitradpla--rvkaiekatervkrqyphffk 55 (56)
T PHA00687 7 VQTTLPPE----AMRLLQQAAQTPITRADPLA--RVKAIEKATERVKRQYPHFFK 55 (56)
T ss_pred ccccCCHH----HHHHHHHHhcCCccccChHH--HHHHHHHHHHHHHHhcchhhc
Confidence 45555654 67788999999999988765 577888888888888998874
No 43
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=40.15 E-value=14 Score=29.18 Aligned_cols=68 Identities=13% Similarity=0.179 Sum_probs=54.5
Q ss_pred CcccccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCCCCchh
Q psy17134 1 MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEA 73 (89)
Q Consensus 1 ~~~g~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~~~~~~ 73 (89)
|||+...++|+. +..+...+||.|-.|-++-.+ ==+.|+.+-....-..-+|+.|+.|+..-+...+|
T Consensus 71 ~~R~tQiIyPKD----~~~I~~~~gi~pg~rVlEAGt-GSG~lt~~La~~vg~~G~v~tyE~r~d~~k~A~~N 138 (256)
T COG2519 71 MKRRTQIIYPKD----AGYIVARLGISPGSRVLEAGT-GSGALTAYLARAVGPEGHVTTYEIREDFAKTAREN 138 (256)
T ss_pred CcCCCceecCCC----HHHHHHHcCCCCCCEEEEccc-CchHHHHHHHHhhCCCceEEEEEecHHHHHHHHHH
Confidence 789999999987 778889999999999999877 33667766666677778999999999855544444
No 44
>PF08518 GIT_SHD: Spa2 homology domain (SHD) of GIT; InterPro: IPR013724 GIT proteins are signalling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase [].
Probab=39.80 E-value=48 Score=18.43 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=15.8
Q ss_pred cccHHHHHHHH-HHHHHHHHh
Q psy17134 34 QLSVQEFGQIC-LAYRDMCEE 53 (89)
Q Consensus 34 qLsv~ef~~Lc-~aY~~~c~~ 53 (89)
.||..+|..|| ++|.++-.+
T Consensus 7 ~Ls~~~F~eL~~DV~~E~~RR 27 (31)
T PF08518_consen 7 RLSNQRFEELATDVYDELDRR 27 (31)
T ss_pred hCCHHHHHHHHHHHHHHHHHh
Confidence 58899999997 588877654
No 45
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=39.26 E-value=1e+02 Score=19.76 Aligned_cols=47 Identities=15% Similarity=0.152 Sum_probs=28.5
Q ss_pred CcccccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHH--HHHHHHHHHhCCCc
Q psy17134 1 MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQI--CLAYRDMCEEMPGL 57 (89)
Q Consensus 1 ~~~g~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~L--c~aY~~~c~~~P~L 57 (89)
|+..++.|=. .---..++|..+||. |+++++.+ +.||..+....+++
T Consensus 1 ~~~~l~~LpN--ig~~~e~~L~~vGI~--------t~~~L~~~Ga~~a~~~Lk~~~~~~ 49 (81)
T PF04994_consen 1 MSNRLKDLPN--IGPKSERMLAKVGIH--------TVEDLRELGAVEAYLRLKASGPSV 49 (81)
T ss_dssp ----GCGSTT----HHHHHHHHHTT----------SHHHHHHHHHHHHHHHHHHH-TT-
T ss_pred CccchhhCCC--CCHHHHHHHHHcCCC--------CHHHHHHhCHHHHHHHHHHHCCCC
Confidence 4445555433 234567899999996 78999887 67899998887664
No 46
>PF08848 DUF1818: Domain of unknown function (DUF1818); InterPro: IPR014947 This entry represents a small family of uncharacterised cyanobacterial proteins. ; PDB: 2IT9_A 2NVN_A.
Probab=36.40 E-value=32 Score=24.44 Aligned_cols=28 Identities=21% Similarity=0.481 Sum_probs=23.1
Q ss_pred ccccccHHHHHHHHHHHHHHHHhCCCcc
Q psy17134 31 RPYQLSVQEFGQICLAYRDMCEEMPGLY 58 (89)
Q Consensus 31 Rp~qLsv~ef~~Lc~aY~~~c~~~P~L~ 58 (89)
-+++||-.||+++|..-..+.+.+-.+.
T Consensus 27 WAiELT~~E~~~f~~Ll~~L~~q~~~i~ 54 (117)
T PF08848_consen 27 WAIELTEAEFNDFCRLLQQLAEQMQAIA 54 (117)
T ss_dssp EEEEE-HHHHHHHHHHHHHHHHHHHCCH
T ss_pred hheeecHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999998876554
No 47
>KOG0700|consensus
Probab=34.70 E-value=22 Score=29.80 Aligned_cols=27 Identities=26% Similarity=0.162 Sum_probs=25.6
Q ss_pred cccccccHHHHHHHHHHHHHHHHhCCC
Q psy17134 30 LRPYQLSVQEFGQICLAYRDMCEEMPG 56 (89)
Q Consensus 30 lRp~qLsv~ef~~Lc~aY~~~c~~~P~ 56 (89)
+.++|||++|-.++-+.=++|-.+||+
T Consensus 237 ~~A~qLS~dHn~~ne~Ev~Rir~eHPd 263 (390)
T KOG0700|consen 237 LVAVQLSTDHNASNEDEVRRIRSEHPD 263 (390)
T ss_pred EEEEecChhhccccHHHHHHHHHhCCC
Confidence 589999999999999999999999994
No 48
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=34.68 E-value=82 Score=22.92 Aligned_cols=47 Identities=21% Similarity=0.311 Sum_probs=40.9
Q ss_pred hH-HHHHHHHHhcCCCCC-cccccccHHHHHHHHHHHHHHHHhCCCccc
Q psy17134 13 KR-QLVVSLLERACVKPV-LRPYQLSVQEFGQICLAYRDMCEEMPGLYE 59 (89)
Q Consensus 13 ~R-elt~~Ll~~AdVDPt-lRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~ 59 (89)
.| ++..++|..-|++|. .|-++.|..|...++++-.++.++--+|..
