Query psy1931
Match_columns 145
No_of_seqs 105 out of 198
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 19:58:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1931hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1869|consensus 100.0 5.2E-37 1.1E-41 268.3 9.6 107 1-107 1-108 (425)
2 PF08312 cwf21: cwf21 domain; 99.7 5.6E-18 1.2E-22 109.7 5.9 45 57-101 1-45 (46)
3 PF02817 E3_binding: e3 bindin 68.2 2.7 5.8E-05 26.1 0.9 19 3-21 16-34 (39)
4 PF04695 Pex14_N: Peroxisomal 66.4 8.1 0.00018 29.4 3.5 25 73-97 27-51 (136)
5 PF04361 DUF494: Protein of un 61.0 18 0.00038 28.5 4.5 25 70-94 24-48 (155)
6 PF06570 DUF1129: Protein of u 56.6 28 0.0006 27.8 5.1 32 70-101 11-42 (206)
7 PRK00117 recX recombination re 55.4 23 0.00049 26.8 4.2 30 66-95 25-54 (157)
8 PF08230 Cpl-7: Cpl-7 lysozyme 54.2 24 0.00053 22.6 3.5 23 71-93 18-40 (42)
9 PF05589 DUF768: Protein of un 53.0 36 0.00078 23.4 4.5 33 67-99 26-62 (64)
10 TIGR03142 cytochro_ccmI cytoch 52.5 47 0.001 24.4 5.4 39 63-101 39-77 (117)
11 PRK03430 hypothetical protein; 51.8 29 0.00064 27.6 4.4 26 70-95 24-49 (157)
12 PRK14137 recX recombination re 50.9 24 0.00052 28.7 3.9 27 69-95 57-83 (195)
13 PRK14136 recX recombination re 50.0 26 0.00057 30.9 4.2 27 69-95 179-205 (309)
14 PF12010 DUF3502: Domain of un 48.1 33 0.00072 25.8 4.1 30 65-94 99-130 (134)
15 PRK12516 RNA polymerase sigma 47.8 41 0.00088 26.0 4.6 46 79-124 142-187 (187)
16 PF06034 DUF919: Nucleopolyhed 46.0 40 0.00087 23.2 3.8 42 59-100 14-57 (62)
17 PF08109 Antimicrobial14: Lact 44.8 8.8 0.00019 22.9 0.4 12 14-25 1-12 (31)
18 PRK14134 recX recombination re 44.2 33 0.00071 29.2 3.9 25 71-95 80-104 (283)
19 TIGR02612 mob_myst_A mobile my 43.8 32 0.0007 26.9 3.5 28 74-101 116-143 (150)
20 PRK07668 hypothetical protein; 43.5 56 0.0012 27.9 5.1 32 70-101 11-42 (254)
21 PF05278 PEARLI-4: Arabidopsis 41.3 88 0.0019 27.2 6.0 40 55-98 192-231 (269)
22 PF10224 DUF2205: Predicted co 39.7 61 0.0013 23.2 4.1 45 52-96 8-52 (80)
23 PRK02539 hypothetical protein; 39.4 86 0.0019 22.9 4.9 70 68-140 8-83 (85)
24 PRK14135 recX recombination re 38.1 52 0.0011 26.9 4.0 25 70-94 75-99 (263)
25 PF04282 DUF438: Family of unk 37.9 62 0.0013 22.7 3.8 23 69-91 34-56 (71)
26 PLN00180 NDF6 (NDH-dependent f 37.9 52 0.0011 26.9 3.9 24 66-95 150-173 (180)
27 TIGR03182 PDH_E1_alph_y pyruva 37.7 87 0.0019 26.7 5.5 36 70-105 263-299 (315)
28 PRK12533 RNA polymerase sigma 37.5 88 0.0019 25.1 5.2 39 79-117 160-202 (216)
29 PF02037 SAP: SAP domain; Int 37.1 74 0.0016 18.8 3.6 26 67-92 4-33 (35)
30 COG0707 MurG UDP-N-acetylgluco 36.6 11 0.00023 33.2 -0.2 18 12-29 7-24 (357)
31 TIGR00012 L29 ribosomal protei 36.5 48 0.001 21.6 2.9 23 80-102 4-26 (55)
32 CHL00154 rpl29 ribosomal prote 36.0 47 0.001 22.8 2.9 23 80-102 11-33 (67)
33 PF01988 VIT1: VIT family; In 34.9 90 0.002 25.0 4.9 28 68-95 81-108 (213)
34 PF11460 DUF3007: Protein of u 34.7 98 0.0021 23.4 4.7 41 48-90 54-99 (104)
35 KOG0151|consensus 34.6 59 0.0013 32.3 4.3 44 57-100 745-789 (877)
36 PF02251 PA28_alpha: Proteasom 33.6 58 0.0012 22.2 3.1 20 84-103 3-22 (64)
37 PF00816 Histone_HNS: H-NS his 33.3 44 0.00096 23.3 2.6 28 59-86 16-43 (93)
38 PF11593 Med3: Mediator comple 33.2 38 0.00083 30.7 2.7 33 66-98 7-39 (379)
39 COG4224 Uncharacterized protei 33.1 1E+02 0.0022 22.2 4.3 33 68-101 8-40 (77)
40 cd00427 Ribosomal_L29_HIP Ribo 33.1 52 0.0011 21.4 2.7 22 80-101 5-26 (57)
41 PF07743 HSCB_C: HSCB C-termin 32.8 92 0.002 20.8 4.0 13 67-79 8-20 (78)
42 PRK13411 molecular chaperone D 32.7 1.4E+02 0.0031 28.0 6.5 46 55-100 550-595 (653)
43 PF00831 Ribosomal_L29: Riboso 32.5 37 0.0008 22.3 1.9 24 80-103 6-29 (58)
44 KOG2629|consensus 31.8 60 0.0013 28.7 3.6 24 69-92 22-45 (300)
45 PF05193 Peptidase_M16_C: Pept 31.7 1.1E+02 0.0024 21.5 4.5 29 65-93 156-184 (184)
46 PRK00306 50S ribosomal protein 31.0 66 0.0014 21.6 3.0 22 80-101 8-29 (66)
47 TIGR03181 PDH_E1_alph_x pyruva 30.8 1.3E+02 0.0027 26.1 5.4 37 69-105 275-312 (341)
48 COG2137 OraA Uncharacterized p 30.3 71 0.0015 25.7 3.6 26 70-95 38-63 (174)
49 PF04405 ScdA_N: Domain of Unk 29.8 72 0.0016 21.1 3.0 23 71-93 33-55 (56)
50 PRK05014 hscB co-chaperone Hsc 29.3 1.1E+02 0.0023 24.2 4.4 36 66-101 92-133 (171)
51 PRK10947 global DNA-binding tr 28.9 97 0.0021 24.0 4.0 23 64-86 53-75 (135)
52 PHA01750 hypothetical protein 27.6 1.2E+02 0.0026 21.6 3.9 30 68-97 43-72 (75)
53 PRK01773 hscB co-chaperone Hsc 27.1 1.1E+02 0.0025 24.3 4.2 37 65-101 93-134 (173)
54 COG1936 Predicted nucleotide k 26.5 85 0.0018 25.8 3.4 27 70-96 94-120 (180)
55 PRK14549 50S ribosomal protein 26.1 90 0.0019 21.4 3.0 22 80-101 11-32 (69)
56 PRK00461 rpmC 50S ribosomal pr 25.8 83 0.0018 22.8 2.9 22 80-101 7-28 (87)
57 COG0255 RpmC Ribosomal protein 25.3 92 0.002 21.7 3.0 25 80-104 10-34 (69)
58 PF01152 Bac_globin: Bacterial 25.0 2.2E+02 0.0048 20.1 5.1 35 65-99 82-119 (120)
59 PRK01356 hscB co-chaperone Hsc 24.9 1.7E+02 0.0038 23.0 4.9 32 68-100 94-128 (166)
60 PF13779 DUF4175: Domain of un 24.8 1.8E+02 0.0039 28.8 5.8 28 71-99 480-507 (820)
61 PLN02269 Pyruvate dehydrogenas 24.8 1.8E+02 0.004 25.7 5.5 33 71-103 291-324 (362)
62 PF00676 E1_dh: Dehydrogenase 24.6 1.1E+02 0.0024 26.0 3.9 36 69-104 255-291 (300)
63 cd02000 TPP_E1_PDC_ADC_BCADC T 24.4 1.9E+02 0.0041 24.2 5.2 33 69-101 257-290 (293)
64 PRK01631 hypothetical protein; 24.3 1.9E+02 0.0041 20.7 4.4 63 68-133 7-75 (76)
65 CHL00149 odpA pyruvate dehydro 24.2 2E+02 0.0043 25.0 5.5 36 69-104 287-323 (341)
66 PRK10328 DNA binding protein, 24.2 1.3E+02 0.0029 23.3 3.9 27 60-86 49-75 (134)
67 PF02631 RecX: RecX family; I 24.1 91 0.002 22.4 2.9 19 76-94 1-19 (121)
68 smart00513 SAP Putative DNA-bi 24.0 1.5E+02 0.0033 17.2 3.4 24 68-91 5-32 (35)
69 PF13837 Myb_DNA-bind_4: Myb/S 23.7 1.5E+02 0.0032 19.7 3.8 30 71-100 39-70 (90)
70 PF04028 DUF374: Domain of unk 23.7 27 0.00059 24.3 0.1 20 5-24 32-51 (74)
71 PF02979 NHase_alpha: Nitrile 23.6 1.7E+02 0.0037 24.2 4.7 30 64-93 4-34 (188)
72 PRK00294 hscB co-chaperone Hsc 23.6 2.1E+02 0.0045 22.8 5.1 38 64-101 92-134 (173)
73 TIGR02302 aProt_lowcomp conser 23.4 2E+02 0.0043 28.8 5.8 28 71-99 511-538 (851)
74 PF12368 DUF3650: Protein of u 22.5 74 0.0016 18.8 1.7 16 77-92 12-27 (28)
75 PF04912 Dynamitin: Dynamitin 22.5 2.5E+02 0.0055 24.6 5.9 41 60-100 94-144 (388)
76 PF13801 Metal_resist: Heavy-m 22.3 1.7E+02 0.0038 19.7 4.0 36 60-95 63-98 (125)
77 PLN02374 pyruvate dehydrogenas 21.9 2.3E+02 0.0049 25.8 5.6 35 70-104 354-389 (433)
78 PF12901 SUZ-C: SUZ-C motif; 21.8 59 0.0013 19.8 1.3 20 2-21 13-33 (34)
79 PRK03578 hscB co-chaperone Hsc 21.7 2.2E+02 0.0048 22.6 4.9 36 66-101 97-137 (176)
80 PF13373 DUF2407_C: DUF2407 C- 21.5 1.3E+02 0.0028 23.3 3.5 24 74-97 4-27 (140)
81 TIGR00718 sda_alpha L-serine d 21.5 3.1E+02 0.0066 24.1 6.1 50 54-103 6-55 (294)
82 PF08006 DUF1700: Protein of u 21.0 2.2E+02 0.0048 21.9 4.7 26 69-94 26-54 (181)
83 PF05120 GvpG: Gas vesicle pro 21.0 3.2E+02 0.0069 19.4 5.4 38 62-99 30-67 (79)
84 KOG4403|consensus 21.0 1.4E+02 0.0031 28.2 4.1 65 62-137 275-348 (575)
85 KOG2759|consensus 20.3 1.5E+02 0.0032 27.6 4.0 32 73-104 295-326 (442)
86 PF03221 HTH_Tnp_Tc5: Tc5 tran 20.2 1.5E+02 0.0032 18.5 3.0 31 64-94 3-35 (66)
87 KOG0299|consensus 20.1 1.7E+02 0.0037 27.5 4.4 70 60-132 74-144 (479)
No 1
