Query psy2660
Match_columns 149
No_of_seqs 193 out of 266
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 21:58:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2660.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2660hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02149 KA1: Kinase associate 99.6 1.8E-15 4E-20 96.3 3.6 33 113-145 3-35 (47)
2 KOG0586|consensus 98.4 9.3E-08 2E-12 87.4 2.4 53 80-138 536-588 (596)
3 PF08385 DHC_N1: Dynein heavy 97.7 6.6E-06 1.4E-10 73.2 -0.4 46 2-47 110-155 (579)
4 PF12949 HeH: HeH/LEM domain; 67.0 2.3 5E-05 25.4 0.4 17 80-96 6-22 (35)
5 TIGR03687 pupylate_cterm ubiqu 60.5 3.4 7.3E-05 24.5 0.3 21 75-95 4-24 (33)
6 PF01193 RNA_pol_L: RNA polyme 51.8 34 0.00074 22.2 4.1 32 58-89 32-63 (66)
7 cd07032 RNAP_I_II_AC40 AC40 su 51.7 17 0.00037 31.1 3.3 32 59-90 253-284 (291)
8 cd00460 RNAP_RPB11_RPB3 RPB11 51.4 22 0.00048 24.5 3.3 27 63-89 55-81 (86)
9 cd07031 RNAP_II_RPB3 RPB3 subu 49.7 19 0.00042 30.1 3.3 29 62-90 226-254 (265)
10 PRK13009 succinyl-diaminopimel 49.2 48 0.001 27.7 5.7 42 55-96 243-284 (375)
11 PRK08652 acetylornithine deace 49.0 51 0.0011 27.2 5.7 46 52-97 212-257 (347)
12 cd03030 GRX_SH3BGR Glutaredoxi 45.6 26 0.00057 24.7 3.0 31 67-97 6-36 (92)
13 PF00924 MS_channel: Mechanose 44.5 1.2E+02 0.0026 23.2 6.8 63 56-122 112-175 (206)
14 PF04908 SH3BGR: SH3-binding, 44.1 23 0.0005 25.5 2.6 29 68-96 8-36 (99)
15 PF07687 M20_dimer: Peptidase 39.8 35 0.00076 23.2 2.9 39 52-90 69-107 (111)
16 KOG1521|consensus 37.2 34 0.00073 29.9 2.9 29 62-90 301-329 (338)
17 PF00101 RuBisCO_small: Ribulo 37.2 63 0.0014 23.4 3.9 38 73-119 10-47 (99)
18 cd05510 Bromo_SPT7_like Bromod 36.7 15 0.00033 26.8 0.6 22 17-38 67-88 (112)
19 cd05860 Ig4_SCFR Fourth immuno 36.1 23 0.0005 25.7 1.5 30 90-121 70-99 (101)
20 cd05516 Bromo_SNF2L2 Bromodoma 35.8 16 0.00034 26.3 0.6 22 18-39 67-88 (107)
21 cd05505 Bromo_WSTF_like Bromod 35.8 16 0.00035 25.9 0.6 23 17-39 59-81 (97)
22 cd06218 DHOD_e_trans FAD/NAD b 35.5 54 0.0012 26.3 3.7 20 75-94 187-206 (246)
23 cd05497 Bromo_Brdt_I_like Brom 35.4 17 0.00037 26.2 0.7 22 18-39 67-88 (107)
24 cd05504 Bromo_Acf1_like Bromod 35.1 16 0.00035 26.7 0.6 23 17-39 71-93 (115)
25 cd05495 Bromo_cbp_like Bromodo 34.8 18 0.00038 26.1 0.7 23 16-38 64-86 (108)
26 cd05502 Bromo_tif1_like Bromod 34.8 16 0.00036 26.1 0.6 23 16-38 64-86 (109)
27 TIGR01246 dapE_proteo succinyl 34.7 1.1E+02 0.0024 25.6 5.7 41 55-95 240-280 (370)
28 PF12046 DUF3529: Protein of u 33.9 1.5E+02 0.0032 23.8 5.8 48 57-119 27-74 (173)
29 cd05517 Bromo_polybromo_II Bro 33.5 18 0.00039 25.9 0.6 23 17-39 65-87 (103)
30 PRK15348 type III secretion sy 32.4 74 0.0016 26.7 4.1 32 72-104 25-59 (249)
31 cd05518 Bromo_polybromo_IV Bro 31.9 19 0.00042 25.8 0.5 22 17-38 65-86 (103)
32 PF11823 DUF3343: Protein of u 31.0 39 0.00085 22.3 1.9 35 59-96 34-68 (73)
33 cd05519 Bromo_SNF2 Bromodomain 30.9 23 0.00049 25.1 0.7 24 17-40 65-88 (103)
34 cd05515 Bromo_polybromo_V Brom 30.5 23 0.0005 25.3 0.7 23 17-39 65-87 (105)
35 PRK00783 DNA-directed RNA poly 30.4 58 0.0013 26.8 3.2 29 62-90 223-251 (263)
36 PF03822 NAF: NAF domain; Int 30.4 61 0.0013 21.6 2.7 25 70-94 37-61 (63)
37 PRK09133 hypothetical protein; 29.8 88 0.0019 27.5 4.4 44 52-95 329-372 (472)
38 PRK00933 ribosomal biogenesis 28.6 51 0.0011 25.9 2.4 32 70-101 4-35 (165)
39 PF00587 tRNA-synt_2b: tRNA sy 28.3 2.4E+02 0.0053 21.1 6.1 45 72-121 123-168 (173)
40 TIGR02544 III_secr_YscJ type I 28.3 98 0.0021 24.7 4.1 31 73-104 25-59 (193)
41 cd05521 Bromo_Rsc1_2_I Bromodo 28.2 25 0.00053 25.4 0.5 24 17-40 64-87 (106)
42 PF01514 YscJ_FliF: Secretory 27.4 47 0.001 26.6 2.1 23 74-97 35-57 (206)
43 cd05498 Bromo_Brdt_II_like Bro 26.7 27 0.00059 24.4 0.6 23 17-39 64-86 (102)
44 TIGR02554 PrgH type III secret 26.7 1.8E+02 0.004 26.0 5.8 59 61-121 279-358 (389)
45 PF00120 Gln-synt_C: Glutamine 26.5 1.8E+02 0.0039 23.7 5.4 42 73-125 64-105 (259)
46 cd05508 Bromo_RACK7 Bromodomai 26.3 28 0.00061 24.8 0.6 21 18-38 62-82 (99)
47 cd05513 Bromo_brd7_like Bromod 26.3 28 0.00061 24.8 0.6 24 16-39 59-82 (98)
48 TIGR01910 DapE-ArgE acetylorni 26.3 1.4E+02 0.0031 25.0 4.9 40 51-90 242-281 (375)
49 TIGR01892 AcOrn-deacetyl acety 25.6 1.4E+02 0.003 24.7 4.7 38 52-89 233-270 (364)
50 PRK08651 succinyl-diaminopimel 25.4 1.3E+02 0.0028 25.4 4.6 40 51-90 250-289 (394)
51 cd05522 Bromo_Rsc1_2_II Bromod 25.2 34 0.00074 24.4 0.8 24 17-40 66-89 (104)
52 smart00662 RPOLD RNA polymeras 24.9 88 0.0019 25.3 3.3 28 62-89 192-219 (224)
53 PRK00466 acetyl-lysine deacety 24.8 1.6E+02 0.0036 24.5 5.0 38 52-89 212-249 (346)
54 PRK14543 nucleoside diphosphat 24.8 79 0.0017 24.9 2.9 54 51-104 99-169 (169)
55 PRK13007 succinyl-diaminopimel 24.6 1.9E+02 0.0042 23.9 5.4 41 51-91 227-267 (352)
56 cd05501 Bromo_SP100C_like Brom 24.4 24 0.00052 25.6 -0.1 19 19-37 61-79 (102)
57 PRK08262 hypothetical protein; 24.3 1.4E+02 0.003 26.3 4.7 44 52-95 342-385 (486)
58 PRK07522 acetylornithine deace 24.1 1.7E+02 0.0036 24.6 5.0 38 52-89 243-280 (385)
59 PF05639 Pup: Pup-like protein 24.1 31 0.00067 23.7 0.4 25 72-96 37-61 (69)
60 PF07137 VDE: Violaxanthin de- 23.7 48 0.001 27.1 1.5 29 68-96 152-180 (198)
61 cd05499 Bromo_BDF1_2_II Bromod 23.4 34 0.00075 24.0 0.6 22 18-39 65-86 (102)
62 cd05512 Bromo_brd1_like Bromod 23.3 35 0.00075 24.2 0.6 24 16-39 59-82 (98)
63 cd05528 Bromo_AAA Bromodomain; 23.2 33 0.00072 25.0 0.4 21 17-37 62-82 (112)
64 PF07927 YcfA: YcfA-like prote 23.0 84 0.0018 19.3 2.3 16 81-96 2-17 (56)
65 PF12691 Minor_capsid_3: Minor 22.9 1.4E+02 0.0029 22.6 3.8 49 56-104 51-101 (135)
66 PRK08201 hypothetical protein; 22.8 1.6E+02 0.0035 25.6 4.8 35 55-89 315-349 (456)
67 cd07030 RNAP_D D subunit of Ar 22.6 1E+02 0.0023 25.2 3.3 28 63-90 224-251 (259)
68 PF13771 zf-HC5HC2H: PHD-like 22.4 1.6E+02 0.0034 19.7 3.7 35 74-108 22-56 (90)
69 PRK06222 ferredoxin-NADP(+) re 22.1 1.1E+02 0.0023 25.2 3.3 20 74-93 187-206 (281)
70 PRK07205 hypothetical protein; 22.0 1.8E+02 0.0039 25.3 4.9 39 57-95 314-352 (444)
71 TIGR01893 aa-his-dipept aminoa 21.7 1.6E+02 0.0036 26.0 4.6 39 58-96 348-386 (477)
72 cd05524 Bromo_polybromo_I Brom 21.7 42 0.00091 24.4 0.7 23 17-39 67-89 (113)
73 PRK08596 acetylornithine deace 21.7 1.9E+02 0.0041 25.0 4.9 39 51-89 262-300 (421)
74 KOG2774|consensus 21.6 61 0.0013 28.0 1.8 33 63-96 276-308 (366)
75 TIGR00106 uncharacterized prot 21.5 1.4E+02 0.003 21.3 3.4 28 72-100 13-40 (97)
76 PRK12778 putative bifunctional 21.4 97 0.0021 29.3 3.3 44 74-117 187-250 (752)
77 PRK08737 acetylornithine deace 21.0 2.3E+02 0.005 24.1 5.3 45 51-95 229-273 (364)
78 PRK07907 hypothetical protein; 20.9 2.2E+02 0.0047 24.8 5.2 38 53-90 305-342 (449)
79 PRK06446 hypothetical protein; 20.8 2.2E+02 0.0047 24.8 5.2 38 54-91 295-332 (436)
80 cd05507 Bromo_brd8_like Bromod 20.7 42 0.00091 23.9 0.6 22 17-38 62-83 (104)
81 PF00101 RuBisCO_small: Ribulo 20.5 1.6E+02 0.0035 21.2 3.6 30 65-94 47-76 (99)
82 PRK15327 type III secretion sy 20.4 3E+02 0.0065 24.7 5.9 57 63-121 286-363 (393)
83 cd05520 Bromo_polybromo_III Br 20.2 44 0.00095 23.9 0.6 22 18-39 66-87 (103)
84 PRK05111 acetylornithine deace 20.2 2E+02 0.0044 24.1 4.7 38 52-89 246-283 (383)
No 1