T Consensus 78 rR~~~lke~l~elgie~eRv~~~wiSa~E~ekf~e~~~efv~~i~~lGp 126 (132)
T COG1908 78 RRMELLKELLKELGIEPERVRVLWISAAEGEKFAETINEFVERIKELGP 126 (132)
T ss_pred HHHHHHHHHHHHhCCCcceEEEEEEehhhHHHHHHHHHHHHHHHHHhCC
Confidence 46 999999999999997 588999999999999999999887655543
No 49
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=34.16 E-value=67 Score=25.10 Aligned_cols=29 Identities=17% Similarity=0.298 Sum_probs=23.2
Q ss_pred HHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 19 SLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 19 ~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
.||+.|||+|..-| -|.+||.++|...++
T Consensus 154 dlf~~aGi~~~~~P--~Twde~~~~a~~l~~ 182 (438)
T PRK10974 154 DAFKKAGLDPEQPP--KTWQDLAAYAAKLRA 182 (438)
T ss_pred HHHHHcCCCCCCCC--CCHHHHHHHHHHHHh
Confidence 68999999875444 489999999988764
No 50
>PF06732 Pescadillo_N: Pescadillo N-terminus; InterPro: IPR010613 Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest []. ; GO: 0042254 ribosome biogenesis, 0005730 nucleolus
Probab=33.20 E-value=24 Score=28.32 Aligned_cols=15 Identities=33% Similarity=0.924 Sum_probs=12.8
Q ss_pred ccccccHHHHHHHHH
Q psy17134 31 RPYQLSVQEFGQICL 45 (89)
Q Consensus 31 Rp~qLsv~ef~~Lc~ 45 (89)
+-.|||..+|+|||-
T Consensus 20 kkLQlsl~dFRRLCI 34 (281)
T PF06732_consen 20 KKLQLSLKDFRRLCI 34 (281)
T ss_pred HHhcCCHHHHhhHHh
Confidence 446999999999994
No 51
>PRK10126 tyrosine phosphatase; Provisional
Probab=31.28 E-value=53 Score=22.57 Aligned_cols=52 Identities=13% Similarity=0.052 Sum_probs=36.6
Q ss_pred cccccCChhhH-HHHHHHHHhcCCCCC-cccccccHHHHHH------H-HHHHHHHHHhCCC
Q psy17134 4 WAILLFPKRKR-QLVVSLLERACVKPV-LRPYQLSVQEFGQ------I-CLAYRDMCEEMPG 56 (89)
Q Consensus 4 g~~~LFP~~~R-elt~~Ll~~AdVDPt-lRp~qLsv~ef~~------L-c~aY~~~c~~~P~ 56 (89)
|+....+ +.- ..|.+.++..|||.. .+|.|||-+++.+ + ...+..+|...|+
T Consensus 36 G~~~~~g-~~~~~~a~~~l~~~Gid~~~h~sr~lt~~~~~~~DlIl~Md~~~~~~l~~~~p~ 96 (147)
T PRK10126 36 GLGALVG-KGADPTAISVAAEHQLSLEGHCARQISRRLCRNYDLILTMEKRHIERLCEMAPE 96 (147)
T ss_pred eccCCCC-CCCCHHHHHHHHHcCCCcCCCccccCCHHHhccCCEEEECCHHHHHHHHHhcCc
Confidence 4444433 334 899999999999976 6999999888765 1 2345677777664
No 52
>cd08541 SAM_PNT-FLI-1 Sterile alpha motif (SAM)/Pointed domain of friend leukemia integration 1 transcription activator. SAM Pointed domain of FLI-1 (Friend Leukemia Integration) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The FLI-1 protein participates in regulation of cellular differentiation, proliferation, and survival. The Fli-1 gene was initially described in Friend virus-induced erythroleukemias as a site for virus integration. It is highly expressed in hematopoietic tissues and at lower level in lungs, heart, and ovaries. Fli-1 is a proto-oncogene implicated in Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=30.94 E-value=29 Score=23.43 Aligned_cols=47 Identities=11% Similarity=0.098 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCCCCccc-------ccccHHHHHHHHHHHH--------HHHHhCCCccccc
Q psy17134 15 QLVVSLLERACVKPVLRP-------YQLSVQEFGQICLAYR--------DMCEEMPGLYEYT 61 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp-------~qLsv~ef~~Lc~aY~--------~~c~~~P~L~~Yd 61 (89)
.-|.+-|.+.+||...=+ +.||.++|.++|-.|. ++.++.|.+-.|+
T Consensus 30 ~Wa~~ef~L~~vd~~~F~~m~Gk~LC~LskedF~~~~p~~~gdiLw~HL~~Lr~~~~~~~~~ 91 (91)
T cd08541 30 EWAIKEYGLMEIDTSFFQNMDGKELCKMNKEDFLRATSLYNTEVLLSHLSYLRESSSLAYNT 91 (91)
T ss_pred HHHHHHcCCCCCChhhccCCCHHHHHhCCHHHHHHHcCCCccHHHHHHHHHHHhCccccccC
Confidence 446667777788776544 5799999999986553 5566666665553
No 53
>KOG0034|consensus
Probab=30.92 E-value=65 Score=23.93 Aligned_cols=31 Identities=19% Similarity=0.237 Sum_probs=26.3
Q ss_pred hhhH-HHHHHHHHhcCCCCCcccccccHHHHHHHH
Q psy17134 11 KRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQIC 44 (89)
Q Consensus 11 ~~~R-elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc 44 (89)
+++| +++..+|..||.|-. =.+|.+||.++-
T Consensus 142 ~e~~~~i~d~t~~e~D~d~D---G~IsfeEf~~~v 173 (187)
T KOG0034|consen 142 DEQLEDIVDKTFEEADTDGD---GKISFEEFCKVV 173 (187)
T ss_pred HHHHHHHHHHHHHHhCCCCC---CcCcHHHHHHHH
Confidence 6888 999999999999977 568999987653
No 54
>PF09448 MmlI: Methylmuconolactone methyl-isomerase ; InterPro: IPR018566 4-methylmuconolactone methyl-isomerase (MmlI) is a short, approx 115 residue, protein of two alpha helices and four beta strands. It is involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria. The enzyme appears to be monomeric in some species [] and tetrameric in others []. The known structure shows two copies of the protein form a dimeric alpha beta barrel. ; PDB: 2IFX_A 3HDS_A 3HF5_A 3HFK_D.