>KOG1869|consensus
Probab=100.00 E-value=5.2e-37 Score=268.35 Aligned_cols=107 Identities=50% Similarity=0.671 Sum_probs=95.8
Q ss_pred CCCCCCCCCCCcCCCccccccccccccccccccccc-cHHHHHHhhhhcCCCCChhHHhHHhhhHHHHHHHHHHHHHHHc
Q psy1931 1 MYNGIGLTTARGSGTNGYVQRNWSLVRKTKEKTNLK-TEKDLERMDAMNNKQPNREILDHEKKRKIELQCLELQELLEEQ 79 (145)
Q Consensus 1 MYNGIGL~TaRGSGTSGyVQrNls~~~~~~~~~~~~-~~~~~~~l~~~~~rkpn~eIleHerKR~IEvk~~ELrd~LEe~ 79 (145)
|||||||+||||||||||||+|||||++++...++. ...+.+.+++...++||+.|++|++||+||+||+||++.|+++
T Consensus 1 mYNGIGL~tarGSgTnGyVQrNLs~vr~rr~~~~~~~~e~enr~~kA~l~Kkpnp~IleHerkRqIE~K~le~ee~lleq 80 (425)
T KOG1869|consen 1 MYNGIGLQTARGSGTNGYVQRNLSHVRRRRGQGPQQRGERENRIKKASLDKKPNPLILEHERKRQIELKLLELEESLLEQ 80 (425)
T ss_pred CccccccccCCCCCccchhhhhhHhhhcccCCCcccchhhHHHHHHhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999998777654 3445666777788999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhhhcCCC
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNVEKINEP 107 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~~~~~~~ 107 (145)
|+++++|+++|.++|..|+.+....++.
T Consensus 81 g~seeei~~k~~e~rknl~~~a~~~nE~ 108 (425)
T KOG1869|consen 81 GLSEEEILSKVQEDRKNLLLRAKLTNEE 108 (425)
T ss_pred hhhHHHHHHHHHHHHHhHHhhccCCccc
Confidence 9999999999999999999986434443
No 2
>PF08312 cwf21: cwf21 domain; InterPro: IPR013170 The cwf21 domain is found in proteins involved in mRNA splicing. Proteins containing this domain have been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) []. In yeast, this domain binds the protein Prp8p [], a large and highly conserved U5 snRNP protein which has been proposed as a protein cofactor at the spliceosomal catalytic centre []. The cwf21 domain is found in, amongst others, the small Cwc21p protein in yeast as well as in the much larger human ortholog SRm300 (serine/arginine repetitive matrix protein). ; PDB: 2E62_A.
Probab=99.73 E-value=5.6e-18 Score=109.73 Aligned_cols=45 Identities=51% Similarity=0.846 Sum_probs=37.8
Q ss_pred HhHHhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh
Q psy1931 57 LDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 57 leHerKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
|+|++||+|||||++|||+||++|+++++|+++|+.+|++|+++.
T Consensus 1 l~HerkR~IElk~~elrd~LEe~g~~~eeIe~kv~~~R~~L~~~~ 45 (46)
T PF08312_consen 1 LEHERKREIELKCLELRDELEEQGYSEEEIEEKVDELRKKLLEEL 45 (46)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHH--
T ss_pred ChHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhcc
Confidence 689999999999999999999999999999999999999999875
No 3
>PF02817 E3_binding: e3 binding domain; InterPro: IPR004167 A small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing this domain include the branched-chain alpha-keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of alpha-keto acids to acyl-CoA and carbon dioxide; and the E-3 binding protein of eukaryotic pyruvate dehydrogenase.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 1BBL_A 1W4H_A 1BAL_A 2WXC_A 2BTH_A 2BTG_A 2CYU_A 2EQ7_C 2EQ8_C 3RNM_E ....
Probab=68.22 E-value=2.7 Score=26.08 Aligned_cols=19 Identities=32% Similarity=0.733 Sum_probs=15.2
Q ss_pred CCCCCCCCCcCCCcccccc
Q psy1931 3 NGIGLTTARGSGTNGYVQR 21 (145)
Q Consensus 3 NGIGL~TaRGSGTSGyVQr 21 (145)
+||-|....|||..|-|.+
T Consensus 16 ~gidl~~v~gtG~~GrI~k 34 (39)
T PF02817_consen 16 LGIDLSQVKGTGPGGRITK 34 (39)
T ss_dssp TT--GGGSSSSSTTSBBCH
T ss_pred cCCCcccccccCCCCcEeH
Confidence 6899999999999998864
No 4
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=66.41 E-value=8.1 Score=29.39 Aligned_cols=25 Identities=24% Similarity=0.260 Sum_probs=16.9
Q ss_pred HHHHHHcCCCHHHHHHHHHHHHHHH
Q psy1931 73 QELLEEQGFNEIEVDAKVMAYRLHL 97 (145)
Q Consensus 73 rd~LEe~G~~eeEIe~kv~~lR~~L 97 (145)
++-|+.+|++++||++-+......-
T Consensus 27 ~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 27 IAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 4568899999999999887765543
No 5
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=60.99 E-value=18 Score=28.51 Aligned_cols=25 Identities=20% Similarity=0.302 Sum_probs=21.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYR 94 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR 94 (145)
.+|.++|++.|++++||.+-++=+-
T Consensus 24 ~~L~~~L~~aGF~~~eI~~Al~WL~ 48 (155)
T PF04361_consen 24 DDLTRELSAAGFEDEEINKALDWLE 48 (155)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4788999999999999999987653
No 6
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=56.56 E-value=28 Score=27.83 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=27.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
..++..|.+.|++|+++++-+.+.-..|++.+
T Consensus 11 ~~l~~~L~~~~~~e~~~e~~L~eil~~LleaQ 42 (206)
T PF06570_consen 11 FDLRKYLRSSGVSEEEIEELLEEILPHLLEAQ 42 (206)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 45677788889999999999999999999874
No 7
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=55.37 E-value=23 Score=26.76 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 66 ELQCLELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 66 Evk~~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
+--..||++.|...|++++.|++-|+.|..
T Consensus 25 ~~s~~el~~kL~~kg~~~~~i~~vl~~l~~ 54 (157)
T PRK00117 25 EHSRAELRRKLAAKGFSEEVIEAVLDRLKE 54 (157)
T ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 344568899999999999999988887754
No 8
>PF08230 Cpl-7: Cpl-7 lysozyme C-terminal domain; InterPro: IPR013168 This domain was originally found in the C-terminal moiety of the Cp-7 lysin (lysozyme, P19385 from SWISSPROT) encoded by Bacteriophage Cp-7. It is assumed that this domain represents a cell wall binding motif although no direct evidence has been obtained so far to support this.
Probab=54.22 E-value=24 Score=22.61 Aligned_cols=23 Identities=26% Similarity=0.343 Sum_probs=19.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHH
Q psy1931 71 ELQELLEEQGFNEIEVDAKVMAY 93 (145)
Q Consensus 71 ELrd~LEe~G~~eeEIe~kv~~l 93 (145)
|-+..|+..|++-++|+.+|+++
T Consensus 18 eRk~~L~~aGydY~~VQ~~VN~~ 40 (42)
T PF08230_consen 18 ERKKRLTAAGYDYDAVQARVNEL 40 (42)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHH
Confidence 34567899999999999999875
No 9
>PF05589 DUF768: Protein of unknown function (DUF768); InterPro: IPR008486 This family consists of several uncharacterised hypothetical proteins from Rhizobium loti (Mesorhizobium loti).
Probab=52.95 E-value=36 Score=23.44 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=25.0
Q ss_pred HHHHHHHHHH----HHcCCCHHHHHHHHHHHHHHHHH
Q psy1931 67 LQCLELQELL----EEQGFNEIEVDAKVMAYRLHLNK 99 (145)
Q Consensus 67 vk~~ELrd~L----Ee~G~~eeEIe~kv~~lR~~Ll~ 99 (145)
+.+.+|-.+| ++.|++-++|++.|....+-.+.
T Consensus 26 is~~~La~kl~adA~a~Gi~~~ei~eEvg~i~e~I~~ 62 (64)
T PF05589_consen 26 ISAAELAEKLFADAEAAGIPREEIEEEVGSIYEAILD 62 (64)
T ss_pred hhHHHHHHHHHHHHHHcCCCHHHHHHHhccHHHHHHh
Confidence 3566666655 55799999999999988776654
No 10
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=52.49 E-value=47 Score=24.42 Aligned_cols=39 Identities=21% Similarity=0.161 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh
Q psy1931 63 RKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 63 R~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
.=..-++.||..++++.-++++|-++-..++...|+++.