>PF02149 KA1: Kinase associated domain 1; InterPro: IPR001772 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Eukaryotic protein kinases [, , , , ] are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme []. Members of the KIN2/PAR-1/MARK kinase subfamily are conserved from yeast to human and share the same domain organisation: an N-terminal kinase domain (IPR000719 from INTERPRO) and a C-terminal kinase associated domain 1 (KA1). Some members of the KIN1/PAR-1/MARK family also contain an UBA domain (IPR000449 from INTERPRO). Members of this kinase subfamily are involved in various biological processes such as cell polarity, cell cycle control, intracellular signalling, microtubule stability and protein stability []. The function of the KA1 domain is not yet known. Some proteins known to contain a KA1 domain are listed below: Mammalian MAP/microtubule affinity-regulating kinases (MARK 1,2,3). They regulate polarity in neuronal cell models and appear to function redundantly in phosphorylating MT-associated proteins and in regulating MT stability []. Mammalian maternal embryonic leucine zipper kinase (MELK). It phosphorylates ZNF622 and may contribute to its redirection to the nucleus. It may be involved in the inhibition of spliceosome assembly during mitosis. Caenorhabditis elegans and drosophila PAR-1 protein. It is required for establishing polarity in embryos where it is asymmetrically distributed []. Fungal Kin1 and Kin2 protein kinases involved in regulation of exocytosis. They localise to the cytoplasmic face of the plasma membrane []. Plant KIN10 and KIN11 proteins, catalytic subunits of the putative trimeric SNF1-related protein kinase (SnRK) complex. This entry represents the KA1 domain.; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 3OSE_A 1V5S_A 1UL7_A.
Probab=99.57 E-value=1.8e-15 Score=96.28 Aligned_cols=33 Identities=58% Similarity=0.876 Sum_probs=29.5
Q ss_pred cceEEEEEEEeeCCCCCceeeEEEecCccceee
Q psy2660 113 SLVQWEIEVCKLPRLSLNGVRFKRISDHIISKI 145 (149)
Q Consensus 113 ~~v~fEmEVCkLp~l~l~GIrfKRisGd~w~~~ 145 (149)
..|+|||||||+|+++++||+||||+||+|+|-
T Consensus 3 ~~v~fEieV~kl~~~~l~Gv~~kRi~Gd~~~yk 35 (47)
T PF02149_consen 3 EVVKFEIEVCKLPRLGLYGVDFKRISGDSWQYK 35 (47)
T ss_dssp C-EEEEEEEEEECCCTCEEEEEEEEES-HHHHH
T ss_pred cceEEEEEEEEecCCCeeEEEEEEeeCCHHHHH
Confidence 579999999999999999999999999999983
No 2
>KOG0586|consensus
Probab=98.44 E-value=9.3e-08 Score=87.37 Aligned_cols=53 Identities=77% Similarity=1.303 Sum_probs=50.1
Q ss_pred HHHHHHHhhhCCCceeeeCCEEEEEEeCCCCCCcceEEEEEEEeeCCCCCceeeEEEec
Q psy2660 80 RAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRIS 138 (149)
Q Consensus 80 ~~EI~rvL~~~~i~y~~~~~y~l~C~~~d~~~~~~v~fEmEVCkLp~l~l~GIrfKRis 138 (149)
+.|+++|++.++++|++.+ .|+|++....++|++|||++|++++||+||+|++
T Consensus 536 ~~~~~~v~~~~~~~~~~~~------~~~~~~a~a~~~~~~~~~~~~~~s~~g~r~~r~s 588 (596)
T KOG0586|consen 536 MREIRKVLDANGCDYEQLR------YHGDPGADAMVQWEMEVCKLPRLSLNGVRFRRIS 588 (596)
T ss_pred hhhhhhccccccccccccc------cCCCCCcccccccccceeecCcccccceeecccc
Confidence 8999999999999999974 6888888899999999999999999999999998
No 3
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=97.71 E-value=6.6e-06 Score=73.17 Aligned_cols=46 Identities=24% Similarity=0.582 Sum_probs=41.2
Q ss_pred ccccccCcCCcccchhhHHHHHHHHhhcCccccCCCCccccCCCce
Q psy2660 2 DKVEGADFNEMEPFLSPMMHTVCLVWANCKYYQGPMAMEPVPKHNV 47 (149)
Q Consensus 2 ~~~E~~~f~~~~~~i~pl~h~v~LiW~~s~yY~~p~ri~vv~~~~~ 47 (149)
+.|+..+|+++...|+|++|+++++|.+|+||+++.||+.+.....
T Consensus 110 ~~l~~~~~~~i~~~i~~l~~~l~~iw~~S~~y~~~~R~~~Ll~~is 155 (579)
T PF08385_consen 110 ELLEASDLSEIQESIPPLFHHLRLIWRISRYYYPPERMTSLLEKIS 155 (579)
T ss_pred HhhccCCHHHHHHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHH
Confidence 5678889999999999999999999999999999999998854433
No 4
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=66.97 E-value=2.3 Score=25.39 Aligned_cols=17 Identities=18% Similarity=0.591 Sum_probs=12.2
Q ss_pred HHHHHHHhhhCCCceee
Q psy2660 80 RAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 80 ~~EI~rvL~~~~i~y~~ 96 (149)
+.||+++|+++||+|..
T Consensus 6 V~~Lk~iL~~~~I~~ps 22 (35)
T PF12949_consen 6 VAQLKRILDEHGIEFPS 22 (35)
T ss_dssp SHHHHHHHHHHT---SS
T ss_pred HHHHHHHHHHcCCCCCC
Confidence 57999999999999964
No 5
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=60.51 E-value=3.4 Score=24.47 Aligned_cols=21 Identities=24% Similarity=0.434 Sum_probs=17.8
Q ss_pred ChHHHHHHHHHHhhhCCCcee
Q psy2660 75 DPNEIRAEIRKVLDANNCDYE 95 (149)
Q Consensus 75 ~P~ei~~EI~rvL~~~~i~y~ 95 (149)
..++++.||-.||+.|.-+|-
T Consensus 4 ~~D~lLDeId~vLe~NAe~FV 24 (33)
T TIGR03687 4 GVDDLLDEIDGVLESNAEEFV 24 (33)
T ss_pred hHHHHHHHHHHHHHHhHHHHH
Confidence 678999999999999876653
No 6
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=51.79 E-value=34 Score=22.22 Aligned_cols=32 Identities=25% Similarity=0.428 Sum_probs=25.7
Q ss_pred CCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 58 KPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 58 kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
.|..=++.|.+.|+.+.+|.+++.+=.+.|.+
T Consensus 32 ~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~ 63 (66)
T PF01193_consen 32 HPNEDKFVFRIETDGSLTPKEALLKAIKILKE 63 (66)
T ss_dssp SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHH
T ss_pred cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHH
Confidence 45666899999999999999999987777654
No 7
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=51.67 E-value=17 Score=31.09 Aligned_cols=32 Identities=22% Similarity=0.317 Sum_probs=27.6
Q ss_pred CeeEeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 59 PRSLRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 59 PR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
.+.=+|.|+|.+|.+.+|++|+.+=.++|.++
T Consensus 253 ~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K 284 (291)
T cd07032 253 RVRDHFIFSIESTGALPPDVLFLEAIKILKEK 284 (291)
T ss_pred EeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHH
Confidence 34448999999999999999999999998764
No 8
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=51.39 E-value=22 Score=24.54 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=23.4
Q ss_pred eeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 63 RFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 63 k~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
++.|.|.|+.+.+|.+++.+-.+.|..
T Consensus 55 ~~~~~VeT~Gs~~P~~al~~Ai~~L~~ 81 (86)
T cd00460 55 KFILRIETVGSIPPEEALRRAVEILRK 81 (86)
T ss_pred eEEEEEEECCCCCHHHHHHHHHHHHHH
Confidence 688999999999999999877777654
No 9
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=49.67 E-value=19 Score=30.08 Aligned_cols=29 Identities=17% Similarity=0.316 Sum_probs=25.5
Q ss_pred EeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 62 LRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 62 lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
=+|.|+|-+|.+.+|++|+.+=.++|.++
T Consensus 226 ~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K 254 (265)
T cd07031 226 DKFYFNVESTGALPPEQIVLSGLEILKKK 254 (265)
T ss_pred CEEEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 36999999999999999999888888763
No 10
>PRK13009 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=49.18 E-value=48 Score=27.74 Aligned_cols=42 Identities=19% Similarity=0.449 Sum_probs=36.1
Q ss_pred CCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCceee
Q psy2660 55 DQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 55 ~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
...-|-.....+++......+++++.++|++++++.++.++-
T Consensus 243 ~nvip~~~~~~~diR~~~~~~~e~i~~~i~~~~~~~~~~~~~ 284 (375)
T PRK13009 243 TNVIPGELEAQFNFRFSTEHTAESLKARVEAILDKHGLDYTL 284 (375)
T ss_pred CcccCCcEEEEEEEecCCCCCHHHHHHHHHHHHHhcCCCeEE
Confidence 356788999999999999999999999999999987665543
No 11
>PRK08652 acetylornithine deacetylase; Provisional
Probab=49.04 E-value=51 Score=27.16 Aligned_cols=46 Identities=17% Similarity=0.272 Sum_probs=39.2
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCceeee
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQR 97 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~~ 97 (149)
+.....-|-..+..+++......+++++.++|++.+...++.++..