Probab=30.72 E-value=37 Score=23.80 Aligned_cols=34 Identities=29% Similarity=0.529 Sum_probs=26.8
Q ss_pred ccccccHHHHHHHHHHHHHHHHhCCCccccccCC
Q psy17134 31 RPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64 (89)
Q Consensus 31 Rp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~ 64 (89)
.|--+|-+.|+.=|-.-.+|-...|+|..|.-|-
T Consensus 9 kpe~ms~e~fr~eclrh~ems~~vpgl~kYEVRL 42 (112)
T PF09448_consen 9 KPEGMSDETFRAECLRHFEMSAGVPGLHKYEVRL 42 (112)
T ss_dssp --TTS-HHHHHHHHHHHHHHCTT-TT-SEEEEEE
T ss_pred ccccCCHHHHHHHHHHHHHhhcCCCcceeeeEEE
Confidence 4667899999999999999999999999999874
No 55
>PF14483 Cut8_M: Cut8 dimerisation domain; PDB: 3Q5W_A 3Q5X_A.
Probab=30.04 E-value=41 Score=19.18 Aligned_cols=18 Identities=22% Similarity=0.527 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHhCCCccc
Q psy17134 42 QICLAYRDMCEEMPGLYE 59 (89)
Q Consensus 42 ~Lc~aY~~~c~~~P~L~~ 59 (89)
.|-..-..+|++||++..
T Consensus 14 qL~~lL~~l~~~HPei~~ 31 (38)
T PF14483_consen 14 QLQSLLQSLCERHPEIQQ 31 (38)
T ss_dssp HHHHHHHHHHHHSTHHHH
T ss_pred HHHHHHHHHHHhChhHHH
Confidence 455567789999998753
No 56
>PF11237 DUF3038: Protein of unknown function (DUF3038); InterPro: IPR021399 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=29.60 E-value=1.4e+02 Score=22.25 Aligned_cols=45 Identities=24% Similarity=0.386 Sum_probs=31.2
Q ss_pred cccccCChhhHHHHHHHHHhcCCCCCcccc---cccHHHHHHHHHHHHHHHHh
Q psy17134 4 WAILLFPKRKRQLVVSLLERACVKPVLRPY---QLSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 4 g~~~LFP~~~Relt~~Ll~~AdVDPtlRp~---qLsv~ef~~Lc~aY~~~c~~ 53 (89)
|+.+.||.. ..+-++-.-+|--|+. .||++|.++|.-.=-+|.++
T Consensus 35 ~L~~~~~nr-----V~LWrlR~~NPlRr~~~r~~L~~eearaLV~Iic~lA~~ 82 (171)
T PF11237_consen 35 GLQSIIPNR-----VELWRLRCTNPLRRSSQRKPLTVEEARALVLIICYLAKQ 82 (171)
T ss_pred CCccccccH-----HHHHHHhcCCcCcccccCCCCCHHHHHHHHHHHHHHHHH
Confidence 566777742 3455666778888877 99999999887655555444
No 57
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=28.96 E-value=20 Score=24.97 Aligned_cols=28 Identities=21% Similarity=0.395 Sum_probs=22.9
Q ss_pred CCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134 27 KPVLRPYQLSVQEFGQICLAYRDMCEEM 54 (89)
Q Consensus 27 DPtlRp~qLsv~ef~~Lc~aY~~~c~~~ 54 (89)
+|..+-+-||.+||..||..|.-.|.-+
T Consensus 36 n~ei~~~GLSTDhltaLa~~~~~~~~~h 63 (104)
T PF05381_consen 36 NPEIRTLGLSTDHLTALAYRYHFQCTFH 63 (104)
T ss_pred chhhhhcCCcHHHHHHHHHHHheEEEEE
Confidence 4567889999999999999998766543
No 58
>KOG3877|consensus
Probab=28.87 E-value=44 Score=27.95 Aligned_cols=63 Identities=13% Similarity=0.203 Sum_probs=40.0
Q ss_pred HHHHHhcCCCCCcccccccHHHHHHHHHHHHHH----HHhCCCccccccCCCCCCCCchhhhhhcCCCccccccc
Q psy17134 18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRDM----CEEMPGLYEYTLEDTPGDIEPEAVAEQEGEGDEIDFNK 88 (89)
Q Consensus 18 ~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~----c~~~P~L~~YdyR~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (89)
.+=.++-|++-...- .|-.-..+|-++|++. ...|-+|-.|+++++... ...+..=+-+|||+
T Consensus 232 ~~~Ik~rg~~~Eik~--~s~aYL~diE~~YK~~fL~e~s~h~eiL~Ydwt~~gdt------~~VVEDIErldfd~ 298 (393)
T KOG3877|consen 232 LENIKRRGNTDEIKT--VSEAYLKDIEESYKDSFLREYSNHSEILAYDWTKPGDT------DAVVEDIERLDFDF 298 (393)
T ss_pred HHHHHhcCCCcceee--hhHHHHHHHHHHHHHHHHHHHhhhhheeeeecccCCCc------hhHHHhhhhhcccc
Confidence 344555666555422 1223467888999877 456788999999998543 33344445677775
No 59
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=28.79 E-value=93 Score=16.02 Aligned_cols=26 Identities=8% Similarity=0.128 Sum_probs=15.2
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHH
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQI 43 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~L 43 (89)
+.+..+++..+.+..- .|+.++|.++
T Consensus 36 ~~~~~~~~~~~~~~~~---~l~~~ef~~~ 61 (63)
T cd00051 36 EEIDEMIREVDKDGDG---KIDFEEFLEL 61 (63)
T ss_pred HHHHHHHHHhCCCCCC---eEeHHHHHHH
Confidence 5555667766665433 3666666543
No 60
>PF08743 Nse4_C: Nse4 C-terminal; InterPro: IPR014854 Nse4 is a component of the Smc5/6 DNA repair complex. It forms interactions with Smc5 and Nse1 [].
Probab=28.40 E-value=47 Score=21.62 Aligned_cols=28 Identities=11% Similarity=0.080 Sum_probs=22.1
Q ss_pred HHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134 21 LERACVKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 21 l~~AdVDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
-...+...+.--+.|+++.|+.|+.+|.