T Consensus 39 ~iyr~qL~ELe~d~~~G~l~~~e~~~~~~El~rrLL~d~ 77 (117)
T TIGR03142 39 AVYRDRLAELERDLAEGLLDEAEAEAARAELQRRLLADI 77 (117)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHCc
Confidence 344556778888877655899999999999999999884
No 11
>PRK03430 hypothetical protein; Validated
Probab=51.84 E-value=29 Score=27.65 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=22.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
-+|.++|.+.|++++||.+-++=|-.
T Consensus 24 ~~L~~~L~~aGF~~~eI~~AL~WLe~ 49 (157)
T PRK03430 24 DKLEDDLTDAGFHREDIYNALLWLEK 49 (157)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 47889999999999999998876543
No 12
>PRK14137 recX recombination regulator RecX; Provisional
Probab=50.93 E-value=24 Score=28.68 Aligned_cols=27 Identities=22% Similarity=0.163 Sum_probs=23.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 69 CLELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 69 ~~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
..||+++|...|++++.|+.-|+.|.+
T Consensus 57 ~~ELr~KL~~kg~~~e~Ie~vI~rL~e 83 (195)
T PRK14137 57 AAELRAKLERRSEDEALVTEVLERVQE 83 (195)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 358899999999999999998887764
No 13
>PRK14136 recX recombination regulator RecX; Provisional
Probab=49.96 E-value=26 Score=30.88 Aligned_cols=27 Identities=19% Similarity=0.019 Sum_probs=23.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 69 CLELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 69 ~~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
..||+++|...|++++.|++-|+.|.+
T Consensus 179 e~ELr~KL~kkG~~ee~IE~VIerLke 205 (309)
T PRK14136 179 RAELARKLAPYADESDSVEPLLDALER 205 (309)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 358999999999999999999988874
No 14
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=48.05 E-value=33 Score=25.80 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHcCCC--HHHHHHHHHHHH
Q psy1931 65 IELQCLELQELLEEQGFN--EIEVDAKVMAYR 94 (145)
Q Consensus 65 IEvk~~ELrd~LEe~G~~--eeEIe~kv~~lR 94 (145)
+|..+-+++++|++.|++ -+|..+++++++
T Consensus 99 ~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~ 130 (134)
T PF12010_consen 99 PEEALPEFNEKLKAAGIDKVIAELQKQLDAFL 130 (134)
T ss_pred HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHH
Confidence 678888999999999974 345555555554
No 15
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=47.76 E-value=41 Score=25.98 Aligned_cols=46 Identities=17% Similarity=0.107 Sum_probs=33.4
Q ss_pred cCCCHHHHHHHHHHHHHHHHHhhhhcCCCCCccCCCcccccCCccc
Q psy1931 79 QGFNEIEVDAKVMAYRLHLNKNVEKINEPPLDELGRVMDDTSLKFP 124 (145)
Q Consensus 79 ~G~~eeEIe~kv~~lR~~Ll~e~~~~~~~~~~~~~r~~~~~~~~f~ 124 (145)
-|+++..|...+...|++|.+..........+..++.+-++|+.|+
T Consensus 142 Lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~~~~~ 187 (187)
T PRK12516 142 CGCAVGTIKSRVNRARQRLQEILQIEGEADYGPDADSARATSRAFA 187 (187)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHHhhcccccCccchhhHHHHhhcC
Confidence 3777777788888888888887755555555666777777777774
No 16
>PF06034 DUF919: Nucleopolyhedrovirus protein of unknown function (DUF919); InterPro: IPR009265 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short baculovirus proteins of unknown function.
Probab=45.99 E-value=40 Score=23.17 Aligned_cols=42 Identities=12% Similarity=0.215 Sum_probs=29.1
Q ss_pred HHhhhHHHHHHHHHHH--HHHHcCCCHHHHHHHHHHHHHHHHHh
Q psy1931 59 HEKKRKIELQCLELQE--LLEEQGFNEIEVDAKVMAYRLHLNKN 100 (145)
Q Consensus 59 HerKR~IEvk~~ELrd--~LEe~G~~eeEIe~kv~~lR~~Ll~e 100 (145)
+..||+|+++..-++- .++..-..-.+|+.++.++|..-++-
T Consensus 14 ~~~K~~l~ik~~H~Ekl~kitK~p~El~~i~~kl~~~R~~FLn~ 57 (62)
T PF06034_consen 14 NQMKRQLTIKSQHWEKLKKITKNPKELQEIEKKLQELRQNFLNF 57 (62)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5678888888766542 22222122288999999999998876
No 17
>PF08109 Antimicrobial14: Lactocin 705 family; InterPro: IPR012517 This family consists of lactocin 705 which is a bacteriocin produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705-alpha and 705-beta) of 33 amino acid residues each. Lactocin 705 is active against several Gram-positive bacteria, including food-borne pathogens and is a good candidate to be used for biopreservation of fermented meats [].
Probab=44.83 E-value=8.8 Score=22.91 Aligned_cols=12 Identities=33% Similarity=0.578 Sum_probs=8.2
Q ss_pred CCcccccccccc
Q psy1931 14 GTNGYVQRNWSL 25 (145)
Q Consensus 14 GTSGyVQrNls~ 25 (145)
|.|||||-=-.|
T Consensus 1 gmsgyiqgipdf 12 (31)
T PF08109_consen 1 GMSGYIQGIPDF 12 (31)
T ss_pred CCcccccccHHH
Confidence 678999964433
No 18
>PRK14134 recX recombination regulator RecX; Provisional
Probab=44.22 E-value=33 Score=29.18 Aligned_cols=25 Identities=16% Similarity=0.216 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 71 ELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 71 ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
||++.|...|++++.|++-|+.|.+
T Consensus 80 Elr~KL~~k~~~~~~Ie~vI~~L~e 104 (283)
T PRK14134 80 QIKEKLYLKEYDEDAVNRVIRFLKE 104 (283)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 8999999999999999998888763
No 19
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=43.81 E-value=32 Score=26.92 Aligned_cols=28 Identities=25% Similarity=0.266 Sum_probs=25.5
Q ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHHhh
Q psy1931 74 ELLEEQGFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 74 d~LEe~G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
-.||+|+++.+++++.+.++=+.|+.+.
T Consensus 116 m~le~q~~~~~~~~~~~~~~~~e~~~~~ 143 (150)
T TIGR02612 116 MALEDQATSKNRTEAEVEALTSELLREM 143 (150)
T ss_pred hhHHhhcCCHHHHHHHHHHHHHHHHHhC
Confidence 5789999999999999999999998873
No 20
>PRK07668 hypothetical protein; Validated
Probab=43.51 E-value=56 Score=27.91 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=27.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
.+|+..|...|++|+|+++-+++....|++.+
T Consensus 11 ~~L~~yL~~~glseeeieeiL~Ei~~hLlEgQ 42 (254)
T PRK07668 11 DDTRVYLIAKGIKEEDIESFLEDAELHLIEGE 42 (254)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Confidence 45667777889999999999999999998864
No 21
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=41.28 E-value=88 Score=27.17 Aligned_cols=40 Identities=35% Similarity=0.390 Sum_probs=27.2
Q ss_pred hHHhHHhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy1931 55 EILDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLN 98 (145)
Q Consensus 55 eIleHerKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll 98 (145)
.......+|+|+++..||...+|+- ++.++++.++++++.
T Consensus 192 e~eke~~~r~l~~~~~ELe~~~EeL----~~~Eke~~e~~~~i~ 231 (269)
T PF05278_consen 192 EEEKEEKDRKLELKKEELEELEEEL----KQKEKEVKEIKERIT 231 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 4556678899999999998888774 444445555544443
No 22
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=39.74 E-value=61 Score=23.18 Aligned_cols=45 Identities=27% Similarity=0.240 Sum_probs=33.1
Q ss_pred CChhHHhHHhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy1931 52 PNREILDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLH 96 (145)
Q Consensus 52 pn~eIleHerKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~ 96 (145)
++-+-++++.+-++--++.+|++.|.+-=---+++.+.|+.|+..
T Consensus 8 ~d~e~~~~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~E 52 (80)
T PF10224_consen 8 EDIEKLEKEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESE 52 (80)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445667888888999999999999987321236777777777743
No 23
>PRK02539 hypothetical protein; Provisional
Probab=39.38 E-value=86 Score=22.92 Aligned_cols=70 Identities=17% Similarity=0.149 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhhh------cCCCCCccCCCcccccCCcccchhhhhhhhccccCCC
Q psy1931 68 QCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEK------INEPPLDELGRVMDDTSLKFPLLQKWQRLSHECEGHP 140 (145)
Q Consensus 68 k~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~~~------~~~~~~~~~~r~~~~~~~~f~~~q~~~~~~~~~~~~~ 140 (145)
++-||--+=.+.|++++|..++ ..||+..++..-. -+-...++-|-.+.+. +....|.+..|.+..-..|
T Consensus 8 RINeLakK~K~~gLT~eEk~Eq-~~LR~eYl~~fR~~~~~~L~~i~ivD~~G~dVTP~--Klk~~q~~~~l~~~~~~~~ 83 (85)
T PRK02539 8 RINELAKKKKTEGLTGEEKVEQ-AKLREEYIEGYRRSVRHHIEGIKIVDEEGNDVTPE--KLRQVQREKGLHGRSLDDP 83 (85)
T ss_pred HHHHHHHHhcccCCCHHHHHHH-HHHHHHHHHHHHHHHHHHhccceEECCCCCCCCHH--HHHHHHHHhCcccCCCCCC
Confidence 3456666656789999998876 4566665554211 1122445556555555 7888888888876553333
No 24
>PRK14135 recX recombination regulator RecX; Provisional
Probab=38.09 E-value=52 Score=26.87 Aligned_cols=25 Identities=12% Similarity=0.251 Sum_probs=22.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYR 94 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR 94 (145)
.||+++|...|++++.|+.-++.|.