T Consensus 212 g~~~nviP~~~~~~~diR~~~~~~~~~v~~~i~~~~~~~~v~~~~~ 257 (347)
T PRK08652 212 GSPEYSIPALCRLRLDARIPPEVEVEDVLDEIDPILDEYTVKYEYT 257 (347)
T ss_pred CCCCCccCCcEEEEEEEEcCCCCCHHHHHHHHHHHHHhcCceEEEe
Confidence 3445677999999999999999999999999999999877777643
No 12
>cd03030 GRX_SH3BGR Glutaredoxin (GRX) family, SH3BGR (SH3 domain binding glutamic acid-rich protein) subfamily; a recently-identified subfamily composed of SH3BGR and similar proteins possessing significant sequence similarity to GRX, but without a redox active CXXC motif. The SH3BGR gene was cloned in an effort to identify genes mapping to chromosome 21, which could be involved in the pathogenesis of congenital heart disease affecting Down syndrome newborns. Several human SH3BGR-like (SH3BGRL) genes have been identified since, mapping to different locations in the chromosome. Of these, SH3BGRL3 was identified as a tumor necrosis factor (TNF) alpha inhibitory protein and was also named TIP-B1. Upregulation of expression of SH3BGRL3 is associated with differentiation. It has been suggested that it functions as a regulator of differentiation-related signal transduction pathways.
Probab=45.56 E-value=26 Score=24.68 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=22.1
Q ss_pred eeecccCCChHHHHHHHHHHhhhCCCceeee
Q psy2660 67 SMKTTSSRDPNEIRAEIRKVLDANNCDYEQR 97 (149)
Q Consensus 67 svsTTSsk~P~ei~~EI~rvL~~~~i~y~~~ 97 (149)
..++++++.--+=-+++++.|++++|+|+..
T Consensus 6 ~ts~~g~~~~k~~~~~v~~lL~~k~I~f~ei 36 (92)
T cd03030 6 IASSSGSTEIKKRQQEVLGFLEAKKIEFEEV 36 (92)
T ss_pred EecccccHHHHHHHHHHHHHHHHCCCceEEE
Confidence 3344444444455568999999999999974
No 13
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=44.52 E-value=1.2e+02 Score=23.17 Aligned_cols=63 Identities=19% Similarity=0.277 Sum_probs=37.4
Q ss_pred CCCCeeEeeeeeeecccC-CChHHHHHHHHHHhhhCCCceeeeCCEEEEEEeCCCCCCcceEEEEEEE
Q psy2660 56 QVKPRSLRFTWSMKTTSS-RDPNEIRAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVC 122 (149)
Q Consensus 56 ~~kPR~lk~~fsvsTTSs-k~P~ei~~EI~rvL~~~~i~y~~~~~y~l~C~~~d~~~~~~v~fEmEVC 122 (149)
..+.+.+...+.++.++. ..++++++++.+.++++.-.+....+......-++ ..+.+++.+.
T Consensus 112 ~~~~~~~~v~~~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~i~~~ 175 (206)
T PF00924_consen 112 SSPYRRVVVEIPVDYDTDPEKIEELREKIEEALRSNPYIFKEPEPRVVVDEIGD----SSLEFRIRVY 175 (206)
T ss_dssp -SSEEEEEEEEEE-TTS----HHHHHHHHHHHHHH-TTC-TTS-EEEEEEEE-S----SSEEEEEEEE
T ss_pred cCCceeeeeeeeEecCCCchHHHHHHHHHHHHHhcCchhhcCCCCeEEEccccC----CceEEEEEEE
Confidence 355677788888877766 78999999999999887655543334555554444 3466766643
No 14
>PF04908 SH3BGR: SH3-binding, glutamic acid-rich protein; InterPro: IPR006993 This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity []. ; PDB: 1SJ6_A 1U6T_A 1WRY_A 1T1V_B 1J0F_A 2CT6_A.
Probab=44.12 E-value=23 Score=25.53 Aligned_cols=29 Identities=17% Similarity=0.349 Sum_probs=18.3
Q ss_pred eecccCCChHHHHHHHHHHhhhCCCceee
Q psy2660 68 MKTTSSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 68 vsTTSsk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
.++|+++.-..=-++|.+.|++++|+|+.
T Consensus 8 ss~sg~~~ikk~q~~v~~iL~a~kI~fe~ 36 (99)
T PF04908_consen 8 SSISGSREIKKRQQRVLMILEAKKIPFEE 36 (99)
T ss_dssp -SS-SSHHHHHHHHHHHHHHHHTT--EEE
T ss_pred ecccCCHHHHHHHHHHHHHHHHcCCCcEE
Confidence 34445544455556999999999999985
No 15
>PF07687 M20_dimer: Peptidase dimerisation domain This family only corresponds to M20 family; InterPro: IPR011650 This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the MEROPS peptidase family M20 []. This family includes a range of zinc exopeptidases: carboxypeptidases, dipeptidases and specialised aminopeptidases [].; GO: 0016787 hydrolase activity; PDB: 3GB0_A 2F7V_A 1R3N_C 2VL1_D 2V8V_C 1R43_B 2V8G_B 2V8H_D 2V8D_A 3PFE_A ....
Probab=39.81 E-value=35 Score=23.17 Aligned_cols=39 Identities=23% Similarity=0.312 Sum_probs=33.6
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
+.....-|-...+.+++......+++++.++|++.+++.
T Consensus 69 G~~~n~ip~~a~~~~~~R~~p~~~~~~i~~~i~~~~~~~ 107 (111)
T PF07687_consen 69 GTAPNVIPDEATLTVDIRYPPGEDLEEIKAEIEAAVEKI 107 (111)
T ss_dssp ESSTTEESSEEEEEEEEEESTCHHHHHHHHHHHHHHHHH
T ss_pred CCcCCEECCEEEEEEEEECCCcchHHHHHHHHHHHHHHh
Confidence 335566788899999999999999999999999999864
No 16
>KOG1521|consensus
Probab=37.23 E-value=34 Score=29.89 Aligned_cols=29 Identities=28% Similarity=0.421 Sum_probs=26.4
Q ss_pred EeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 62 LRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 62 lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
=+|.|++.+|..+.|+.+..|-.+||..+
T Consensus 301 dHfIFsvestgal~p~~lf~eavkvle~K 329 (338)
T KOG1521|consen 301 DHFIFSVESTGALKPEVLFEEAVKVLEEK 329 (338)
T ss_pred ceEEEEeecccCCCchhhHHHHHHHHHHH
Confidence 37999999999999999999999999863
No 17
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=37.17 E-value=63 Score=23.39 Aligned_cols=38 Identities=21% Similarity=0.421 Sum_probs=25.6
Q ss_pred CCChHHHHHHHHHHhhhCCCceeeeCCEEEEEEeCCCCCCcceEEEE
Q psy2660 73 SRDPNEIRAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEI 119 (149)
Q Consensus 73 sk~P~ei~~EI~rvL~~~~i~y~~~~~y~l~C~~~d~~~~~~v~fEm 119 (149)
.++.++|.++|+..|.+ ||.....|.|++.-..-.|+|
T Consensus 10 ~l~~~~i~~Qv~~ll~q---------G~~i~iE~ad~r~~r~~~W~m 47 (99)
T PF00101_consen 10 PLTDEEIAKQVRYLLSQ---------GWIIGIEHADPRRFRTSYWQM 47 (99)
T ss_dssp ---HHHHHHHHHHHHHT---------T-EEEEEEESCGGSTSSS-EE
T ss_pred CCCHHHHHHHHHhhhhc---------CceeeEEecCCCCCCCCEeec
Confidence 34458999999999985 788888888876555556665
No 18
>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=36.70 E-value=15 Score=26.80 Aligned_cols=22 Identities=23% Similarity=0.685 Sum_probs=17.8
Q ss_pred hhHHHHHHHHhhcCccccCCCC
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMA 38 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~r 38 (149)
.-+.+-+-|||.||+-||.+..
T Consensus 67 ~ef~~D~~Li~~N~~~yN~~~s 88 (112)
T cd05510 67 AEFVDDLNLIWKNCLLYNSDPS 88 (112)
T ss_pred HHHHHHHHHHHHHHHHHCCCCC
Confidence 4567788899999999998643
No 19
>cd05860 Ig4_SCFR Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). Ig4_SCFR: The fourth Immunoglobulin (Ig)-like domain in stem cell factor receptor (SCFR). SCFR is organized as an extracellular component having five IG-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR. This fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth domain abolishes the ligand-induced dimerization of SCFR and completely inhibits signal transduction.
Probab=36.11 E-value=23 Score=25.71 Aligned_cols=30 Identities=13% Similarity=0.251 Sum_probs=23.1
Q ss_pred CCCceeeeCCEEEEEEeCCCCCCcceEEEEEE
Q psy2660 90 NNCDYEQRERFLLLCVHGDPNTDSLVQWEIEV 121 (149)
Q Consensus 90 ~~i~y~~~~~y~l~C~~~d~~~~~~v~fEmEV 121 (149)
..+.-++.|.|.+.+.+.|.. ..+.|+++|
T Consensus 70 ~Rlk~~E~G~YTf~a~N~~~~--~s~tF~l~v 99 (101)
T cd05860 70 TRLKGTEGGTYTFLVSNSDAS--ASVTFNVYV 99 (101)
T ss_pred eecChhhCcEEEEEEECCCCe--EEEEEEEEE
Confidence 344456678899999999854 569999986
No 20
>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=35.81 E-value=16 Score=26.33 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=17.8
Q ss_pred hHHHHHHHHhhcCccccCCCCc
Q psy2660 18 PMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 18 pl~h~v~LiW~~s~yY~~p~ri 39 (149)
-+.+-+-|||.||+.||.+...