T Consensus 57 ~~~~~~~~~q~I~~ld~~~W~~li~~~~ 84 (93)
T PF08743_consen 57 QESDNDSRSQFILSLDYEDWQELIEKYN 84 (93)
T ss_pred hhccCCCCceEEEEcCHHHHHHHHHHhC
Confidence 3445566666678999999999999986
No 61
>PRK11391 etp phosphotyrosine-protein phosphatase; Provisional
Probab=28.39 E-value=78 Score=21.88 Aligned_cols=42 Identities=7% Similarity=-0.038 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCCCC-cccccccHHHHHH------HH-HHHHHHHHhCCC
Q psy17134 15 QLVVSLLERACVKPV-LRPYQLSVQEFGQ------IC-LAYRDMCEEMPG 56 (89)
Q Consensus 15 elt~~Ll~~AdVDPt-lRp~qLsv~ef~~------Lc-~aY~~~c~~~P~ 56 (89)
..|.+.++..|+|.. .|+-|||-+++.. ++ ..+..+.+..|.
T Consensus 47 ~~a~~~l~~~Gid~~~h~s~~lt~~~~~~~DlIl~M~~~~~~~l~~~~p~ 96 (144)
T PRK11391 47 ATAADVAANHGVSLEGHAGRKLTAEMARNYDLILAMESEHIAQVTAIAPE 96 (144)
T ss_pred HHHHHHHHHcCCCcCCCccCcCCHHHHhhCCEEEECCHHHHHHHHHHCCC
Confidence 789999999999987 4999999988764 12 345566666664
No 62
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=28.27 E-value=28 Score=22.96 Aligned_cols=23 Identities=26% Similarity=0.394 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHhCCCcccccc
Q psy17134 40 FGQICLAYRDMCEEMPGLYEYTL 62 (89)
Q Consensus 40 f~~Lc~aY~~~c~~~P~L~~Ydy 62 (89)
++.||+.=++-++++|++..|++
T Consensus 51 V~~iCe~C~eaL~~nPe~~~~~~ 73 (76)
T PF10955_consen 51 VKVICEDCQEALERNPEYHEYDK 73 (76)
T ss_pred EEEecHHHHHHHHhCcchhhhhh
Confidence 56789999999999999999986
No 63
>PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []. ; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A.
Probab=28.02 E-value=29 Score=26.74 Aligned_cols=63 Identities=17% Similarity=0.360 Sum_probs=40.2
Q ss_pred CcccccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCC
Q psy17134 1 MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGD 68 (89)
Q Consensus 1 ~~~g~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~ 68 (89)
|||+-..+||+. +..++..+||-|-.|-++=.+ ==++|+.+-...+--.=.|+.|++|+..-.
T Consensus 17 l~rrtQIiYpkD----~~~I~~~l~i~pG~~VlEaGt-GSG~lt~~l~r~v~p~G~v~t~E~~~~~~~ 79 (247)
T PF08704_consen 17 LPRRTQIIYPKD----ISYILMRLDIRPGSRVLEAGT-GSGSLTHALARAVGPTGHVYTYEFREDRAE 79 (247)
T ss_dssp S-SSS----HHH----HHHHHHHTT--TT-EEEEE---TTSHHHHHHHHHHTTTSEEEEEESSHHHHH
T ss_pred ccCCcceeeCch----HHHHHHHcCCCCCCEEEEecC-CcHHHHHHHHHHhCCCeEEEccccCHHHHH
Confidence 789999999976 677888999999999998665 234556666666666678999999987543
No 64
>PRK13530 arsenate reductase; Provisional
Probab=27.83 E-value=65 Score=21.99 Aligned_cols=42 Identities=10% Similarity=0.236 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCCCCC-cccccccHHHHHH------HHHHHHHHHHhCCC
Q psy17134 15 QLVVSLLERACVKPV-LRPYQLSVQEFGQ------ICLAYRDMCEEMPG 56 (89)
Q Consensus 15 elt~~Ll~~AdVDPt-lRp~qLsv~ef~~------Lc~aY~~~c~~~P~ 56 (89)
..|.+.++..|||.. .+|-||+-+++.. +|....++|...|.
T Consensus 46 ~~a~~~l~e~Gi~~~~~~s~~l~~~~~~~~D~ii~m~~~~~~~~~~~p~ 94 (133)
T PRK13530 46 PNAIKAMKEVGIDISNQTSDIIDNDILNNADLVVTLCSHADDVCPSTPP 94 (133)
T ss_pred HHHHHHHHHcCCCcCCCccccCChhHhccCCEEEEechHhhhhccccCC
Confidence 788999999999965 7999999877765 57777788887774
No 65
>smart00555 GIT Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins. Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins, and in yeast Spa2p and Sph1p (CPP; unpublished results). In p95-APP1 the N-terminal GIT motif might be involved in binding PIX.
Probab=27.82 E-value=1.1e+02 Score=16.76 Aligned_cols=21 Identities=14% Similarity=0.202 Sum_probs=16.5
Q ss_pred cccHHHHHHH-HHHHHHHHHhC
Q psy17134 34 QLSVQEFGQI-CLAYRDMCEEM 54 (89)
Q Consensus 34 qLsv~ef~~L-c~aY~~~c~~~ 54 (89)
-|+-.+|..| .++|.++-.+.
T Consensus 7 ~L~~~~F~~L~~Dv~~El~RR~ 28 (31)
T smart00555 7 RLSDEQFQKLLTDLNDELKRRE 28 (31)
T ss_pred hcCHHHHHHHHHHHHHHHHHhh
Confidence 4788899999 68888887654
No 66
>PF02229 PC4: Transcriptional Coactivator p15 (PC4); InterPro: IPR003173 p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain []. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.; GO: 0003677 DNA binding, 0003713 transcription coactivator activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3PM7_B 2LTD_A 2LTT_B 3OBH_B 2L3A_B 2PHE_B 1PCF_B 2C62_B.
Probab=27.68 E-value=31 Score=20.78 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=14.9
Q ss_pred CCcccccccHHHHHHHHHH
Q psy17134 28 PVLRPYQLSVQEFGQICLA 46 (89)
Q Consensus 28 PtlRp~qLsv~ef~~Lc~a 46 (89)
|+..=+.|+.+||..|+.+
T Consensus 37 P~kKGIsL~~~q~~~l~~~ 55 (56)
T PF02229_consen 37 PTKKGISLTPEQWKELKEA 55 (56)
T ss_dssp EEEEEEEE-HHHHHHHHHH
T ss_pred CcCCEEEcCHHHHHHHHhh
Confidence 5666788999999999876
No 67
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline []. Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein [] involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Y30_B 3ZQL_C 2Y31_B 2Y2Z_A 2VPR_A 3B6A_A 3B6C_A 2OPT_A 2NS7_B 2NS8_C ....