T Consensus 75 ~el~~kL~~kg~~~~~Ie~vl~~l~ 99 (263)
T PRK14135 75 KEVRDYLKKHEISEEIISEVIDKLK 99 (263)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 5899999999999999998888775
No 25
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=37.93 E-value=62 Score=22.65 Aligned_cols=23 Identities=13% Similarity=0.085 Sum_probs=18.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Q psy1931 69 CLELQELLEEQGFNEIEVDAKVM 91 (145)
Q Consensus 69 ~~ELrd~LEe~G~~eeEIe~kv~ 91 (145)
++.++.+|=.+|++.+||..-|+
T Consensus 34 I~~~Eq~Li~eG~~~eeiq~LCd 56 (71)
T PF04282_consen 34 ISAAEQELIQEGMPVEEIQKLCD 56 (71)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhH
Confidence 45566677778999999999997
No 26
>PLN00180 NDF6 (NDH-dependent flow 6); Provisional
Probab=37.88 E-value=52 Score=26.94 Aligned_cols=24 Identities=25% Similarity=0.145 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 66 ELQCLELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 66 Evk~~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
+.+-..||++|- +|||+||.-||+
T Consensus 150 sAReeL~REELi------EEIEQkVGGLRE 173 (180)
T PLN00180 150 SARAELWREELI------EEIEQKVGGLRE 173 (180)
T ss_pred HHHHHHHHHHHH------HHHHHHhhhHHH
Confidence 334456787776 489999999997
No 27
>TIGR03182 PDH_E1_alph_y pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc.
Probab=37.71 E-value=87 Score=26.73 Aligned_cols=36 Identities=28% Similarity=0.234 Sum_probs=29.5
Q ss_pred HHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHhhhhcC
Q psy1931 70 LELQELLEEQG-FNEIEVDAKVMAYRLHLNKNVEKIN 105 (145)
Q Consensus 70 ~ELrd~LEe~G-~~eeEIe~kv~~lR~~Ll~e~~~~~ 105 (145)
.-|+..|.++| ++++++++--++.++.+.+......
T Consensus 263 ~~~~~~L~~~g~~~~~~~~~~~~~~~~~v~~a~~~a~ 299 (315)
T TIGR03182 263 EKLKARLIEQGIASEEELKEIDKEVRAEVEEAVEFAE 299 (315)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46888999999 6999999999999999888654433
No 28
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=37.50 E-value=88 Score=25.08 Aligned_cols=39 Identities=15% Similarity=0.068 Sum_probs=29.6
Q ss_pred cCCCHHHHHHHHHHHHHHHHHhhhhcCC----CCCccCCCccc
Q psy1931 79 QGFNEIEVDAKVMAYRLHLNKNVEKINE----PPLDELGRVMD 117 (145)
Q Consensus 79 ~G~~eeEIe~kv~~lR~~Ll~e~~~~~~----~~~~~~~r~~~ 117 (145)
-|+++..|...+...|++|.+..++++. |...++|||--
T Consensus 160 LgiS~~tVk~~L~RAr~~Lr~~l~~~~~~~~~~~~~~~~~~~~ 202 (216)
T PRK12533 160 ADVPVGTVMSRLARARRRLAALLGGASAAQAAPGERAAGRPRR 202 (216)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHcccchhhcCCcccccCCCCC
Confidence 4778888888889999999988877774 35566777743
No 29
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=37.12 E-value=74 Score=18.77 Aligned_cols=26 Identities=31% Similarity=0.482 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHcCC----CHHHHHHHHHH
Q psy1931 67 LQCLELQELLEEQGF----NEIEVDAKVMA 92 (145)
Q Consensus 67 vk~~ELrd~LEe~G~----~eeEIe~kv~~ 92 (145)
+++.||++.|.+.|+ +-+++-+++.+
T Consensus 4 l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~ 33 (35)
T PF02037_consen 4 LTVAELKEELKERGLSTSGKKAELIERLKE 33 (35)
T ss_dssp SHHHHHHHHHHHTTS-STSSHHHHHHHHHH
T ss_pred CcHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Confidence 467899999999887 35555555543
No 30
>COG0707 MurG UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]
Probab=36.63 E-value=11 Score=33.17 Aligned_cols=18 Identities=28% Similarity=0.357 Sum_probs=14.9
Q ss_pred cCCCcccccccccccccc
Q psy1931 12 GSGTNGYVQRNWSLVRKT 29 (145)
Q Consensus 12 GSGTSGyVQrNls~~~~~ 29 (145)
|+||.|||+..+|....-
T Consensus 7 ~gGTGGHv~pAlAl~~~l 24 (357)
T COG0707 7 AGGTGGHVFPALALAEEL 24 (357)
T ss_pred eCCCccchhHHHHHHHHH
Confidence 789999999999975443
No 31
>TIGR00012 L29 ribosomal protein L29. called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.
Probab=36.50 E-value=48 Score=21.57 Aligned_cols=23 Identities=13% Similarity=-0.052 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNVE 102 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~~ 102 (145)
.++.+|+.+++.++|++|.+-..
T Consensus 4 ~~s~~EL~~~l~~lr~eLf~Lr~ 26 (55)
T TIGR00012 4 EKSKEELAKKLDELKKELFELRF 26 (55)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999999999998643
No 32
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=35.96 E-value=47 Score=22.81 Aligned_cols=23 Identities=9% Similarity=0.144 Sum_probs=20.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNVE 102 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~~ 102 (145)
+++.+|+.+++.+++++|.+=..
T Consensus 11 ~ls~~eL~~~l~elk~elf~LRf 33 (67)
T CHL00154 11 DLTDSEISEEIIKTKKELFDLRL 33 (67)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHH
Confidence 48899999999999999998643
No 33
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=34.91 E-value=90 Score=25.02 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 68 QCLELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 68 k~~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
...|+.+.+.+.|++++++++-++.+-+
T Consensus 81 e~~el~~iy~~~Gl~~~~a~~i~~~l~~ 108 (213)
T PF01988_consen 81 EKEELVEIYRAKGLSEEDAEEIAEELSK 108 (213)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHh
Confidence 3348889999999999999988887644
No 34
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=34.75 E-value=98 Score=23.38 Aligned_cols=41 Identities=20% Similarity=0.175 Sum_probs=28.5
Q ss_pred cCCCCChhHHhHHhhhHHHHHHHH-----HHHHHHHcCCCHHHHHHHH
Q psy1931 48 NNKQPNREILDHEKKRKIELQCLE-----LQELLEEQGFNEIEVDAKV 90 (145)
Q Consensus 48 ~~rkpn~eIleHerKR~IEvk~~E-----Lrd~LEe~G~~eeEIe~kv 90 (145)
..|-.+..+--|+.+|..|-.+.. ++..+++ +++||.++-.
T Consensus 54 lfRV~t~~MTy~~Q~k~Ye~a~~~~~~~~lqkRle~--l~~eE~~~L~ 99 (104)
T PF11460_consen 54 LFRVVTGKMTYMQQRKDYEEAVDQLTNEELQKRLEE--LSPEELEALQ 99 (104)
T ss_pred HhhhccCCCcHHHHHHHHHHHHHHHhHHHHHHHHHh--CCHHHHHHHH
Confidence 346677888899999999988844 4444444 7777766433
No 35
>KOG0151|consensus
Probab=34.60 E-value=59 Score=32.29 Aligned_cols=44 Identities=25% Similarity=0.266 Sum_probs=37.0
Q ss_pred HhHHhhhHHHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHHh
Q psy1931 57 LDHEKKRKIELQCLELQELLEEQGFN-EIEVDAKVMAYRLHLNKN 100 (145)
Q Consensus 57 leHerKR~IEvk~~ELrd~LEe~G~~-eeEIe~kv~~lR~~Ll~e 100 (145)
+.-..+|.+++...|+++.++|+|+. -++|+.+|.-.|..+-.+
T Consensus 745 ~l~q~~r~~~~a~~e~~e~~~e~~~k~s~~~~rk~e~~~~r~e~~ 789 (877)
T KOG0151|consen 745 LLRQDVRVEAIALIEYREADEEQGMKRSEDKERKVEIERKRKERK 789 (877)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhhccchhhhhhhcchhHHHHHhh
Confidence 44556778889999999999999985 569999999999888776
No 36
>PF02251 PA28_alpha: Proteasome activator pa28 alpha subunit; InterPro: IPR003185 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the alpha subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_K.
Probab=33.61 E-value=58 Score=22.25 Aligned_cols=20 Identities=35% Similarity=0.395 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q psy1931 84 IEVDAKVMAYRLHLNKNVEK 103 (145)
Q Consensus 84 eEIe~kv~~lR~~Ll~e~~~ 103 (145)
.|...+|++||+.|..++|.
T Consensus 3 ~e~~~kV~~fr~~l~~eAE~ 22 (64)
T PF02251_consen 3 PENKKKVDEFRQSLTKEAEN 22 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 35567777777777777654
No 37
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=33.29 E-value=44 Score=23.34 Aligned_cols=28 Identities=29% Similarity=0.432 Sum_probs=21.0
Q ss_pred HHhhhHHHHHHHHHHHHHHHcCCCHHHH
Q psy1931 59 HEKKRKIELQCLELQELLEEQGFNEIEV 86 (145)
Q Consensus 59 HerKR~IEvk~~ELrd~LEe~G~~eeEI 86 (145)
=.++++.+-.+.++++.|++.|++.+||
T Consensus 16 ~~~~~e~~~~~~~i~~~~~~~Gis~~el 43 (93)
T PF00816_consen 16 ERRKQEREEAIAEIRELMAEYGISPEEL 43 (93)
T ss_dssp HHHHHCCHHHHHHHHHHHHHTT--HHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCHHHh
Confidence 3445566778889999999999999998
No 38
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=33.23 E-value=38 Score=30.74 Aligned_cols=33 Identities=21% Similarity=0.136 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy1931 66 ELQCLELQELLEEQGFNEIEVDAKVMAYRLHLN 98 (145)
Q Consensus 66 Evk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll 98 (145)
-|++.||+|+|.+..-+.|.|..+|.+.|..+|
T Consensus 7 ~~~LeeLe~kLa~~d~~Kd~V~~~I~ea~~sIL 39 (379)
T PF11593_consen 7 NLKLEELEEKLASNDNSKDSVMDKISEAQDSIL 39 (379)
T ss_pred CCcHHHHHHHHhcCCchHHHHHHHHHHHHhccc
Confidence 367889999998765688999999988886654
No 39
>COG4224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.14 E-value=1e+02 Score=22.25 Aligned_cols=33 Identities=21% Similarity=0.236 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh
Q psy1931 68 QCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 68 k~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
++-||--+=.+.|++++|+.++ ..||+..++..