T Consensus 67 ef~~D~~li~~Na~~yN~~~s~ 88 (107)
T cd05516 67 DLEKDVMLLCQNAQTFNLEGSL 88 (107)
T ss_pred HHHHHHHHHHHHHHHHCCCCCH
Confidence 3566788999999999988654
No 21
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=35.78 E-value=16 Score=25.90 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=18.4
Q ss_pred hhHHHHHHHHhhcCccccCCCCc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
.-..+-+-|||.||+-||.+...
T Consensus 59 ~ef~~D~~li~~Na~~yN~~~s~ 81 (97)
T cd05505 59 QEFLDDMKLVFSNAEKYYENGSY 81 (97)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCH
Confidence 34567788999999999987653
No 22
>cd06218 DHOD_e_trans FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 cofactors: FMN, FAD, and an [2Fe-2S] cluster.
Probab=35.49 E-value=54 Score=26.31 Aligned_cols=20 Identities=5% Similarity=0.194 Sum_probs=16.7
Q ss_pred ChHHHHHHHHHHhhhCCCce
Q psy2660 75 DPNEIRAEIRKVLDANNCDY 94 (149)
Q Consensus 75 ~P~ei~~EI~rvL~~~~i~y 94 (149)
-|..+++.+++.|.+.|++.
T Consensus 187 Gp~~mv~~~~~~L~~~Gv~~ 206 (246)
T cd06218 187 GPEPMLKAVAELAAERGVPC 206 (246)
T ss_pred CCHHHHHHHHHHHHhcCCCE
Confidence 47789999999999987663
No 23
>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=35.38 E-value=17 Score=26.19 Aligned_cols=22 Identities=18% Similarity=0.392 Sum_probs=17.7
Q ss_pred hHHHHHHHHhhcCccccCCCCc
Q psy2660 18 PMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 18 pl~h~v~LiW~~s~yY~~p~ri 39 (149)
-+..-+-|||.||+-||.|...
T Consensus 67 ef~~D~~li~~Na~~yN~~~s~ 88 (107)
T cd05497 67 ECIQDFNTMFTNCYIYNKPGDD 88 (107)
T ss_pred HHHHHHHHHHHHHHHHCCCCCH
Confidence 4566778899999999988654
No 24
>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=35.07 E-value=16 Score=26.67 Aligned_cols=23 Identities=22% Similarity=0.479 Sum_probs=18.4
Q ss_pred hhHHHHHHHHhhcCccccCCCCc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
.-++.-+-|||.||+-||.+...
T Consensus 71 ~~f~~Dv~LI~~Na~~yN~~~s~ 93 (115)
T cd05504 71 EEFLSDIQLVFSNCFLYNPEHTS 93 (115)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCH
Confidence 45677788899999999987643
No 25
>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=34.83 E-value=18 Score=26.12 Aligned_cols=23 Identities=17% Similarity=0.226 Sum_probs=18.5
Q ss_pred hhhHHHHHHHHhhcCccccCCCC
Q psy2660 16 LSPMMHTVCLVWANCKYYQGPMA 38 (149)
Q Consensus 16 i~pl~h~v~LiW~~s~yY~~p~r 38 (149)
+.-+.+-+-|||.||+-||.+..
T Consensus 64 ~~ef~~D~~li~~Na~~yN~~~s 86 (108)
T cd05495 64 PWQYVDDVWLMFDNAWLYNRKTS 86 (108)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCC
Confidence 34567788899999999998754
No 26
>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=34.83 E-value=16 Score=26.11 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=18.8
Q ss_pred hhhHHHHHHHHhhcCccccCCCC
Q psy2660 16 LSPMMHTVCLVWANCKYYQGPMA 38 (149)
Q Consensus 16 i~pl~h~v~LiW~~s~yY~~p~r 38 (149)
+.-+.+-+-|||.||+-||.|..
T Consensus 64 ~~~f~~D~~li~~Na~~yN~~~s 86 (109)
T cd05502 64 PEEFVADVRLMFKNCYKFNEEDS 86 (109)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCC
Confidence 34467788899999999999874
No 27
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase, proteobacterial clade. This model describes a proteobacterial subset of succinyl-diaminopimelate desuccinylases. An experimentally confirmed Gram-positive lineage succinyl-diaminopimelate desuccinylase has been described for Corynebacterium glutamicum, and a neighbor-joining tree shows the seed members, SP:Q59284, and putative archaeal members such as TrEMBL:O58003 in a single clade. However, the archaeal members differ substantially, share a number of motifs with acetylornithine deacetylases rather than succinyl-diaminopimelate desuccinylases, and are not taken as trusted examples of succinyl-diaminopimelate desuccinylases. This model is limited to proteobacterial members for this reason.
Probab=34.68 E-value=1.1e+02 Score=25.56 Aligned_cols=41 Identities=17% Similarity=0.456 Sum_probs=35.5
Q ss_pred CCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCcee
Q psy2660 55 DQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYE 95 (149)
Q Consensus 55 ~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~ 95 (149)
...-|-.....+++..+...+++++.++|++.+++.++..+
T Consensus 240 ~nvvP~~~~~~~diR~~~~~~~~~v~~~i~~~~~~~~~~~~ 280 (370)
T TIGR01246 240 NNVIPGELYVQFNLRFSTEVSDEILKQRVEAILDQHGLDYD 280 (370)
T ss_pred CcccCCceEEEEEEecCCCCCHHHHHHHHHHHHHHcCCCEE
Confidence 35678899999999999999999999999999998766554
No 28
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=33.89 E-value=1.5e+02 Score=23.78 Aligned_cols=48 Identities=21% Similarity=0.434 Sum_probs=30.8
Q ss_pred CCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCceeeeCCEEEEEEeCCCCCCcceEEEE
Q psy2660 57 VKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEI 119 (149)
Q Consensus 57 ~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~~~~y~l~C~~~d~~~~~~v~fEm 119 (149)
+|-|+-+-. -.|..+|++++.+|+.-++++ +|. -.-+|+ .++.++||=
T Consensus 27 ~KdRt~~~~----~~s~~p~~~~~~~l~~yf~~r--------~y~--v~~~d~-~~~~itFeG 74 (173)
T PF12046_consen 27 VKDRTEQVT----FESPQPPDEVLEQLKAYFEQR--------NYR--VAEGDA-EGEVITFEG 74 (173)
T ss_pred ccccEEEEE----EEcCCCHHHHHHHHHHHHHhc--------Cce--ecccCc-cccEEEEEE
Confidence 345555544 347889999999999999874 453 222333 345677773
No 29
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=33.50 E-value=18 Score=25.88 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=18.0
Q ss_pred hhHHHHHHHHhhcCccccCCCCc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
.-+..-+-|||.||+-||.|...
T Consensus 65 ~~f~~D~~lm~~Na~~yN~~~s~ 87 (103)
T cd05517 65 EDMEKDLDLMVKNAKTFNEPGSQ 87 (103)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCH
Confidence 34556788899999999987653
No 30
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=32.39 E-value=74 Score=26.69 Aligned_cols=32 Identities=19% Similarity=0.203 Sum_probs=24.4
Q ss_pred cCCChHHHHHHHHHHhhhCCCceee---eCCEEEEE
Q psy2660 72 SSRDPNEIRAEIRKVLDANNCDYEQ---RERFLLLC 104 (149)
Q Consensus 72 Ssk~P~ei~~EI~rvL~~~~i~y~~---~~~y~l~C 104 (149)
+-.+++| .++|...|+++||+|+. ++|+.+.-
T Consensus 25 sgL~~~d-A~~I~a~L~~~gI~y~~~~~~~G~tI~V 59 (249)
T PRK15348 25 RSLPEDE-ANQMLALLMQHHIDAEKKQEEDGVTLRV 59 (249)
T ss_pred cCCCHHH-HHHHHHHHHHcCCCceEeeCCCCeEEEe
Confidence 4566666 78999999999999975 45776654
No 31
>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=31.92 E-value=19 Score=25.76 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=17.8
Q ss_pred hhHHHHHHHHhhcCccccCCCC
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMA 38 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~r 38 (149)
.-+.+-+-|||.||+-||.+..
T Consensus 65 ~ef~~D~~li~~Na~~yN~~~s 86 (103)
T cd05518 65 EELMDDFKLMFRNARHYNEEGS 86 (103)
T ss_pred HHHHHHHHHHHHHHHHHCCCCC
Confidence 3466778889999999998754
No 32
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=30.97 E-value=39 Score=22.33 Aligned_cols=35 Identities=26% Similarity=0.417 Sum_probs=24.9
Q ss_pred CeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCceee
Q psy2660 59 PRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 59 PR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
||.+..-.+++. +-+.+-...+.+.|+++|+.|+.
T Consensus 34 P~~i~~~CG~al---~~~~~d~~~i~~~l~~~~i~~~~ 68 (73)
T PF11823_consen 34 PREISAGCGLAL---RFEPEDLEKIKEILEENGIEYEG 68 (73)
T ss_pred ChhccCCCCEEE---EEChhhHHHHHHHHHHCCCCeeE
Confidence 666655555544 22346678899999999999985
No 33
>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=30.93 E-value=23 Score=25.12 Aligned_cols=24 Identities=17% Similarity=0.351 Sum_probs=19.3
Q ss_pred hhHHHHHHHHhhcCccccCCCCcc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAME 40 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri~ 40 (149)
..+.+-+-|||.||+-||.|....
T Consensus 65 ~~f~~D~~li~~Na~~yn~~~s~i 88 (103)
T cd05519 65 EEFLEDFHLMFANARTYNQEGSIV 88 (103)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHH
Confidence 456688899999999999886543
No 34
>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=30.47 E-value=23 Score=25.29 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=18.2
Q ss_pred hhHHHHHHHHhhcCccccCCCCc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
.-+..-+.|||.||+-||.+...