Probab=27.62 E-value=75 Score=20.52 Aligned_cols=26 Identities=27% Similarity=0.314 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHhCCCccccccC
Q psy17134 38 QEFGQICLAYRDMCEEMPGLYEYTLE 63 (89)
Q Consensus 38 ~ef~~Lc~aY~~~c~~~P~L~~YdyR 63 (89)
+.+..+|.+|+....+||.+..+--.
T Consensus 10 ~~l~~~a~~~r~~~~~hP~~~~~~~~ 35 (139)
T PF02909_consen 10 ERLRALARAYRAALLRHPWLAELLLA 35 (139)
T ss_dssp HHHHHHHHHHHHHHHTSTTHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHCcCHHHHHHh
Confidence 57889999999999999999876443
No 68
>TIGR03851 chitin_NgcE carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein. Members of this protein family are the substrate-binding protein, a lipid-anchored protein of Gram-positive bacteria in all examples found so far, that include NgcE of the chitin-degrader, Streptomyces olivaceoviridis, and close homologs from other species likely to share the same function. NgcE binds both N-acetylglucosamine and the chitin dimer, N,N'-diacetylchitobiose.
Probab=27.39 E-value=1e+02 Score=24.14 Aligned_cols=27 Identities=19% Similarity=0.181 Sum_probs=21.8
Q ss_pred HHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 18 ~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
..||+.|||+|-. |.++|..+|.+-++
T Consensus 169 kdl~~~aGl~~P~-----Twde~~~~~~~l~~ 195 (450)
T TIGR03851 169 ATLFEENGWTPPK-----TWDEFLALGEEAKA 195 (450)
T ss_pred HHHHHHcCCCCCC-----CHHHHHHHHHHHHH
Confidence 3689999998432 99999999988765
No 69
>PF14841 FliG_M: FliG middle domain; PDB: 3HJL_A 3AJC_A 1LKV_X 3SOH_D 3USY_B 3USW_A.
Probab=27.34 E-value=38 Score=21.41 Aligned_cols=25 Identities=20% Similarity=0.359 Sum_probs=19.3
Q ss_pred ccccCChhhH-HHHHHHHHhcCCCCC
Q psy17134 5 AILLFPKRKR-QLVVSLLERACVKPV 29 (89)
Q Consensus 5 ~~~LFP~~~R-elt~~Ll~~AdVDPt 29 (89)
|-..||++.| +....|.+...|+|.
T Consensus 32 VL~~lp~e~r~~v~~Ria~~~~v~~~ 57 (79)
T PF14841_consen 32 VLSQLPEELRAEVVRRIARLESVSPE 57 (79)
T ss_dssp HHHTS-HHHHHHHHHHHHTCCCCSHH
T ss_pred HHHHCCHHHHHHHHHHHHccCCCCHH
Confidence 3457999999 999999888888764
No 70
>KOG0372|consensus
Probab=27.21 E-value=29 Score=28.26 Aligned_cols=36 Identities=31% Similarity=0.374 Sum_probs=31.2
Q ss_pred cccccccCChhhHHHHHHHHHhcCCCCCcccccccHHHH
Q psy17134 2 PLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEF 40 (89)
Q Consensus 2 ~~g~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef 40 (89)
|||.+-||-+ +.+.+.++.-|++--.|+.||-|+-+
T Consensus 206 PRGaGylFG~---dvv~~F~~~N~~~~I~RaHQLv~eGy 241 (303)
T KOG0372|consen 206 PRGAGYLFGE---DVVESFLEANGLSLICRAHQLVMEGY 241 (303)
T ss_pred CCCccccccH---HHHHHHHHhCChHHHHHHHHHHHhhH
Confidence 9999999985 46778889999999999999998643
No 71
>PF09075 STb_secrete: Heat-stable enterotoxin B, secretory; InterPro: IPR015160 Members of this family assume a helical secondary structure, with two alpha helices forming a disulphide cross-linked alpha-helical hairpin. The disulphide bonds are crucial for the toxic activity of the protein, and are required for maintenance of the tertiary structure, and subsequent interaction with the particulate form of guanylate cyclase, increasing cyclic GMP levels within the host intestinal epithelial cells []. ; PDB: 1EHS_A.
Probab=27.17 E-value=28 Score=21.04 Aligned_cols=14 Identities=29% Similarity=0.676 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHh
Q psy17134 40 FGQICLAYRDMCEE 53 (89)
Q Consensus 40 f~~Lc~aY~~~c~~ 53 (89)
=++||+.|+.+..+
T Consensus 6 kkdlcehyrqiake 19 (48)
T PF09075_consen 6 KKDLCEHYRQIAKE 19 (48)
T ss_dssp T-SSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 36799999988765
No 72
>PHA00542 putative Cro-like protein
Probab=26.99 E-value=62 Score=20.48 Aligned_cols=35 Identities=3% Similarity=-0.120 Sum_probs=24.4
Q ss_pred HHHHhcCCCCCcc-------cccccHHHHHHHHHHHHHHHHh
Q psy17134 19 SLLERACVKPVLR-------PYQLSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 19 ~Ll~~AdVDPtlR-------p~qLsv~ef~~Lc~aY~~~c~~ 53 (89)
++-+..||.+.+= ....+.+....||++|++.+.-
T Consensus 36 elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~~~~~~ 77 (82)
T PHA00542 36 QIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVLNLDDF 77 (82)
T ss_pred HHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHHHhchh
Confidence 3455666665431 1346889999999999998763
No 73
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=26.35 E-value=53 Score=23.38 Aligned_cols=35 Identities=14% Similarity=0.137 Sum_probs=27.9
Q ss_pred HHHHHHHHHhcC-------CCCCcccccccHHHHHHHHHHHH
Q psy17134 14 RQLVVSLLERAC-------VKPVLRPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 14 Relt~~Ll~~Ad-------VDPtlRp~qLsv~ef~~Lc~aY~ 48 (89)
++....|++.-| -|..|=+.|+|.-+++++|..|.
T Consensus 122 ~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 122 IEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred HHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 366666666555 57888999999999999999886
No 74
>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function.; PDB: 3LKU_E 2WPV_G.