T Consensus 8 rINeLAkk~K~~gLTeeEk~eQ-~~LR~eYl~~f 40 (77)
T COG4224 8 RINELAKKKKEEGLTEEEKKEQ-AKLRREYLESF 40 (77)
T ss_pred HHHHHHHHhcccCCCHHHHHHH-HHHHHHHHHHH
Confidence 3778887778889999999876 56777777653
No 40
>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat
Probab=33.06 E-value=52 Score=21.44 Aligned_cols=22 Identities=14% Similarity=0.045 Sum_probs=19.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
.++.+|+.+++.++|++|.+-.
T Consensus 5 ~ls~~eL~~~l~~l~~elf~Lr 26 (57)
T cd00427 5 EKSDEELQEKLDELKKELFNLR 26 (57)
T ss_pred HCCHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999998864
No 41
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=32.76 E-value=92 Score=20.82 Aligned_cols=13 Identities=46% Similarity=0.662 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHc
Q psy1931 67 LQCLELQELLEEQ 79 (145)
Q Consensus 67 vk~~ELrd~LEe~ 79 (145)
..+||||+.|++-
T Consensus 8 me~mE~rE~le~~ 20 (78)
T PF07743_consen 8 MEQMELREELEEA 20 (78)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 4689999999995
No 42
>PRK13411 molecular chaperone DnaK; Provisional
Probab=32.71 E-value=1.4e+02 Score=28.05 Aligned_cols=46 Identities=17% Similarity=0.272 Sum_probs=36.1
Q ss_pred hHHhHHhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHh
Q psy1931 55 EILDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKN 100 (145)
Q Consensus 55 eIleHerKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e 100 (145)
+.+..+.+-+|+-+|.++++.|++...+.++|+++.++|++.+..=
T Consensus 550 ~~~~~~er~~i~~~l~~~~~wL~~~~~~~~~~~~~~~el~~~~~~i 595 (653)
T PRK13411 550 ELISEELKQRAEQKVEQLEAALTDPNISLEELKQQLEEFQQALLAI 595 (653)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 3456667778888888999999885567899999999999876553
No 43
>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 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 L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....
Probab=32.47 E-value=37 Score=22.31 Aligned_cols=24 Identities=13% Similarity=0.095 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNVEK 103 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~~~ 103 (145)
+++.+|+.+++.+++.+|.+-..+
T Consensus 6 ~ls~~eL~~~l~elk~eL~~Lr~q 29 (58)
T PF00831_consen 6 ELSDEELQEKLEELKKELFNLRFQ 29 (58)
T ss_dssp HSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHH
Confidence 478899999999999999986544
No 44
>KOG2629|consensus
Probab=31.81 E-value=60 Score=28.69 Aligned_cols=24 Identities=21% Similarity=0.414 Sum_probs=20.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHH
Q psy1931 69 CLELQELLEEQGFNEIEVDAKVMA 92 (145)
Q Consensus 69 ~~ELrd~LEe~G~~eeEIe~kv~~ 92 (145)
+.+-|+-|+..|++++||++-+..
T Consensus 22 li~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 22 LIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHh
Confidence 345578899999999999998875
No 45
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=31.69 E-value=1.1e+02 Score=21.47 Aligned_cols=29 Identities=21% Similarity=0.141 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q psy1931 65 IELQCLELQELLEEQGFNEIEVDAKVMAY 93 (145)
Q Consensus 65 IEvk~~ELrd~LEe~G~~eeEIe~kv~~l 93 (145)
+.-.+.+.-+.|.+.|++++|+++-...|
T Consensus 156 ~~~~~~~~l~~l~~~~~s~~el~~~k~~L 184 (184)
T PF05193_consen 156 AIEAILQELKRLREGGISEEELERAKNQL 184 (184)
T ss_dssp HHHHHHHHHHHHHHHCS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 44455555556666699999999876654
No 46
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=30.96 E-value=66 Score=21.58 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
.++.+|+.+++.+++++|++-.
T Consensus 8 ~ls~~eL~~~l~~lkkeL~~lR 29 (66)
T PRK00306 8 ELSVEELNEKLLELKKELFNLR 29 (66)
T ss_pred hCCHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999865
No 47
>TIGR03181 PDH_E1_alph_x pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc.
Probab=30.83 E-value=1.3e+02 Score=26.12 Aligned_cols=37 Identities=22% Similarity=0.278 Sum_probs=29.8
Q ss_pred HHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHhhhhcC
Q psy1931 69 CLELQELLEEQGF-NEIEVDAKVMAYRLHLNKNVEKIN 105 (145)
Q Consensus 69 ~~ELrd~LEe~G~-~eeEIe~kv~~lR~~Ll~e~~~~~ 105 (145)
+.-++..|.+.|+ +++++++--++.+..+.+......
T Consensus 275 i~~~~~~L~~~g~~~~~e~~~i~~~~~~~v~~a~~~a~ 312 (341)
T TIGR03181 275 ILRLRKYLERKGLWDEEQEEALEEEAEAEVAEAVAEAL 312 (341)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568889999994 999999999999998888765443
No 48
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=30.31 E-value=71 Score=25.68 Aligned_cols=26 Identities=19% Similarity=0.226 Sum_probs=21.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
.||++.|...|+++++|++=++.+.+
T Consensus 38 ~ELr~kL~k~~~~~~~Ie~Vi~~l~~ 63 (174)
T COG2137 38 KELRRKLAKKEFSEEIIEEVIDRLAE 63 (174)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHHH
Confidence 47889999999999999888877654
No 49
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=29.85 E-value=72 Score=21.06 Aligned_cols=23 Identities=35% Similarity=0.426 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHH
Q psy1931 71 ELQELLEEQGFNEIEVDAKVMAY 93 (145)
Q Consensus 71 ELrd~LEe~G~~eeEIe~kv~~l 93 (145)
-|.+..+++|++.++|-++++++
T Consensus 33 ~L~eA~~~~~ld~~~vl~~L~~l 55 (56)
T PF04405_consen 33 SLEEACEEKGLDPEEVLEELNAL 55 (56)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHc
Confidence 36778889999999998888764
No 50
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=29.26 E-value=1.1e+02 Score=24.18 Aligned_cols=36 Identities=17% Similarity=0.066 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHcCC--C----HHHHHHHHHHHHHHHHHhh
Q psy1931 66 ELQCLELQELLEEQGF--N----EIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 66 Evk~~ELrd~LEe~G~--~----eeEIe~kv~~lR~~Ll~e~ 101 (145)
=..+||+|++||+..- + -++|..+|+...+.+.++.
T Consensus 92 Lme~me~rE~le~~~~~~d~~~~l~~l~~~~~~~~~~~~~~l 133 (171)
T PRK05014 92 LMEQMELREELEDIEQSKDPEAALESFIKRVKKMFKTRLQQM 133 (171)
T ss_pred HHHHHHHHHHHHhhccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999987432 1 2355566666655555554
No 51
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=28.86 E-value=97 Score=24.02 Aligned_cols=23 Identities=17% Similarity=0.271 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHH
Q psy1931 64 KIELQCLELQELLEEQGFNEIEV 86 (145)
Q Consensus 64 ~IEvk~~ELrd~LEe~G~~eeEI 86 (145)
+-+-++.++++.|.+.|++.+|+
T Consensus 53 er~~kl~~~r~~m~~~Gis~~eL 75 (135)
T PRK10947 53 ERTRKLQQYREMLIADGIDPNEL 75 (135)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHH
Confidence 34447888999999999998888
No 52
>PHA01750 hypothetical protein
Probab=27.58 E-value=1.2e+02 Score=21.59 Aligned_cols=30 Identities=20% Similarity=0.216 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q psy1931 68 QCLELQELLEEQGFNEIEVDAKVMAYRLHL 97 (145)
Q Consensus 68 k~~ELrd~LEe~G~~eeEIe~kv~~lR~~L 97 (145)
.+--|+-++++-..-.|+|+++|.++..++
T Consensus 43 ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 43 ELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 445566677776677788999999888776
No 53
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=27.06 E-value=1.1e+02 Score=24.30 Aligned_cols=37 Identities=19% Similarity=0.185 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHcC--CCHHH---HHHHHHHHHHHHHHhh
Q psy1931 65 IELQCLELQELLEEQG--FNEIE---VDAKVMAYRLHLNKNV 101 (145)
Q Consensus 65 IEvk~~ELrd~LEe~G--~~eeE---Ie~kv~~lR~~Ll~e~ 101 (145)
.=..+|||||.||+-. -+.++ |..+|.+..+.+..+.
T Consensus 93 fLme~ME~rE~lee~~~~~d~~~L~~l~~~v~~~~~~~~~~l 134 (173)
T PRK01773 93 FLMQQMEWREQLEEIEQQQDEDALTAFSKEIKQEQQAILTEL 134 (173)
T ss_pred HHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467899999999842 23333 3455555555555544
No 54
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=26.51 E-value=85 Score=25.79 Aligned_cols=27 Identities=30% Similarity=0.281 Sum_probs=22.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy1931 70 LELQELLEEQGFNEIEVDAKVMAYRLH 96 (145)
Q Consensus 70 ~ELrd~LEe~G~~eeEIe~kv~~lR~~ 96 (145)
..|.+.|++.||+++-|.+-+++..--
T Consensus 94 ~~L~~RLk~RGy~~eKI~ENveAEi~~ 120 (180)
T COG1936 94 EVLYERLKGRGYSEEKILENVEAEILD 120 (180)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 478999999999999999888765533
No 55
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=26.06 E-value=90 Score=21.36 Aligned_cols=22 Identities=23% Similarity=0.244 Sum_probs=19.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
.++.+|+.+++.+++++|.+=.