T Consensus 65 ~ef~~D~~l~~~Na~~yN~~~s~ 87 (105)
T cd05515 65 DDMVSDFVLMFDNACKYNEPDSQ 87 (105)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCH
Confidence 44566788999999999987653
No 35
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=30.39 E-value=58 Score=26.78 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=25.2
Q ss_pred EeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 62 LRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 62 lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
-++.|++.+|.+.+|++++.+=.++|.++
T Consensus 223 ~~~if~vEs~G~l~p~~iv~~A~~~l~~k 251 (263)
T PRK00783 223 NKFIFTVESDGSLPVEEILLEALKILKRK 251 (263)
T ss_pred CeEEEEeccCCCCCHHHHHHHHHHHHHHH
Confidence 36889999999999999999888888753
No 36
>PF03822 NAF: NAF domain; InterPro: IPR004041 The NAF domain is a 24 amino acid domain that is found in a plant-specific subgroup of serine-threonine protein kinases (CIPKs), that interact with calcineurin B-like calcium sensor proteins (CBLs). Whereas the N-terminal part of CIPKs comprises a conserved catalytic domain typical of Ser-Thr kinases, the much less conserved C-terminal domain appears to be unique to this subgroup of kinases. The only exception is the NAF domain that forms an 'island of conservation' in this otherwise variable region. The NAF domain has been named after the prominent conserved amino acids Asn-Ala-Phe. It represents a minimum protein interaction module that is both necessary and sufficient to mediate the interaction with the CBL calcium sensor proteins []. The secondary structure of the NAF domain is currently not known, but secondary structure computation of the C-terminal region of Arabidopsis thaliana CBL-interacting protein kinase 1 revealed a long helical structure [].; GO: 0007165 signal transduction; PDB: 2ZFD_B 2EHB_D.
Probab=30.37 E-value=61 Score=21.62 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=19.4
Q ss_pred cccCCChHHHHHHHHHHhhhCCCce
Q psy2660 70 TTSSRDPNEIRAEIRKVLDANNCDY 94 (149)
Q Consensus 70 TTSsk~P~ei~~EI~rvL~~~~i~y 94 (149)
-||..+|++|+..|..+....|...
T Consensus 37 F~S~~~~~~Ii~klEe~a~~~~~~V 61 (63)
T PF03822_consen 37 FTSKEPASEIIEKLEEIAKKLGFRV 61 (63)
T ss_dssp EEESS-HHHHHHHHHHHHHHTTEEE
T ss_pred EecCCCHHHHHHHHHHHHHhcCcee
Confidence 4588999999999999998765443
No 37
>PRK09133 hypothetical protein; Provisional
Probab=29.83 E-value=88 Score=27.50 Aligned_cols=44 Identities=9% Similarity=0.153 Sum_probs=36.9
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCcee
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYE 95 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~ 95 (149)
+.....-|-..++.+++..+...+++++.++|++.++..++.++
T Consensus 329 G~~~NvVP~~a~~~lDiR~~p~~~~e~v~~~I~~~i~~~~v~v~ 372 (472)
T PRK09133 329 GHAENALPQRATANVNCRIFPGDTIEAVRATLKQVVADPAIKIT 372 (472)
T ss_pred CCcCccCCCceEEEEEEEeCCchhHHHHHHHHHHHhcCCCEEEE
Confidence 34456788899999999999999999999999999987555554
No 38
>PRK00933 ribosomal biogenesis protein; Validated
Probab=28.57 E-value=51 Score=25.92 Aligned_cols=32 Identities=25% Similarity=0.446 Sum_probs=23.4
Q ss_pred cccCCChHHHHHHHHHHhhhCCCceeeeCCEE
Q psy2660 70 TTSSRDPNEIRAEIRKVLDANNCDYEQRERFL 101 (149)
Q Consensus 70 TTSsk~P~ei~~EI~rvL~~~~i~y~~~~~y~ 101 (149)
|||.++-+.+++-.+......|+.|-.+|.+.
T Consensus 4 TTSrkPs~~t~~fAkeLa~~ln~~yv~Rgk~S 35 (165)
T PRK00933 4 TTSRKPSQRTRSLVKDLARFLNCKYVNRGKMS 35 (165)
T ss_pred ECCCCCCHHHHHHHHHHHHHhCCEEEccCCcc
Confidence 66666666677777776667799998877665
No 39
>PF00587 tRNA-synt_2b: tRNA synthetase class II core domain (G, H, P, S and T) This Prosite entry contains all class II enzymes. seryl tRNA synthetase structure; InterPro: IPR002314 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain includes the glycine, histidine, proline, threonine and serine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3UH0_A 3UGT_C 3UGQ_A 1B76_B 1GGM_B 1ATI_A 1ADY_C 1ADJ_C 2I4O_A 2I4M_B ....
Probab=28.33 E-value=2.4e+02 Score=21.07 Aligned_cols=45 Identities=18% Similarity=0.282 Sum_probs=29.7
Q ss_pred cCCChHHHHHHHHHHhhhCCC-ceeeeCCEEEEEEeCCCCCCcceEEEEEE
Q psy2660 72 SSRDPNEIRAEIRKVLDANNC-DYEQRERFLLLCVHGDPNTDSLVQWEIEV 121 (149)
Q Consensus 72 Ssk~P~ei~~EI~rvL~~~~i-~y~~~~~y~l~C~~~d~~~~~~v~fEmEV 121 (149)
+...-+++++-+.++++..|+ +|+.. .+..++..+...-.|.+|+
T Consensus 123 ~~~~~~~~~~~~~~i~~~lgl~~~~~~-----~~~~~~~~~~~~~~~d~e~ 168 (173)
T PF00587_consen 123 SEEEFEELLELYKEILEKLGLEPYRIV-----LSSSGELGAYAKYEFDIEA 168 (173)
T ss_dssp HHHHHHHHHHHHHHHHHHTTSGCEEEE-----EEETCTSCTTSSEEEEEEE
T ss_pred cHHHHHHHHHHHHHHHHHcCCceEEEE-----EcCCCccCCCHHHcccHHH
Confidence 334456667777888889999 77753 2334454455677888886
No 40
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=28.26 E-value=98 Score=24.68 Aligned_cols=31 Identities=19% Similarity=0.238 Sum_probs=22.0
Q ss_pred CCChHHHHHHHHHHhhhCCCceee----eCCEEEEE
Q psy2660 73 SRDPNEIRAEIRKVLDANNCDYEQ----RERFLLLC 104 (149)
Q Consensus 73 sk~P~ei~~EI~rvL~~~~i~y~~----~~~y~l~C 104 (149)
..++++ .++|...|+++||.|+. ++|+.+.-
T Consensus 25 ~L~~~d-a~~I~~~L~~~gI~y~~~~~~~~g~~I~V 59 (193)
T TIGR02544 25 GLSERE-ANEMLAVLMRHGIDAEKEGSGKGGYTISV 59 (193)
T ss_pred CCCHHH-HHHHHHHHHHCCCCeEEeecCCCCeEEEE
Confidence 345555 67889999999999986 24565554
No 41
>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=28.20 E-value=25 Score=25.43 Aligned_cols=24 Identities=8% Similarity=0.135 Sum_probs=19.0
Q ss_pred hhHHHHHHHHhhcCccccCCCCcc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAME 40 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri~ 40 (149)
.-+.+-+.|||.||+-||.+....
T Consensus 64 ~ef~~D~~li~~Na~~yN~~~s~i 87 (106)
T cd05521 64 QEFVNDLAQIPWNARLYNTKGSVI 87 (106)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCHH
Confidence 345678899999999999877543
No 42
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=27.36 E-value=47 Score=26.65 Aligned_cols=23 Identities=30% Similarity=0.411 Sum_probs=17.5
Q ss_pred CChHHHHHHHHHHhhhCCCceeee
Q psy2660 74 RDPNEIRAEIRKVLDANNCDYEQR 97 (149)
Q Consensus 74 k~P~ei~~EI~rvL~~~~i~y~~~ 97 (149)
.++.+ .++|...|+++||+|+..
T Consensus 35 l~~~d-a~~i~~~L~~~gI~y~~~ 57 (206)
T PF01514_consen 35 LDEED-ANEIVAALDENGIPYKLS 57 (206)
T ss_dssp E-HHH-HHHHHHHHHHTT--EEEE
T ss_pred CCHHH-HHHHHHHHHHCCCCcEec
Confidence 56777 799999999999999984
No 43
>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.68 E-value=27 Score=24.44 Aligned_cols=23 Identities=26% Similarity=0.446 Sum_probs=18.1
Q ss_pred hhHHHHHHHHhhcCccccCCCCc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
.-+..-+-|||.||+-||.|...
T Consensus 64 ~ef~~D~~li~~Na~~yn~~~s~ 86 (102)
T cd05498 64 QEFAADVRLMFSNCYKYNPPDHP 86 (102)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCH
Confidence 44566778899999999987643
No 44
>TIGR02554 PrgH type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex.
Probab=26.66 E-value=1.8e+02 Score=25.99 Aligned_cols=59 Identities=17% Similarity=0.307 Sum_probs=43.5
Q ss_pred eEeeeeeeecccCCChHHHHHHHHHHhhhCCCceee---eCCEEEEEEeCC------------------CCCCcceEEEE
Q psy2660 61 SLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQ---RERFLLLCVHGD------------------PNTDSLVQWEI 119 (149)
Q Consensus 61 ~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~---~~~y~l~C~~~d------------------~~~~~~v~fEm 119 (149)
.+.+.-+++..+ ++.+++.++=+.-|++.+|.|++ .+++.|. ..+. ..|+..|+|-+
T Consensus 279 ~~pya~~v~I~~-~s~~~l~~~Ae~GL~~~ni~yr~i~~~~~vtFi-I~~aL~D~~l~~l~~Fv~~F~~~WG~~~VqFsI 356 (389)
T TIGR02554 279 LMPYARDVRIID-ADDGAAEQQAENGLDKQALPYRRLARRGGVTFV-IAGALDDEELARARQFVDSYYRKWGGRYVQFAI 356 (389)
T ss_pred hCCccceeEEEE-cCHHHHHHHHHhhHHhcCCceEEEecCCcEEEE-EcCCCCHHHHHHHHHHHHHHHHhhCccEEEEEE
Confidence 444555565544 89999999999999999999998 3566654 3443 14568899998
Q ss_pred EE
Q psy2660 120 EV 121 (149)
Q Consensus 120 EV 121 (149)
+.