Probab=25.67 E-value=23 Score=26.96 Aligned_cols=38 Identities=21% Similarity=0.395 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCcccc
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEY 60 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~Y 60 (89)
...+-|+..+.-+ +.+-|..||+.|+..++++|.+..|
T Consensus 193 nF~~lLl~t~e~~--------~~~~F~~L~~~Y~~~L~rd~~~~~~ 230 (260)
T PF04190_consen 193 NFLQLLLLTCERD--------NLPLFKKLCEKYKPSLKRDPSFKEY 230 (260)
T ss_dssp HHHHHHHHHHHHT---------HHHHHHHHHHTHH---HHHHTHHH
T ss_pred HHHHHHHHHHhcC--------cHHHHHHHHHHhCccccccHHHHHH
Confidence 5555566555554 2468999999999999999988764
No 75
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=25.06 E-value=95 Score=14.88 Aligned_cols=19 Identities=5% Similarity=0.331 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHhCCC
Q psy17134 38 QEFGQICLAYRDMCEEMPG 56 (89)
Q Consensus 38 ~ef~~Lc~aY~~~c~~~P~ 56 (89)
.++..-...|+++++++|+
T Consensus 14 g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 14 GDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp CHHHHHHHHHHHHHHHSTT
T ss_pred cCHHHHHHHHHHHHHHCcC
Confidence 4667778889999999986
No 76
>cd02518 GT2_SpsF SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration.
Probab=24.92 E-value=68 Score=22.88 Aligned_cols=26 Identities=23% Similarity=0.507 Sum_probs=16.4
Q ss_pred cHHHHHHHHHHHH---------------HHHHhCCCccccc
Q psy17134 36 SVQEFGQICLAYR---------------DMCEEMPGLYEYT 61 (89)
Q Consensus 36 sv~ef~~Lc~aY~---------------~~c~~~P~L~~Yd 61 (89)
|.++|..+-..|+ ++|++||+|+.=|
T Consensus 191 t~eD~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p~l~~~~ 231 (233)
T cd02518 191 TPEDFELIKEIYEALYPKNPDFSLEDIIELLDKNPELFEIN 231 (233)
T ss_pred CHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHhChhHHHHh
Confidence 3457777776675 4567777776533
No 77
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=24.90 E-value=48 Score=22.71 Aligned_cols=18 Identities=50% Similarity=0.988 Sum_probs=14.9
Q ss_pred ccccccHHHHHHHHHHHH
Q psy17134 31 RPYQLSVQEFGQICLAYR 48 (89)
Q Consensus 31 Rp~qLsv~ef~~Lc~aY~ 48 (89)
||-++|.+||+.+=..|.
T Consensus 1 RPl~isTeeFG~~W~s~~ 18 (104)
T PF14807_consen 1 RPLQISTEEFGQLWLSFS 18 (104)
T ss_pred CCccccHHHHHHHHHcCC
Confidence 899999999998766553
No 78
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=23.62 E-value=88 Score=26.97 Aligned_cols=35 Identities=17% Similarity=0.352 Sum_probs=30.2
Q ss_pred HHHHHhcCCCCCc-ccccccHHHHHHHHHHHHHHHH
Q psy17134 18 VSLLERACVKPVL-RPYQLSVQEFGQICLAYRDMCE 52 (89)
Q Consensus 18 ~~Ll~~AdVDPtl-Rp~qLsv~ef~~Lc~aY~~~c~ 52 (89)
.++++.+|||.++ -|.+-++..|.+.-+.|..+..
T Consensus 562 ~ell~~~GiD~~~~~~~~~a~~~~~~~ide~~~l~~ 597 (598)
T COG1164 562 LELLKIAGIDLTTPDPWEEALAEFERLIDELEELLK 597 (598)
T ss_pred HHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHHHhc
Confidence 4789999999999 7889999999999888887653
No 79
>smart00226 LMWPc Low molecular weight phosphatase family.
Probab=23.55 E-value=1.1e+02 Score=20.27 Aligned_cols=53 Identities=15% Similarity=0.173 Sum_probs=36.4
Q ss_pred cccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHH------HHHH-HHHHHHhCCC
Q psy17134 4 WAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQ------ICLA-YRDMCEEMPG 56 (89)
Q Consensus 4 g~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~------Lc~a-Y~~~c~~~P~ 56 (89)
|+....+...-..|.++++..|||..-+..+|+-+++.. +|.. .+.+|...|+
T Consensus 33 G~~~~~g~~~~~~a~~~l~~~Gid~~~~~~~l~~~~~~~~DlIv~m~~~~~~~~~~~~p~ 92 (140)
T smart00226 33 GTGAWVGGGADPRAVEVLKEHGIALSHHASQLTSSDFKNADLVLAMDHSHLRNICRLKPR 92 (140)
T ss_pred cccCCCCCCCCHHHHHHHHHcCcCccceeccCCHHHHHhCCEEEEeCHHHHHHHHHHccc
Confidence 455443322228999999999999877777999877654 2443 4577777775
No 80
>PF05939 Phage_min_tail: Phage minor tail protein; InterPro: IPR010265 This entry is represented by Bacteriophage lambda, GpM, the minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of a series of phage minor tail proteins and related sequences from several bacterial species.
Probab=23.01 E-value=39 Score=22.72 Aligned_cols=49 Identities=12% Similarity=0.142 Sum_probs=39.6
Q ss_pred hcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCCCCc
Q psy17134 23 RACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEP 71 (89)
Q Consensus 23 ~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~~~~ 71 (89)
..||++.+|...||..-=..-+.+-...+++|-+..++.|+.+......