T Consensus 11 ~ls~~eL~~~l~elk~eLf~LR 32 (69)
T PRK14549 11 EMSPEEREEKLEELKLELLKER 32 (69)
T ss_pred hCCHHHHHHHHHHHHHHHHHHH
Confidence 3788999999999999998854
No 56
>PRK00461 rpmC 50S ribosomal protein L29; Reviewed
Probab=25.85 E-value=83 Score=22.77 Aligned_cols=22 Identities=14% Similarity=0.022 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHhh
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
+++.+|+.+++.+++++|.+-.
T Consensus 7 ~lS~eEL~e~L~elkkELf~LR 28 (87)
T PRK00461 7 KKSVEELEKLVIELKAELFTLR 28 (87)
T ss_pred hCCHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999998864
No 57
>COG0255 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]
Probab=25.30 E-value=92 Score=21.67 Aligned_cols=25 Identities=8% Similarity=-0.001 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhhhc
Q psy1931 80 GFNEIEVDAKVMAYRLHLNKNVEKI 104 (145)
Q Consensus 80 G~~eeEIe~kv~~lR~~Ll~e~~~~ 104 (145)
++|.+|+.+++.+++.+|++-..+.
T Consensus 10 ~~s~eeL~~~l~eLK~ELf~LR~q~ 34 (69)
T COG0255 10 EKSVEELEEELRELKKELFNLRFQL 34 (69)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999875443
No 58
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=24.98 E-value=2.2e+02 Score=20.09 Aligned_cols=35 Identities=20% Similarity=0.232 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHH
Q psy1931 65 IELQCLELQELLEEQGFNEIEVDA---KVMAYRLHLNK 99 (145)
Q Consensus 65 IEvk~~ELrd~LEe~G~~eeEIe~---kv~~lR~~Ll~ 99 (145)
-+.=+..+++.|++.|++++.|++ .++.+|..+.+
T Consensus 82 f~~~~~~~~~al~~~~v~~~~~~~~~~~~~~~~~~i~n 119 (120)
T PF01152_consen 82 FDRWLELLKQALDELGVPEELIDELLARLESLRDDIVN 119 (120)
T ss_dssp HHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhcC
Confidence 345566788999999999866664 45566655544
No 59
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=24.91 E-value=1.7e+02 Score=22.95 Aligned_cols=32 Identities=9% Similarity=-0.114 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHcCCCHHH---HHHHHHHHHHHHHHh
Q psy1931 68 QCLELQELLEEQGFNEIE---VDAKVMAYRLHLNKN 100 (145)
Q Consensus 68 k~~ELrd~LEe~G~~eeE---Ie~kv~~lR~~Ll~e 100 (145)
.+||++|.||+.+ ++++ |..++....+.+.++
T Consensus 94 e~me~rE~le~~~-~~~~L~~l~~~~~~~~~~~~~~ 128 (166)
T PRK01356 94 IFWDEMERIENTI-LFSDLEKIKNKYELMYKNEIDS 128 (166)
T ss_pred HHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999998864 4433 334444444444443
No 60
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=24.85 E-value=1.8e+02 Score=28.85 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Q psy1931 71 ELQELLEEQGFNEIEVDAKVMAYRLHLNK 99 (145)
Q Consensus 71 ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~ 99 (145)
.|++.|+. |-+++||++.+++||+-+-+
T Consensus 480 ~L~eAL~~-gAs~eEI~rLm~eLR~A~~~ 507 (820)
T PF13779_consen 480 ALREALER-GASDEEIARLMQELREAMQD 507 (820)
T ss_pred HHHHHHHc-CCCHHHHHHHHHHHHHHHHH
Confidence 45555544 99999999999999987633
No 61
>PLN02269 Pyruvate dehydrogenase E1 component subunit alpha
Probab=24.85 E-value=1.8e+02 Score=25.67 Aligned_cols=33 Identities=21% Similarity=0.295 Sum_probs=27.2
Q ss_pred HHHHHHHHcCC-CHHHHHHHHHHHHHHHHHhhhh
Q psy1931 71 ELQELLEEQGF-NEIEVDAKVMAYRLHLNKNVEK 103 (145)
Q Consensus 71 ELrd~LEe~G~-~eeEIe~kv~~lR~~Ll~e~~~ 103 (145)
-|+..|.++|+ +++++++--++.++.+.+..+.
T Consensus 291 ~~~~~L~~~g~~te~e~~~i~~e~~~~v~~a~~~ 324 (362)
T PLN02269 291 RVRKLLLAHELATEAELKDIEKEIRKEVDDAVAK 324 (362)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 47888999995 9999999888888888876544
No 62
>PF00676 E1_dh: Dehydrogenase E1 component; InterPro: IPR001017 This entry includes a number of dehydrogenases all of which use thiamine pyrophosphate as a cofactor and are members of a multienzyme complex. Pyruvate dehydrogenase (1.2.4.1 from EC), a component of the multienzyme pyruvate dehydrogenase complex; 2-oxoglutarate dehydrogenase (1.2.4.2 from EC), a component of the multienzyme 2-oxoglutarate dehydrogenase which contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3); and 2-oxoisovalerate dehydrogenase (1.2.4.4 from EC), a component of the multienzyme branched-chain alpha-keto dehydrogenase complex all belong to this family.; GO: 0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 0008152 metabolic process; PDB: 1X7Y_A 1V1M_A 1X7W_A 1OLU_A 2J9F_A 2BEW_A 1V11_A 2BFE_A 1U5B_A 2BEU_A ....
Probab=24.60 E-value=1.1e+02 Score=26.02 Aligned_cols=36 Identities=25% Similarity=0.291 Sum_probs=27.7
Q ss_pred HHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHhhhhc
Q psy1931 69 CLELQELLEEQGF-NEIEVDAKVMAYRLHLNKNVEKI 104 (145)
Q Consensus 69 ~~ELrd~LEe~G~-~eeEIe~kv~~lR~~Ll~e~~~~ 104 (145)
+.-++..|.++|+ +++++++--++.++.+.+..+..
T Consensus 255 i~~~~~~L~~~g~~t~~~~~~i~~e~~~~v~~a~~~a 291 (300)
T PF00676_consen 255 IKRFRRYLIEEGVLTEEELDAIEAEIKAEVEEAVEFA 291 (300)
T ss_dssp HHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467889999996 99999998888888887765443
No 63
>cd02000 TPP_E1_PDC_ADC_BCADC Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC). PDC catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. ADC participates in the breakdown of acetoin while BCADC participates in the breakdown of branched chain amino acids. BCADC catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate (branched chain 2-oxo acids derived from the transamination of leucine, valine and isoleucine).
Probab=24.41 E-value=1.9e+02 Score=24.20 Aligned_cols=33 Identities=27% Similarity=0.358 Sum_probs=27.1
Q ss_pred HHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHhh
Q psy1931 69 CLELQELLEEQG-FNEIEVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 69 ~~ELrd~LEe~G-~~eeEIe~kv~~lR~~Ll~e~ 101 (145)
+..|++.|.+.| ++++++++--++.++.+.+..
T Consensus 257 i~~~~~~L~~~g~~~~~~~~~~~~~~~~~v~~a~ 290 (293)
T cd02000 257 ILRLRKYLIEAGILTEEELAAIEAEVKAEVEEAV 290 (293)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 456889999999 599999998888888877653
No 64
>PRK01631 hypothetical protein; Provisional
Probab=24.26 E-value=1.9e+02 Score=20.72 Aligned_cols=63 Identities=17% Similarity=0.159 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhhh------cCCCCCccCCCcccccCCcccchhhhhhhh
Q psy1931 68 QCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEK------INEPPLDELGRVMDDTSLKFPLLQKWQRLS 133 (145)
Q Consensus 68 k~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~~~------~~~~~~~~~~r~~~~~~~~f~~~q~~~~~~ 133 (145)
++-||--.=.++|++++|..++ ..||+..++..-. -+-...++-|--+.+. +..+.|+.-.||
T Consensus 7 RINeLakK~K~~gLT~eE~~Eq-~~LR~eYl~~fR~~~~~~L~~i~ivD~~G~dvTP~--Klk~~q~~~~~~ 75 (76)
T PRK01631 7 RINELSKKEKATGLTVDEKQEQ-QMLRQNYTQTFRGSLDSILLNTKIVDQNGLNVTPA--ALQDAQIRLKLS 75 (76)
T ss_pred HHHHHHHHhcccCCCHHHHHHH-HHHHHHHHHHHHHHHHHHhcCceeECCCCCcCCHH--HHHHHHHHHhcc
Confidence 3445555556789999998876 4566665554211 1122344445444444 666677765554
No 65
>CHL00149 odpA pyruvate dehydrogenase E1 component alpha subunit; Reviewed
Probab=24.19 E-value=2e+02 Score=25.03 Aligned_cols=36 Identities=8% Similarity=0.161 Sum_probs=28.0
Q ss_pred HHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHhhhhc
Q psy1931 69 CLELQELLEEQG-FNEIEVDAKVMAYRLHLNKNVEKI 104 (145)
Q Consensus 69 ~~ELrd~LEe~G-~~eeEIe~kv~~lR~~Ll~e~~~~ 104 (145)
+.-++..|.++| ++++++++--++.++.+.+..+..
T Consensus 287 i~~~~~~L~~~g~~~~~~~~~i~~e~~~~v~~a~~~a 323 (341)
T CHL00149 287 IKKLKSYIIDNELASQKELNKIQREVKIEIEQAVQFA 323 (341)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 356888999999 599999888888888877765443
No 66
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=24.16 E-value=1.3e+02 Score=23.26 Aligned_cols=27 Identities=19% Similarity=0.220 Sum_probs=21.4
Q ss_pred HhhhHHHHHHHHHHHHHHHcCCCHHHH
Q psy1931 60 EKKRKIELQCLELQELLEEQGFNEIEV 86 (145)
Q Consensus 60 erKR~IEvk~~ELrd~LEe~G~~eeEI 86 (145)
..+++.+-++.++++.|++.|++.+|+
T Consensus 49 ~~~~er~~~l~~i~~~~~~~Git~eeL 75 (134)
T PRK10328 49 RELAERQEKINTWLELMKADGINPEEL 75 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCHHHH
Confidence 445556667888999999999998888
No 67
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=24.06 E-value=91 Score=22.44 Aligned_cols=19 Identities=21% Similarity=0.506 Sum_probs=9.2
Q ss_pred HHHcCCCHHHHHHHHHHHH
Q psy1931 76 LEEQGFNEIEVDAKVMAYR 94 (145)
Q Consensus 76 LEe~G~~eeEIe~kv~~lR 94 (145)
|.+.|++++.|++-|+.|.