T Consensus 357 ~L 358 (389)
T TIGR02554 357 EL 358 (389)
T ss_pred Ee
Confidence 83
No 45
>PF00120 Gln-synt_C: Glutamine synthetase, catalytic domain; InterPro: IPR008146 Glutamine synthetase (6.3.1.2 from EC) (GS) [] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [, , ]: Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637 from INTERPRO). Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast. Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.; GO: 0004356 glutamate-ammonia ligase activity, 0006807 nitrogen compound metabolic process; PDB: 2J9I_E 3ZXV_D 1HTQ_D 1HTO_F 2BVC_F 2WGS_G 3ZXR_B 2WHI_D 3NG0_A 1LGR_C ....
Probab=26.51 E-value=1.8e+02 Score=23.68 Aligned_cols=42 Identities=21% Similarity=0.139 Sum_probs=28.6
Q ss_pred CCChHHHHHHHHHHhhhCCCceeeeCCEEEEEEeCCCCCCcceEEEEEEEeeC
Q psy2660 73 SRDPNEIRAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLP 125 (149)
Q Consensus 73 sk~P~ei~~EI~rvL~~~~i~y~~~~~y~l~C~~~d~~~~~~v~fEmEVCkLp 125 (149)
....+++++||.+.|.+.||+.++- -|+.. .=|||+.+--.+
T Consensus 64 ~~~~~~~~~~i~~~l~~~Gi~ve~~-------h~E~g----pgQ~Ei~~~~~~ 105 (259)
T PF00120_consen 64 LDAGEDFLEEIVDALEQAGIPVEQI-------HHEVG----PGQYEINLGPCD 105 (259)
T ss_dssp TSTTHHHHHHHHHHHHHCT--EEEE-------EEESS----TTEEEEEEEEEE
T ss_pred hhHHHHHHHHHHHHHHHhhcccccc-------ccccc----hHhhccccccCc
Confidence 4578999999999999999988752 12221 128998876544
No 46
>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.29 E-value=28 Score=24.82 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=17.0
Q ss_pred hHHHHHHHHhhcCccccCCCC
Q psy2660 18 PMMHTVCLVWANCKYYQGPMA 38 (149)
Q Consensus 18 pl~h~v~LiW~~s~yY~~p~r 38 (149)
-..+=+-|||.||+-||.|.-
T Consensus 62 ef~~Dv~LI~~Na~~YN~~~s 82 (99)
T cd05508 62 AFLADAKWILHNAIIYNGGDH 82 (99)
T ss_pred HHHHHHHHHHHHHHHHCCCCC
Confidence 356677889999999998763
No 47
>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.28 E-value=28 Score=24.77 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=19.3
Q ss_pred hhhHHHHHHHHhhcCccccCCCCc
Q psy2660 16 LSPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 16 i~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
+.-+.+-+-|||.||+=||.|...
T Consensus 59 ~~~f~~D~~li~~Na~~yN~~~s~ 82 (98)
T cd05513 59 IEEFKDDFKLMCENAMKYNKPDTI 82 (98)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCH
Confidence 344678889999999999988654
No 48
>TIGR01910 DapE-ArgE acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase. This group of sequences contains annotations for both acetylornithine deacetylase and succinyl-diaminopimelate desuccinylase, but does not contain any members with experimental characterization. Bacillus, Staphylococcus and Sulfolobus species contain multiple hits to this subfamily and each may have a separate activity. Determining which is which must await further laboratory research.
Probab=26.25 E-value=1.4e+02 Score=25.05 Aligned_cols=40 Identities=15% Similarity=0.198 Sum_probs=35.2
Q ss_pred CCCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 51 AVNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 51 ~~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
++.....-|-.....+++......+++++.++|++++++.
T Consensus 242 gG~~~nviP~~~~~~~diR~~~~~~~~~~~~~i~~~~~~~ 281 (375)
T TIGR01910 242 GGDWVNSVPDYCEFSIDVRIIPEENLDEVKQIIEDVVKAL 281 (375)
T ss_pred CCCCcCcCCCEEEEEEEeeeCCCCCHHHHHHHHHHHHHHH
Confidence 3455667899999999999999999999999999999874
No 49
>TIGR01892 AcOrn-deacetyl acetylornithine deacetylase (ArgE). This model represents a clade of acetylornithine deacetylases from proteobacteria. This enzyme is the final step of the "acetylated" ornithine biosynthesis pathway. The enzyme is closely related to dapE, succinyl-diaminopimelate desuccinylase, and outside of this clade annotation is very inaccurate as to which function should be ascribed to genes.
Probab=25.64 E-value=1.4e+02 Score=24.70 Aligned_cols=38 Identities=16% Similarity=0.323 Sum_probs=33.5
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
+.....-|-..+..+++.+....++++++++|++++++
T Consensus 233 g~~~nviP~~~~~~~diR~~p~~~~~~v~~~i~~~~~~ 270 (364)
T TIGR01892 233 GKAVNIIPGACEFVFEWRPIPGMDPEELLQLLETIAQA 270 (364)
T ss_pred CCCCcccCCeEEEEEEeecCCCCCHHHHHHHHHHHHHH
Confidence 44556788899999999999999999999999999986
No 50
>PRK08651 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=25.41 E-value=1.3e+02 Score=25.38 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=34.5
Q ss_pred CCCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 51 AVNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 51 ~~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
++.....-|-...+.+++.+.+..++++++++|++++++.
T Consensus 250 gG~~~nviP~~a~~~~diR~~~~~~~e~i~~~i~~~~~~~ 289 (394)
T PRK08651 250 GGTKTNIVPGYCAFSIDRRLIPEETAEEVRDELEALLDEV 289 (394)
T ss_pred CCCCCCccCCEEEEEEEeeeCCCCCHHHHHHHHHHHHHHH
Confidence 3445567888999999999999999999999999999873
No 51
>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=25.25 E-value=34 Score=24.40 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=19.3
Q ss_pred hhHHHHHHHHhhcCccccCCCCcc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAME 40 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri~ 40 (149)
.-+..-+.|||.||+-|+.|....
T Consensus 66 ~~f~~D~~li~~Na~~yn~~~s~i 89 (104)
T cd05522 66 DQFLNDLNLMFENAKLYNENDSQE 89 (104)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHH
Confidence 446778889999999999887643
No 52
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=24.89 E-value=88 Score=25.31 Aligned_cols=28 Identities=25% Similarity=0.382 Sum_probs=24.6
Q ss_pred EeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 62 LRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 62 lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
=|+.|.+.|+.+.+|++++.+=.++|.+
T Consensus 192 d~l~f~IeT~G~i~p~~al~~A~~iL~~ 219 (224)
T smart00662 192 DKLIFDVETNGSLKPEEAVLEAAKILKE 219 (224)
T ss_pred CEEEEEEEecCCcCHHHHHHHHHHHHHH
Confidence 3689999999999999999888887765
No 53
>PRK00466 acetyl-lysine deacetylase; Validated
Probab=24.85 E-value=1.6e+02 Score=24.47 Aligned_cols=38 Identities=13% Similarity=0.309 Sum_probs=33.6
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
+.....-|-..++.+++......++++++++|++.++.
T Consensus 212 G~~~NvvP~~a~~~~diR~~p~~~~~~v~~~i~~~~~~ 249 (346)
T PRK00466 212 GESYNVTPAKLYLHFDVRYAINNKRDDLISEIKDKFQE 249 (346)
T ss_pred CCcCcccCCceEEEEEEEeCCCCCHHHHHHHHHHHHhh
Confidence 44556778899999999999999999999999999987
No 54
>PRK14543 nucleoside diphosphate kinase; Provisional
Probab=24.84 E-value=79 Score=24.93 Aligned_cols=54 Identities=19% Similarity=0.288 Sum_probs=37.6
Q ss_pred CCCCCCCCCeeEeeeeeeec---------------ccCCChHHHHHHHHHHhhhCC-Cceee-eCCEEEEE
Q psy2660 51 AVNDDQVKPRSLRFTWSMKT---------------TSSRDPNEIRAEIRKVLDANN-CDYEQ-RERFLLLC 104 (149)
Q Consensus 51 ~~~~~~~kPR~lk~~fsvsT---------------TSsk~P~ei~~EI~rvL~~~~-i~y~~-~~~y~l~C 104 (149)
+.....+.|.+||+.|..+. =.|.+|+.-.+||.-.+.... .+|.. .+.|+..|
T Consensus 99 pt~p~~a~p~tIR~~fg~~~~~~~~~~~~~~rN~vH~SDs~esA~rEi~~fF~~~e~~~~~~~~~~~~~~~ 169 (169)
T PRK14543 99 STEPKLAIPGTIRGDFSYHSFNYANEKGFSVYNVIHASANEDDALREIPIWFKDNEILTYKRDDECEHYYC 169 (169)
T ss_pred CCCccccCCCcchhhhcccccccccccccceeeEEECCCCHHHHHHHHHHhCCcccccccccccceeEeeC
Confidence 34456678999999999752 246789999999999997543 34544 34455444
No 55
>PRK13007 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=24.59 E-value=1.9e+02 Score=23.87 Aligned_cols=41 Identities=20% Similarity=0.204 Sum_probs=35.1
Q ss_pred CCCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCC
Q psy2660 51 AVNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANN 91 (149)
Q Consensus 51 ~~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~ 91 (149)
++.....-|...++.+++.+....++++++++|++++...+
T Consensus 227 gG~~~nviP~~a~~~~diR~~p~~~~~~v~~~i~~~~~~~~ 267 (352)
T PRK13007 227 GGVAGNVIPDECVVNVNYRFAPDRSLEEALAHVREVFDGFA 267 (352)
T ss_pred cCCcCccCCCeEEEEEEEeeCCCCCHHHHHHHHHHHhcccc
Confidence 34455678899999999999999999999999999998754
No 56
>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=24.40 E-value=24 Score=25.58 Aligned_cols=19 Identities=16% Similarity=0.307 Sum_probs=15.9
Q ss_pred HHHHHHHHhhcCccccCCC
Q psy2660 19 MMHTVCLVWANCKYYQGPM 37 (149)
Q Consensus 19 l~h~v~LiW~~s~yY~~p~ 37 (149)
..+=+-|||.||+-||.+.