T Consensus 34 ~~GiN~~~~~~~ltf~~~~~~~~~I~~FL~~h~G~~sF~WtpP~~~~~~ 82 (109)
T PF05939_consen 34 PDGINNKLRSWSLTFTGTEAEIRAIEAFLDRHGGVKSFLWTPPGGEKGL 82 (109)
T ss_pred hhhccccccEEEEEEEECHHHHHHHHHHHHHCCCceEEEEECCCCCEEE
Confidence 4589999999999876555556668889999999999999999776443
No 81
>PHA02135 hypothetical protein
Probab=22.78 E-value=61 Score=23.08 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHhCCCc
Q psy17134 42 QICLAYRDMCEEMPGL 57 (89)
Q Consensus 42 ~Lc~aY~~~c~~~P~L 57 (89)
.++.-|+++|.++|+=
T Consensus 76 e~~~d~r~wc~~npg~ 91 (122)
T PHA02135 76 ENNKDWRKWCRENPGK 91 (122)
T ss_pred hhhhHHHHHHhcCCCc
Confidence 4678899999999973
No 82
>PF08344 TRP_2: Transient receptor ion channel II; InterPro: IPR013555 TRP (transient receptor potential) channels can be described as tetramers formed by subunits with six transmembrane domains and containing cation-selective pores, which in several cases show high calcium permeability. The molecular architecture of TRP channels is reminiscent of voltage-gated channels and comprises six putative transmembrane segments (S1-S6), intracellular N- and C-termini, and a pore-forming reentrant loop between S5 and S6 []. TRP channels represent a superfamily conserved from worms to humans that comprise seven subfamilies []: TRPC (canonical), TRPV (vanilloid), TRPM (melastatin or long TRPs), TRPA (ankyrin), whose only member is the transmembrane protein 1, TRPP(polycystin), TRPML (mucolipin) and TRPN (Nomp-C homologues), which has a single member that can be found in worms, flies, and zebrafish. TRPs are classified essentially according to their primary amino acid sequence rather than selectivity or ligand affinity, due to their heterogenous properties and complex regulation. TRP channels are involved in many physiological functions, ranging from pure sensory functions, such as pheromone signalling, taste transduction, nociception, and temperature sensation, over homeostatic functions, such as Ca2+ and Mg2+ reabsorption and osmoregulation, to many other motile functions, such as muscle contraction and vaso-motor control []. This domain is found in Trp proteins, generally located to the C terminus of the Ankyrin repeats (IPR002110 from INTERPRO).
Probab=22.52 E-value=30 Score=21.90 Aligned_cols=29 Identities=17% Similarity=0.337 Sum_probs=22.8
Q ss_pred HHHHHHhcCCCCCcccccccHHHHHHHHHH
Q psy17134 17 VVSLLERACVKPVLRPYQLSVQEFGQICLA 46 (89)
Q Consensus 17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~a 46 (89)
+.-.+-++--||-++.|+||- +.++|+..
T Consensus 30 Spayi~Lts~DPi~~AF~Ls~-eL~~la~~ 58 (63)
T PF08344_consen 30 SPAYISLTSDDPILTAFELSW-ELRELARI 58 (63)
T ss_pred CHHHHHHcCccHHHHHHHHHH-HHHHHHHc
Confidence 345677889999999999997 67777653
No 83
>PF02828 L27: L27 domain; InterPro: IPR014775 The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein.; PDB: 1ZL8_B 1VA8_A 3LRA_A 3UIT_A 1Y74_D 1RSO_B.
Probab=22.37 E-value=72 Score=18.72 Aligned_cols=39 Identities=13% Similarity=0.152 Sum_probs=25.8
Q ss_pred HHHHHHHHhcCCC-CCccccc--ccHHHHHHHHHHHHHHHHh
Q psy17134 15 QLVVSLLERACVK-PVLRPYQ--LSVQEFGQICLAYRDMCEE 53 (89)
Q Consensus 15 elt~~Ll~~AdVD-PtlRp~q--Lsv~ef~~Lc~aY~~~c~~ 53 (89)
|+..+|-...+.+ +..+-.+ |+-.+|+.|-.||..+..+
T Consensus 7 e~L~~L~~~~~~~~~~~~eL~~lL~~p~~~aLl~~hD~va~~ 48 (56)
T PF02828_consen 7 ELLEELQSLSSASQEDAQELQQLLQSPHFQALLEVHDKVAQK 48 (56)
T ss_dssp HHHHHHHHHTSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhccCCChHHHHHHHHHHcCHHHHHHHHHHHHHHhh
Confidence 5555555555555 2222221 6778999999999998876
No 84
>PF10964 DUF2766: Protein of unknown function (DUF2766); InterPro: IPR020262 This entry contains proteins with no known function.
Probab=22.19 E-value=47 Score=22.10 Aligned_cols=25 Identities=28% Similarity=0.405 Sum_probs=18.0
Q ss_pred ccCChhhH-HHHHHHHHh------cCCCCCcc
Q psy17134 7 LLFPKRKR-QLVVSLLER------ACVKPVLR 31 (89)
Q Consensus 7 ~LFP~~~R-elt~~Ll~~------AdVDPtlR 31 (89)
..-|-+.| .++.+|=.. |+.||.++
T Consensus 31 vIAP~EvR~KM~~QLKsIdf~~hpa~~DpvT~ 62 (79)
T PF10964_consen 31 VIAPVEVRDKMASQLKSIDFSTHPAGADPVTR 62 (79)
T ss_pred HhchHHHHHHHHHHHhcCcccCCCCCCChHHH
Confidence 35688899 999987432 78888653
No 85
>PF13232 Complex1_LYR_1: Complex1_LYR-like
Probab=22.07 E-value=71 Score=18.76 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhCCCccccccC
Q psy17134 43 ICLAYRDMCEEMPGLYEYTLE 63 (89)
Q Consensus 43 Lc~aY~~~c~~~P~L~~YdyR 63 (89)
....|+.+..+-..++.|++|
T Consensus 3 vL~LYR~lLR~~~~~~~~~~r 23 (61)
T PF13232_consen 3 VLSLYRQLLREASKFPDYNFR 23 (61)
T ss_pred HHHHHHHHHHHhhhcCCcchH
Confidence 346799999999999999999
No 86
>cd00818 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases. Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=21.58 E-value=1.9e+02 Score=22.65 Aligned_cols=34 Identities=9% Similarity=0.153 Sum_probs=26.0
Q ss_pred HHHHHhcCCCCCcccccccHHHHHHHHHHHHHHH
Q psy17134 18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRDMC 51 (89)
Q Consensus 18 ~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c 51 (89)
.+..+.++++|...+.+++.++|...|..|.+.+
T Consensus 56 ~ka~k~lg~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (338)
T cd00818 56 LKVEKELGISGKKDIEKMGIAEFNAKCREFALRY 89 (338)
T ss_pred HHHHHHhCCCCCcchhhcCHHHHHHHHHHHHHHH
Confidence 3455667999999999999999988887775433
No 87
>PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional
Probab=21.55 E-value=2e+02 Score=22.38 Aligned_cols=45 Identities=13% Similarity=0.148 Sum_probs=35.7
Q ss_pred HHHHHHHHhcCCCC---CcccccccHHHHHHHHHHHHHHHHhCCCccccc
Q psy17134 15 QLVVSLLERACVKP---VLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYT 61 (89)
Q Consensus 15 elt~~Ll~~AdVDP---tlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~Yd 61 (89)
+.+.++++..|+++ ...|.+||--+-.|++-|= .+-.+|+|--.|
T Consensus 132 ~~~~~~l~~~gL~~~~~~~~p~~LSgGq~QRv~iAr--AL~~~P~lLilD 179 (327)
T PRK11308 132 EKALAMMAKVGLRPEHYDRYPHMFSGGQRQRIAIAR--ALMLDPDVVVAD 179 (327)
T ss_pred HHHHHHHHHCCCChHHhcCCCccCCHHHHHHHHHHH--HHHcCCCEEEEE
Confidence 78899999999986 6789999999999998774 344467765544
No 88
>TIGR03850 bind_CPR_0540 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family. Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1-3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus.