T Consensus 1 L~~kg~~~e~I~~vi~~l~ 19 (121)
T PF02631_consen 1 LKRKGFSEEAIEEVIDRLK 19 (121)
T ss_dssp HHHTT--HHHHHHHHHHHH
T ss_pred CcccCCCHHHHHHHHHHHH
Confidence 3455566666665555553
No 68
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=24.01 E-value=1.5e+02 Score=17.16 Aligned_cols=24 Identities=21% Similarity=0.497 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHcCCC----HHHHHHHHH
Q psy1931 68 QCLELQELLEEQGFN----EIEVDAKVM 91 (145)
Q Consensus 68 k~~ELrd~LEe~G~~----eeEIe~kv~ 91 (145)
.+.+|++.|.+.|++ -+++.+++.
T Consensus 5 ~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~ 32 (35)
T smart00513 5 KVSELKDELKKRGLSTSGTKAELVDRLL 32 (35)
T ss_pred cHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 467888888888763 445554443
No 69
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=23.69 E-value=1.5e+02 Score=19.69 Aligned_cols=30 Identities=23% Similarity=0.304 Sum_probs=23.1
Q ss_pred HHHHHHHHcCC--CHHHHHHHHHHHHHHHHHh
Q psy1931 71 ELQELLEEQGF--NEIEVDAKVMAYRLHLNKN 100 (145)
Q Consensus 71 ELrd~LEe~G~--~eeEIe~kv~~lR~~Ll~e 100 (145)
+..+.|.+.|+ +..++..|.+.|+....+.
T Consensus 39 ~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 39 EIAEELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp HHHHHHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 34566777897 9999999999999998765
No 70
>PF04028 DUF374: Domain of unknown function (DUF374); InterPro: IPR007172 This is a bacterial domain of unknown function.
Probab=23.68 E-value=27 Score=24.30 Aligned_cols=20 Identities=30% Similarity=0.435 Sum_probs=14.6
Q ss_pred CCCCCCCcCCCccccccccc
Q psy1931 5 IGLTTARGSGTNGYVQRNWS 24 (145)
Q Consensus 5 IGL~TaRGSGTSGyVQrNls 24 (145)
.|+.|+|||.+-|-++-=+.
T Consensus 32 ~G~~~iRGSs~rgg~~Alr~ 51 (74)
T PF04028_consen 32 FGFRTIRGSSSRGGARALRE 51 (74)
T ss_pred cCCCeEEeCCCCcHHHHHHH
Confidence 58999999977776654433
No 71
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=23.62 E-value=1.7e+02 Score=24.24 Aligned_cols=30 Identities=33% Similarity=0.500 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHcC-CCHHHHHHHHHHH
Q psy1931 64 KIELQCLELQELLEEQG-FNEIEVDAKVMAY 93 (145)
Q Consensus 64 ~IEvk~~ELrd~LEe~G-~~eeEIe~kv~~l 93 (145)
.+++++.-|+.-|.++| ++.++|+..++.+
T Consensus 4 ~~~~~~~al~~ll~ekg~~~~~~~~~~~~~~ 34 (188)
T PF02979_consen 4 EIAARVRALESLLIEKGLITPAEVDRIIETY 34 (188)
T ss_dssp HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 46888899999999999 5899999877643
No 72
>PRK00294 hscB co-chaperone HscB; Provisional
Probab=23.57 E-value=2.1e+02 Score=22.81 Aligned_cols=38 Identities=26% Similarity=0.237 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHcCCCHH-----HHHHHHHHHHHHHHHhh
Q psy1931 64 KIELQCLELQELLEEQGFNEI-----EVDAKVMAYRLHLNKNV 101 (145)
Q Consensus 64 ~IEvk~~ELrd~LEe~G~~ee-----EIe~kv~~lR~~Ll~e~ 101 (145)
.+=..+||+|+.|++..-+++ ++..++....+.|....
T Consensus 92 ~fLme~me~rE~le~~~~~~d~~~l~~~~~~i~~~~~~l~~~~ 134 (173)
T PRK00294 92 EFLLQQMQLREELEELQDEADLAGVATFKRRLKAAQDELNESF 134 (173)
T ss_pred HHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 345688999999998643322 23445555555554443
No 73
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=23.41 E-value=2e+02 Score=28.81 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=20.8
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Q psy1931 71 ELQELLEEQGFNEIEVDAKVMAYRLHLNK 99 (145)
Q Consensus 71 ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~ 99 (145)
.|++.|+ .|-|++||++-.++||+-+-+
T Consensus 511 aL~eAL~-~gAsdeEI~~Lm~eLR~Am~~ 538 (851)
T TIGR02302 511 ALKDALE-RGASDEEIKQLTDKLRAAMQT 538 (851)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHHHHHHHH
Confidence 3444444 499999999999999976543
No 74
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=22.52 E-value=74 Score=18.81 Aligned_cols=16 Identities=38% Similarity=0.611 Sum_probs=13.1
Q ss_pred HHcCCCHHHHHHHHHH
Q psy1931 77 EEQGFNEIEVDAKVMA 92 (145)
Q Consensus 77 Ee~G~~eeEIe~kv~~ 92 (145)
.+.|+|++|+.+++..
T Consensus 12 ~eh~ls~ee~~~RL~~ 27 (28)
T PF12368_consen 12 KEHGLSEEEVAERLAA 27 (28)
T ss_pred HhcCCCHHHHHHHHHc
Confidence 4678999999998764
No 75
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=22.48 E-value=2.5e+02 Score=24.56 Aligned_cols=41 Identities=20% Similarity=0.272 Sum_probs=30.9
Q ss_pred HhhhHHHHHHHHHHHHHHH----------cCCCHHHHHHHHHHHHHHHHHh
Q psy1931 60 EKKRKIELQCLELQELLEE----------QGFNEIEVDAKVMAYRLHLNKN 100 (145)
Q Consensus 60 erKR~IEvk~~ELrd~LEe----------~G~~eeEIe~kv~~lR~~Ll~e 100 (145)
.+..++-..+.||.++|+. ++.+..++...+..+.+.|-.=
T Consensus 94 ~kl~RL~~Ev~EL~eEl~~~~~~~~~~~~e~~~~~~l~~~~~~L~~~L~~l 144 (388)
T PF04912_consen 94 QKLQRLRREVEELKEELEKRKADSKESDEEKISPEELAQQLEELSKQLDSL 144 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccccccccCChhhHHHHHHHHHHHHHHh
Confidence 4556677777888888876 3567788888999998887663
No 76
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=22.34 E-value=1.7e+02 Score=19.69 Aligned_cols=36 Identities=19% Similarity=0.232 Sum_probs=24.9
Q ss_pred HhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy1931 60 EKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRL 95 (145)
Q Consensus 60 erKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~ 95 (145)
.-++++..+-.+|...|...-++++.|++.+++.++
T Consensus 63 ~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~ 98 (125)
T PF13801_consen 63 ALRQELRAARQELRALLAAPPPDEAAIEALLEEIRE 98 (125)
T ss_dssp HHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 344666777777777777778899999876666553
No 77
>PLN02374 pyruvate dehydrogenase (acetyl-transferring)
Probab=21.90 E-value=2.3e+02 Score=25.83 Aligned_cols=35 Identities=26% Similarity=0.204 Sum_probs=28.3
Q ss_pred HHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHhhhhc
Q psy1931 70 LELQELLEEQG-FNEIEVDAKVMAYRLHLNKNVEKI 104 (145)
Q Consensus 70 ~ELrd~LEe~G-~~eeEIe~kv~~lR~~Ll~e~~~~ 104 (145)
..+++.|.++| ++++++++--++.++.+.+..+..
T Consensus 354 ~~~~~~L~~~gi~te~e~~~i~~~~~~~v~~a~~~A 389 (433)
T PLN02374 354 AALKKYLIENGLATEAELKAIEKKIDEVVEDAVEFA 389 (433)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44889999999 599999998888888888765443
No 78
>PF12901 SUZ-C: SUZ-C motif; InterPro: IPR024642 The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins []. It is always found at the C terminus of the protein and appears to be required for localization of the protein to specific subcellular structures. The domain was first characterised in the C.elegans protein SZY-20 which localizes to the centrosome. This domain is widely distributed in eukaryotes.
Probab=21.76 E-value=59 Score=19.82 Aligned_cols=20 Identities=45% Similarity=0.682 Sum_probs=15.0
Q ss_pred CCCCCCCCCCcC-CCcccccc
Q psy1931 2 YNGIGLTTARGS-GTNGYVQR 21 (145)
Q Consensus 2 YNGIGL~TaRGS-GTSGyVQr 21 (145)
+|+.+|..|||= ||.|+-|+
T Consensus 13 ~~~~vir~P~gPd~~~gf~~~ 33 (34)
T PF12901_consen 13 PNGAVIRQPRGPDGTWGFQQR 33 (34)
T ss_pred CCCcceecCCCCCCCcccccc
Confidence 578888889873 67787765
No 79
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=21.67 E-value=2.2e+02 Score=22.62 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHcC--CCHHHHH---HHHHHHHHHHHHhh
Q psy1931 66 ELQCLELQELLEEQG--FNEIEVD---AKVMAYRLHLNKNV 101 (145)
Q Consensus 66 Evk~~ELrd~LEe~G--~~eeEIe---~kv~~lR~~Ll~e~ 101 (145)
=..+||||+.|++.. -+.++|+ .++.+..+.+.++.