T Consensus 61 f~~D~~Lif~N~~~yN~~~ 79 (102)
T cd05501 61 FVRDMRLIFHNHKLFYKDD 79 (102)
T ss_pred HHHHHHHHHHHHHHHcCCC
Confidence 4566788999999999876
No 57
>PRK08262 hypothetical protein; Provisional
Probab=24.28 E-value=1.4e+02 Score=26.34 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=36.2
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCcee
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYE 95 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~ 95 (149)
+.....-|=...+.+++.++...+++++.++|++.+++.+++++
T Consensus 342 G~~~NvIP~~a~~~~diR~~p~~~~~~i~~~i~~~~~~~~~~v~ 385 (486)
T PRK08262 342 SPKDNVLPQRATATVNFRILPGDSVESVLAHVRRAVADDRVEIE 385 (486)
T ss_pred CCccccCCCccEEEEEEEeCCCCCHHHHHHHHHHHhccCceEEE
Confidence 33445677788999999999999999999999999998655544
No 58
>PRK07522 acetylornithine deacetylase; Provisional
Probab=24.08 E-value=1.7e+02 Score=24.55 Aligned_cols=38 Identities=24% Similarity=0.394 Sum_probs=33.3
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
+.....-|....+.+++......+++++.++|++.+++
T Consensus 243 G~~~nviP~~a~~~~diR~~~~~~~~~i~~~i~~~i~~ 280 (385)
T PRK07522 243 GTALNIVPAECEFDFEFRNLPGDDPEAILARIRAYAEA 280 (385)
T ss_pred CccccccCCceEEEEEEccCCCCCHHHHHHHHHHHHHh
Confidence 34456778899999999999999999999999999987
No 59
>PF05639 Pup: Pup-like protein; InterPro: IPR008515 This family consists of several short bacterial proteins formely known as (DUF797). It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD) []. Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages []. The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup []). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. ; PDB: 3M91_D 3M9D_I.
Probab=24.05 E-value=31 Score=23.66 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=17.0
Q ss_pred cCCChHHHHHHHHHHhhhCCCceee
Q psy2660 72 SSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 72 Ssk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
.+-+.++|+.||-.||+.|-=.|-+
T Consensus 37 ~~~~vD~lLDeID~vLE~NAeeFVr 61 (69)
T PF05639_consen 37 LTDDVDDLLDEIDSVLETNAEEFVR 61 (69)
T ss_dssp CHCCHHHHHHHHTTTSSSC------
T ss_pred hHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568899999999999999877764
No 60
>PF07137 VDE: Violaxanthin de-epoxidase (VDE); InterPro: IPR010788 This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [].; GO: 0046422 violaxanthin de-epoxidase activity, 0055114 oxidation-reduction process, 0009507 chloroplast; PDB: 3CQN_B 3CQR_A.
Probab=23.71 E-value=48 Score=27.10 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=20.8
Q ss_pred eecccCCChHHHHHHHHHHhhhCCCceee
Q psy2660 68 MKTTSSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 68 vsTTSsk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
|-|+|+.=|++++-||++++++.|+++.+
T Consensus 152 VYtrs~~lP~s~~p~l~~aa~k~G~d~~~ 180 (198)
T PF07137_consen 152 VYTRSPTLPESIVPELRRAAKKAGIDFSK 180 (198)
T ss_dssp EEESSSS--GGGHHHHHHHHHHTT--GGG
T ss_pred EEeCCCCCChHHhHHHHHHHHHhCCCHHH
Confidence 34566666999999999999999999874
No 61
>cd05499 Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=23.41 E-value=34 Score=24.02 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=17.5
Q ss_pred hHHHHHHHHhhcCccccCCCCc
Q psy2660 18 PMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 18 pl~h~v~LiW~~s~yY~~p~ri 39 (149)
-+..-+-|||.||+-||.+...
T Consensus 65 ef~~D~~li~~N~~~yn~~~s~ 86 (102)
T cd05499 65 EFERDVRLIFKNCYTFNPEGTD 86 (102)
T ss_pred HHHHHHHHHHHHHHHHCCCCCH
Confidence 4556778899999999987753
No 62
>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=23.35 E-value=35 Score=24.19 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHhhcCccccCCCCc
Q psy2660 16 LSPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 16 i~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
+.-+.+-+-|||.||.-||.|...
T Consensus 59 ~~ef~~D~~li~~Na~~yN~~~s~ 82 (98)
T cd05512 59 LEDFEADFNLIINNCLAYNAKDTI 82 (98)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCH
Confidence 344677888999999999988654
No 63
>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver
Probab=23.16 E-value=33 Score=24.96 Aligned_cols=21 Identities=14% Similarity=0.215 Sum_probs=16.9
Q ss_pred hhHHHHHHHHhhcCccccCCC
Q psy2660 17 SPMMHTVCLVWANCKYYQGPM 37 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ 37 (149)
.-+..-+-|||.||+-||.|.
T Consensus 62 ~ef~~Dv~li~~Na~~yN~~~ 82 (112)
T cd05528 62 KDFLKDIDLIVTNALEYNPDR 82 (112)
T ss_pred HHHHHHHHHHHHHHHHHCCCC
Confidence 345677888999999999764
No 64
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=23.03 E-value=84 Score=19.28 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=13.2
Q ss_pred HHHHHHhhhCCCceee
Q psy2660 81 AEIRKVLDANNCDYEQ 96 (149)
Q Consensus 81 ~EI~rvL~~~~i~y~~ 96 (149)
+|+.++|.+.|+.+..
T Consensus 2 ~el~k~L~~~G~~~~r 17 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVR 17 (56)
T ss_dssp HHHHHHHHHTT-EEEE
T ss_pred hHHHHHHHHCCCEEec
Confidence 6899999999998775
No 65
>PF12691 Minor_capsid_3: Minor capsid protein from bacteriophage; InterPro: IPR024411 This entry represents a minor capsid protein from bacteriophages.
Probab=22.89 E-value=1.4e+02 Score=22.65 Aligned_cols=49 Identities=22% Similarity=0.262 Sum_probs=37.4
Q ss_pred CCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhC-CCcee-eeCCEEEEE
Q psy2660 56 QVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDAN-NCDYE-QRERFLLLC 104 (149)
Q Consensus 56 ~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~-~i~y~-~~~~y~l~C 104 (149)
-.+.+.+.|...++++....+...+.+|-+.|+.. .-+.. ..|.|.|.=
T Consensus 51 G~~~~~~~feI~~K~~d~~~a~~tl~~Is~~Ld~~~~~~L~S~dgSy~f~~ 101 (135)
T PF12691_consen 51 GTREISLPFEIAIKSKDQQKANNTLWEISDYLDNLNDRDLPSQDGSYEFES 101 (135)
T ss_pred CceEeeeeEEEEEecCcHhHHHHHHHHHHHHHHHhhhcCcCcCCCcEEEEE
Confidence 34677888888999999999999999999999985 22333 356786654
No 66
>PRK08201 hypothetical protein; Provisional
Probab=22.78 E-value=1.6e+02 Score=25.64 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=32.4
Q ss_pred CCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 55 DQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 55 ~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
...-|....+.+++......++++++++|++.|++
T Consensus 315 ~NvVP~~a~~~~diR~~p~~~~e~v~~~i~~~l~~ 349 (456)
T PRK08201 315 KTVIPAEAHAKITCRLVPDQDPQEILDLIEAHLQA 349 (456)
T ss_pred ceEECcceEEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence 45679999999999999999999999999999987
No 67
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=22.56 E-value=1e+02 Score=25.21 Aligned_cols=28 Identities=29% Similarity=0.515 Sum_probs=24.5
Q ss_pred eeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 63 RFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 63 k~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
++.|.+.++.+.+|++++.+=.++|.++
T Consensus 224 ~~if~vEs~Gsl~p~~il~~A~~~l~~k 251 (259)
T cd07030 224 RFIFEVESDGSLPPKEILLEALRILKEK 251 (259)
T ss_pred EEEEEEeCCCCCCHHHHHHHHHHHHHHH
Confidence 5889999999999999999888888753
No 68
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=22.36 E-value=1.6e+02 Score=19.71 Aligned_cols=35 Identities=11% Similarity=0.169 Sum_probs=24.1
Q ss_pred CChHHHHHHHHHHhhhCCCceeeeCCEEEEEEeCC
Q psy2660 74 RDPNEIRAEIRKVLDANNCDYEQRERFLLLCVHGD 108 (149)
Q Consensus 74 k~P~ei~~EI~rvL~~~~i~y~~~~~y~l~C~~~d 108 (149)
.+...|-+++++.....-.-.++++|-.+.|.+.+
T Consensus 22 ~~i~~v~~~~~~~~~~~C~~C~~~~Ga~i~C~~~~ 56 (90)
T PF13771_consen 22 FSIEDVEKEIKRRRKLKCSICKKKGGACIGCSHPG 56 (90)
T ss_pred ccHHhHHHHHHHHhCCCCcCCCCCCCeEEEEeCCC
Confidence 34566677777777665555566658999998765
No 69
>PRK06222 ferredoxin-NADP(+) reductase subunit alpha; Reviewed
Probab=22.14 E-value=1.1e+02 Score=25.22 Aligned_cols=20 Identities=5% Similarity=0.008 Sum_probs=16.6
Q ss_pred CChHHHHHHHHHHhhhCCCc
Q psy2660 74 RDPNEIRAEIRKVLDANNCD 93 (149)
Q Consensus 74 k~P~ei~~EI~rvL~~~~i~ 93 (149)
--|..+|+.+.+.|.+.|+.