Probab=21.52 E-value=1.5e+02 Score=22.77 Aligned_cols=26 Identities=12% Similarity=-0.010 Sum_probs=20.9
Q ss_pred HHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134 19 SLLERACVKPVLRPYQLSVQEFGQICLAYRD 49 (89)
Q Consensus 19 ~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~ 49 (89)
.||+.+||+|- =|.++|..+|.+.++
T Consensus 168 dl~~~aG~~~P-----~Twde~~~~~~~l~~ 193 (437)
T TIGR03850 168 TLFEEKGWEVP-----TTWDEMFALGDKAKA 193 (437)
T ss_pred HHHHHcCCCCC-----CCHHHHHHHHHHHHh
Confidence 57899999753 289999999998765
No 89
>PF03819 MazG: MazG nucleotide pyrophosphohydrolase domain; InterPro: IPR004518 This domain is found in a group of prokaryotic proteins which includes Escherichia coli MazG. The domain is about 100 amino acid residues in length and contains four conserved negatively charged residues that probably form an active site or metal binding site.; PDB: 1VMG_A 2YXH_B 2OIE_B 2OIG_C 2Q4P_A 2A3Q_B 2Q9L_C 2Q5Z_B 2Q73_A 3CRC_B ....
Probab=21.33 E-value=93 Score=19.01 Aligned_cols=18 Identities=6% Similarity=0.194 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHhCCCcc
Q psy17134 41 GQICLAYRDMCEEMPGLY 58 (89)
Q Consensus 41 ~~Lc~aY~~~c~~~P~L~ 58 (89)
..+..++.++..++|.+|
T Consensus 57 ~~~~~~~~K~~~R~p~~f 74 (74)
T PF03819_consen 57 EALERKMEKLERRYPHVF 74 (74)
T ss_dssp HHHHHHHHHHHHHSGGGG
T ss_pred HHHHHHHHHHhccCCCCC
Confidence 456778899999999886
No 90
>PF11090 DUF2833: Protein of unknown function (DUF2833); InterPro: IPR020335 This entry contains proteins with no known function.
Probab=21.29 E-value=1e+02 Score=20.78 Aligned_cols=31 Identities=23% Similarity=0.461 Sum_probs=23.6
Q ss_pred cccHH---HHHHHHHHHHHHH-HhCCCccccccCC
Q psy17134 34 QLSVQ---EFGQICLAYRDMC-EEMPGLYEYTLED 64 (89)
Q Consensus 34 qLsv~---ef~~Lc~aY~~~c-~~~P~L~~YdyR~ 64 (89)
+|+-. +|.+++.-|.+.+ +.+|.|..|-|-+
T Consensus 32 ~~~~~~~~eF~k~i~~~~d~~l~~Y~~l~N~V~~~ 66 (86)
T PF11090_consen 32 SLTKKERREFRKLIKEYLDKMLKQYPVLWNFVWVG 66 (86)
T ss_pred hcCHhhhHHHHHHHHHHHHHHHHHhhheeEEEEeC
Confidence 45555 4999999998777 8899987776644
No 91
>PF09068 EF-hand_2: EF hand; InterPro: IPR015153 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=21.25 E-value=2.9e+02 Score=19.10 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCCCCcccccccHHHHHH-HHHHHHHHHHhCCCcc
Q psy17134 15 QLVVSLLERACVKPVLRPYQLSVQEFGQ-ICLAYRDMCEEMPGLY 58 (89)
Q Consensus 15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~-Lc~aY~~~c~~~P~L~ 58 (89)
....+.|+..|+....-+. |++.+... |.+.|...+++.|.+-
T Consensus 41 ~~v~~~f~~~~l~~~~d~~-l~v~~l~~~L~~iy~~l~~~~p~~~ 84 (127)
T PF09068_consen 41 SNVIEAFREHGLNQSNDSS-LSVSQLETLLSSIYEFLNKRLPTLH 84 (127)
T ss_dssp HHHHHHHHHTT---T-TSE-EEHHHHHHHHHHHHHHHHHHSTTS-
T ss_pred HHHHHHHHHcCCCcccCCC-CCHHHHHHHHHHHHHHHHHHCCCCC
Confidence 4567889999988883333 99999766 6789999999999865
No 92
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=20.94 E-value=1.2e+02 Score=18.85 Aligned_cols=28 Identities=7% Similarity=0.172 Sum_probs=23.1
Q ss_pred ccccHHHHHHHHHHHHHHHHhCCCcccc
Q psy17134 33 YQLSVQEFGQICLAYRDMCEEMPGLYEY 60 (89)
Q Consensus 33 ~qLsv~ef~~Lc~aY~~~c~~~P~L~~Y 60 (89)
-.+|.+++..+.....+.++.++.+..|
T Consensus 9 g~~t~ed~~~~~~~~~~~~~~~~~~~ll 36 (109)
T PF11964_consen 9 GKLTEEDYKELLPALEELIADHGKIRLL 36 (109)
T ss_dssp EEE-HHHHHHHHHHHHHHHTTSSSEEEE
T ss_pred eeeCHHHHHHHHHHHHHHHhcCCceEEE
Confidence 3689999999999999999988877654
Done!