T Consensus 97 Lme~mE~rE~lee~~~~~d~~~L~~l~~e~~~~~~~~~~~l 137 (176)
T PRK03578 97 LMQQMEWREAIEDARAARDVDALDALLAELRDERRERYAEL 137 (176)
T ss_pred HHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999742 2445444 34444444444443
No 80
>PF13373 DUF2407_C: DUF2407 C-terminal domain
Probab=21.53 E-value=1.3e+02 Score=23.34 Aligned_cols=24 Identities=17% Similarity=0.224 Sum_probs=17.7
Q ss_pred HHHHHcCCCHHHHHHHHHHHHHHH
Q psy1931 74 ELLEEQGFNEIEVDAKVMAYRLHL 97 (145)
Q Consensus 74 d~LEe~G~~eeEIe~kv~~lR~~L 97 (145)
|.|-++|+|++||+.-=..+|...
T Consensus 4 DRLl~~GFS~~eI~~LR~QF~~~~ 27 (140)
T PF13373_consen 4 DRLLSAGFSPEEIQDLRSQFHSIY 27 (140)
T ss_pred hHHHHcCCCHHHHHHHHHHHHHHh
Confidence 678889999999886655555444
No 81
>TIGR00718 sda_alpha L-serine dehydratase, iron-sulfur-dependent, alpha subunit. This enzyme is also called serine deaminase. L-serine dehydratase converts serine into pyruvate in the gluconeogenesis pathway from serine. This model describes the alpha chain of an iron-sulfur-dependent L-serine dehydratase, found in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of alpha chains from the homologous region of single chain forms such as found in Escherichia coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases.
Probab=21.50 E-value=3.1e+02 Score=24.07 Aligned_cols=50 Identities=24% Similarity=0.250 Sum_probs=37.8
Q ss_pred hhHHhHHhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhhh
Q psy1931 54 REILDHEKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEK 103 (145)
Q Consensus 54 ~eIleHerKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~~~ 103 (145)
.+|+++-++..+-+-=.-|+.+++..|.+++||.++....-+-+.+-.+.
T Consensus 6 ~el~~~c~~~~~~l~e~vl~~E~~~~g~~~~ei~~~m~~~~~vM~~~v~~ 55 (294)
T TIGR00718 6 KEIIDICKEKGIKISDLMIAEEIENSEKTEEDIFKKLDANIDVMEAAAQK 55 (294)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 36777777776666656677888889999999999988877776665443
No 82
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.04 E-value=2.2e+02 Score=21.95 Aligned_cols=26 Identities=23% Similarity=0.244 Sum_probs=16.2
Q ss_pred HHHHHHHHH---HcCCCHHHHHHHHHHHH
Q psy1931 69 CLELQELLE---EQGFNEIEVDAKVMAYR 94 (145)
Q Consensus 69 ~~ELrd~LE---e~G~~eeEIe~kv~~lR 94 (145)
+.++++..+ ++|.+|+||-++...=+
T Consensus 26 l~~Y~e~f~d~~~~G~sEeeii~~LG~P~ 54 (181)
T PF08006_consen 26 LEYYEEYFDDAGEEGKSEEEIIAELGSPK 54 (181)
T ss_pred HHHHHHHHHHhhhCCCCHHHHHHHcCCHH
Confidence 445555444 45788888888764433
No 83
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=21.00 E-value=3.2e+02 Score=19.44 Aligned_cols=38 Identities=26% Similarity=0.221 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Q psy1931 62 KRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNK 99 (145)
Q Consensus 62 KR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~ 99 (145)
.-.|.-++++|+..++.--+|++|-+++=++|=..|..
T Consensus 30 p~~i~~~L~~L~~~~e~GEIseeEf~~~E~eLL~rL~~ 67 (79)
T PF05120_consen 30 PAAIRRELAELQEALEAGEISEEEFERREDELLDRLEE 67 (79)
T ss_pred HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 34677889999999998779999999988888777664
No 84
>KOG4403|consensus
Probab=20.98 E-value=1.4e+02 Score=28.21 Aligned_cols=65 Identities=35% Similarity=0.552 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHHHHHH--------cCCCHHHHHHHHHHHHHHHHHhhhhcCCCCCccCCCcccccCCcccc-hhhhhhh
Q psy1931 62 KRKIELQCLELQELLEE--------QGFNEIEVDAKVMAYRLHLNKNVEKINEPPLDELGRVMDDTSLKFPL-LQKWQRL 132 (145)
Q Consensus 62 KR~IEvk~~ELrd~LEe--------~G~~eeEIe~kv~~lR~~Ll~e~~~~~~~~~~~~~r~~~~~~~~f~~-~q~~~~~ 132 (145)
-|.|+|.-+.|+-.|.+ +|+.-+.-.+++..+|..|-+. |.-.+..+ +-.-++ +|+|-++
T Consensus 275 ~rnvavek~~lerkl~ea~rl~elreg~e~e~~rkelE~lR~~L~kA-Ekele~nS----------~wsaP~aLQ~wLq~ 343 (575)
T KOG4403|consen 275 QRNVAVEKLDLERKLDEAPRLSELREGVENETSRKELEQLRVALEKA-EKELEANS----------SWSAPLALQKWLQL 343 (575)
T ss_pred hhchhhhhhhHHHHHhhhhhhhhhhcchhHHHHHHHHHHHHHHHHHH-HHHHHhcc----------CCCCcHHHHHHHHH
Confidence 34555555555555443 1433333334566667666543 22222222 112223 9999999
Q ss_pred hcccc
Q psy1931 133 SHECE 137 (145)
Q Consensus 133 ~~~~~ 137 (145)
.||.|
T Consensus 344 T~E~E 348 (575)
T KOG4403|consen 344 THEVE 348 (575)
T ss_pred HHHHH
Confidence 99976
No 85
>KOG2759|consensus
Probab=20.27 E-value=1.5e+02 Score=27.59 Aligned_cols=32 Identities=16% Similarity=0.301 Sum_probs=27.6
Q ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHhhhhc
Q psy1931 73 QELLEEQGFNEIEVDAKVMAYRLHLNKNVEKI 104 (145)
Q Consensus 73 rd~LEe~G~~eeEIe~kv~~lR~~Ll~e~~~~ 104 (145)
-+-|+++++++++|..-++-++++|-+.....
T Consensus 295 l~~L~~rkysDEDL~~di~~L~e~L~~svq~L 326 (442)
T KOG2759|consen 295 LQSLEERKYSDEDLVDDIEFLTEKLKNSVQDL 326 (442)
T ss_pred HHHHHhcCCCcHHHHHHHHHHHHHHHHHHHhh
Confidence 35789999999999999999999999876443
No 86
>PF03221 HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain; InterPro: IPR006600 This entry represents a DNA-binding helix-turn-helix domain found in the pogo family of transposable elements, the centromere protein Cenp-B, and yeast PCD2. There is extensive sequence similarity between Cenp-B and transposase proteins encoded by the pogo superfamily of transposable elements, which includes the human Tigger and Jerky elements []. The HTH domain is composed of three alpha-helices, with the second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, as in other HTHs []. This conserved DNA-binding domain is found in the following proteins: Cenp-B (major centromere autoantigen B or centromere protein B), which appears to organise arrays of centromere satellite DNA into a higher order structure that then direct centromere formation and kinetochore assembly in mammalian chromosomes. The N terminus of Cenp-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA: a psq-type HTH domain followed by a CenpB-type HTH domain, which together bind specifically to the Cenp-B box, which occurs in alpha-satellite DNA in human centromeres []. Pogo family transposable elements includes both Tigger and Jerky elements []. Pogo contains two open reading frames flanked by inverted repeats. The N-terminal region of pogo transposase contains a Cenp-B-type HTH DNA-binding domain []. Mammalian jerky protein, involved in epileptic seizures in mice []. PDC2 (Pyruvate DeCarboxylase 2), which is a transcription factor required for the synthesis of the glycolytic enzyme pyruvate decarboxylase, required for high level expression of both the THI and the PDC genes. PDC2 may be important for a high basal level of PDC gene expression or play a positive role in the autoregulation control of PDC1 and PDC5 [, ]. ; PDB: 1HLV_A 1IUF_A.
Probab=20.19 E-value=1.5e+02 Score=18.51 Aligned_cols=31 Identities=13% Similarity=0.185 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHcC--CCHHHHHHHHHHHH
Q psy1931 64 KIELQCLELQELLEEQG--FNEIEVDAKVMAYR 94 (145)
Q Consensus 64 ~IEvk~~ELrd~LEe~G--~~eeEIe~kv~~lR 94 (145)
++|-.+.++=..+...| ++.+.|.++..++.
T Consensus 3 ~~E~~L~~wi~~~~~~g~~vt~~~i~~~A~~i~ 35 (66)
T PF03221_consen 3 ELEKALVEWIKRMRRKGFPVTREMIREKAKEIA 35 (66)
T ss_dssp HHHHHHHHHHHHHCGCT---SCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 57888889988888888 58999999998887
No 87
>KOG0299|consensus
Probab=20.09 E-value=1.7e+02 Score=27.47 Aligned_cols=70 Identities=20% Similarity=0.163 Sum_probs=43.2
Q ss_pred HhhhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhhhcCCC-CCccCCCcccccCCcccchhhhhhh
Q psy1931 60 EKKRKIELQCLELQELLEEQGFNEIEVDAKVMAYRLHLNKNVEKINEP-PLDELGRVMDDTSLKFPLLQKWQRL 132 (145)
Q Consensus 60 erKR~IEvk~~ELrd~LEe~G~~eeEIe~kv~~lR~~Ll~e~~~~~~~-~~~~~~r~~~~~~~~f~~~q~~~~~ 132 (145)
.++|--|..+.+.+ +.+|.+.++++.++ +..-++|++++-.++.. -...+.+.-...+..|..+..|++-
T Consensus 74 kr~RlA~e~L~~i~-e~~E~~~d~~~~~~--e~va~rLked~le~~Gr~~r~~a~~v~~~~s~~~~~~~~H~~s 144 (479)
T KOG0299|consen 74 KRLRLAEEYLDEIR-EIEEDNFDADDLDD--ELVASRLKEDVLEQSGRVRRLVADKVQAPESSDFRVIGKHQLS 144 (479)
T ss_pred HHHHHHHHHHHHHH-hhhhcccccchhhH--HHHHHHHHHHHHHhcceeehhhhhhccccccccceeeccccCc
Confidence 36788888888888 55556676666664 33334555554444433 3445555555566668888888763
Done!