T Consensus 187 CGP~~M~~~v~~~l~~~gv~ 206 (281)
T PRK06222 187 IGPVIMMKFVAELTKPYGIK 206 (281)
T ss_pred ECCHHHHHHHHHHHHhcCCC
Confidence 35888999999999988764
No 70
>PRK07205 hypothetical protein; Provisional
Probab=22.00 E-value=1.8e+02 Score=25.32 Aligned_cols=39 Identities=8% Similarity=0.185 Sum_probs=34.6
Q ss_pred CCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCcee
Q psy2660 57 VKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYE 95 (149)
Q Consensus 57 ~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~ 95 (149)
..|-..++.+++.+....++++++++|++++++.++.++
T Consensus 314 vvP~~a~~~ld~R~~p~~~~e~v~~~i~~~~~~~~v~~~ 352 (444)
T PRK07205 314 ITKEKSEIRIDIRIPVLADKEKLVQQLSQKAQEYGLTYE 352 (444)
T ss_pred EECCEEEEEEEEeCCCCCCHHHHHHHHHHHHHHcCcEEE
Confidence 467888999999999999999999999999998887765
No 71
>TIGR01893 aa-his-dipept aminoacyl-histidine dipeptidase.
Probab=21.72 E-value=1.6e+02 Score=25.96 Aligned_cols=39 Identities=15% Similarity=0.304 Sum_probs=33.7
Q ss_pred CCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCceee
Q psy2660 58 KPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 58 kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
+|...+..+++......+|+++++.|++.+...++.++.
T Consensus 348 ~~~~~~~~i~~R~~~~~~~~~i~~~i~~~~~~~~~~v~~ 386 (477)
T TIGR01893 348 KENKVIFTFLIRSSVESDKDYVTEKIESIAKLAGARVEV 386 (477)
T ss_pred cCCEEEEEEEeCCCCchhHHHHHHHHHHHhhhcCeEEEE
Confidence 356788888999999999999999999999987777665
No 72
>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=21.71 E-value=42 Score=24.38 Aligned_cols=23 Identities=22% Similarity=0.228 Sum_probs=17.9
Q ss_pred hhHHHHHHHHhhcCccccCCCCc
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~ri 39 (149)
.-+..-+-|+|.||+-||.|...
T Consensus 67 ~~f~~D~~lm~~Na~~yN~~~s~ 89 (113)
T cd05524 67 DDLTADFELLINNAKAYYKPDSP 89 (113)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCH
Confidence 34566788899999999987653
No 73
>PRK08596 acetylornithine deacetylase; Validated
Probab=21.66 E-value=1.9e+02 Score=24.98 Aligned_cols=39 Identities=8% Similarity=0.064 Sum_probs=33.9
Q ss_pred CCCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 51 AVNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 51 ~~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
++.....-|-..+..+++......++++++++|++++++
T Consensus 262 gG~~~nvvP~~~~~~~d~R~~p~~~~~~v~~~i~~~~~~ 300 (421)
T PRK08596 262 GGRHAAFIADECRLWITVHFYPNETYEQVIKEIEEYIGK 300 (421)
T ss_pred CCCCCCccCceEEEEEEeeeCCCCCHHHHHHHHHHHHHH
Confidence 344556778899999999999999999999999999986
No 74
>KOG2774|consensus
Probab=21.64 E-value=61 Score=27.98 Aligned_cols=33 Identities=33% Similarity=0.490 Sum_probs=27.7
Q ss_pred eeeeeeecccCCChHHHHHHHHHHhhhCCCceee
Q psy2660 63 RFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQ 96 (149)
Q Consensus 63 k~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~ 96 (149)
|-+|||.. -|-.|||+...|+|+.....|+|.-
T Consensus 276 rr~ynvt~-~sftpee~~~~~~~~~p~~~i~y~~ 308 (366)
T KOG2774|consen 276 RRTYNVTG-FSFTPEEIADAIRRVMPGFEIDYDI 308 (366)
T ss_pred hheeeece-eccCHHHHHHHHHhhCCCceeeccc
Confidence 35788844 4578999999999999999999975
No 75
>TIGR00106 uncharacterized protein, MTH1187 family. This protein has been crystallized in both Methanobacterium thermoautotrophicum and yeast, but its function remains unknown. Both crystal structures showed sulfate ions bound at the interface of two dimers to form a tetramer.
Probab=21.52 E-value=1.4e+02 Score=21.29 Aligned_cols=28 Identities=18% Similarity=0.188 Sum_probs=23.3
Q ss_pred cCCChHHHHHHHHHHhhhCCCceeeeCCE
Q psy2660 72 SSRDPNEIRAEIRKVLDANNCDYEQRERF 100 (149)
Q Consensus 72 Ssk~P~ei~~EI~rvL~~~~i~y~~~~~y 100 (149)
.+-+..+.+++..++|++.|+.|+.. ++
T Consensus 13 ~~~s~s~yVa~~i~~l~~sGl~y~~~-pm 40 (97)
T TIGR00106 13 VGASVSSYVAAAIEVLKESGLKYELH-PM 40 (97)
T ss_pred CCCcHHHHHHHHHHHHHHcCCCeEec-CC
Confidence 34578889999999999999999984 44
No 76
>PRK12778 putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional
Probab=21.44 E-value=97 Score=29.29 Aligned_cols=44 Identities=14% Similarity=0.144 Sum_probs=31.1
Q ss_pred CChHHHHHHHHHHhhhCCCce--------------------eeeCCEEEEEEeCCCCCCcceEE
Q psy2660 74 RDPNEIRAEIRKVLDANNCDY--------------------EQRERFLLLCVHGDPNTDSLVQW 117 (149)
Q Consensus 74 k~P~ei~~EI~rvL~~~~i~y--------------------~~~~~y~l~C~~~d~~~~~~v~f 117 (149)
--|..||+.+.+.|.+.|++. +..+++.+.|+.|+-...+.|.|
T Consensus 187 CGP~~M~~~v~~~l~~~gv~~~~Sle~~M~CG~G~C~~C~v~~~~~~~~~C~dGPvF~~~~v~~ 250 (752)
T PRK12778 187 IGPAIMMKFVCLLTKKYGIPTIVSLNTIMVDGTGMCGACRVTVGGKTKFACVDGPEFDGHLVDF 250 (752)
T ss_pred ECCHHHHHHHHHHHHHcCCCEEEeCcccccCcccccCcceeEeCCCeEEEECCCCeecccEEeH
Confidence 468899999999999877653 33344677888887555455555
No 77
>PRK08737 acetylornithine deacetylase; Provisional
Probab=21.02 E-value=2.3e+02 Score=24.13 Aligned_cols=45 Identities=9% Similarity=0.160 Sum_probs=36.6
Q ss_pred CCCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCCCcee
Q psy2660 51 AVNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYE 95 (149)
Q Consensus 51 ~~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~ 95 (149)
++.....-|-...+.+++.++...++++++++|+++++.....++
T Consensus 229 GG~~~NvVP~~a~~~~d~R~~p~~~~e~v~~~i~~~~~~~~~~~~ 273 (364)
T PRK08737 229 GGIKANMIAPAAELRFGFRPLPSMDVDGLLATFAGFAEPAAATFE 273 (364)
T ss_pred cCCCCCcCCCceEEEEEeeeCCCCCHHHHHHHHHHHHHHcCCceE
Confidence 344556778899999999999999999999999988887554443
No 78
>PRK07907 hypothetical protein; Provisional
Probab=20.94 E-value=2.2e+02 Score=24.85 Aligned_cols=38 Identities=21% Similarity=0.322 Sum_probs=33.5
Q ss_pred CCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhC
Q psy2660 53 NDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDAN 90 (149)
Q Consensus 53 ~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~ 90 (149)
+....-|-.....+++.+....++++++++|++.++..
T Consensus 305 ~~~nvIP~~a~~~~diR~~p~~~~e~v~~~l~~~l~~~ 342 (449)
T PRK07907 305 GASNALPPSARARLSLRVAPGQDAAEAQDALVAHLEAH 342 (449)
T ss_pred CCCCEecCceEEEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence 44566788899999999999999999999999999874
No 79
>PRK06446 hypothetical protein; Provisional
Probab=20.85 E-value=2.2e+02 Score=24.77 Aligned_cols=38 Identities=16% Similarity=0.248 Sum_probs=33.9
Q ss_pred CCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhhCC
Q psy2660 54 DDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDANN 91 (149)
Q Consensus 54 ~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~~~ 91 (149)
....-|-..++.+++.+....++++++++|++.+++.+
T Consensus 295 ~~nvvP~~a~~~~d~R~~p~~~~~~v~~~l~~~~~~~~ 332 (436)
T PRK06446 295 SKTIVPSRAFAKLDFRLVPNQDPYKIFELLKKHLQKVG 332 (436)
T ss_pred CCcEecCceEEEEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence 34677899999999999999999999999999999844
No 80
>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=20.74 E-value=42 Score=23.89 Aligned_cols=22 Identities=18% Similarity=0.307 Sum_probs=17.7
Q ss_pred hhHHHHHHHHhhcCccccCCCC
Q psy2660 17 SPMMHTVCLVWANCKYYQGPMA 38 (149)
Q Consensus 17 ~pl~h~v~LiW~~s~yY~~p~r 38 (149)
.-+.+-+-|||.||+=||.|.-
T Consensus 62 ~ef~~D~~li~~Na~~yN~~~s 83 (104)
T cd05507 62 AEFQRDVLLMFQNAIMYNSSDH 83 (104)
T ss_pred HHHHHHHHHHHHHHHHHCCCCC
Confidence 3466778899999999998763
No 81
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=20.52 E-value=1.6e+02 Score=21.24 Aligned_cols=30 Identities=23% Similarity=0.548 Sum_probs=23.0
Q ss_pred eeeeecccCCChHHHHHHHHHHhhhCCCce
Q psy2660 65 TWSMKTTSSRDPNEIRAEIRKVLDANNCDY 94 (149)
Q Consensus 65 ~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y 94 (149)
+|+..+--..+|++++.||...+.+..=.|
T Consensus 47 mW~~p~~~~~~~~~Vl~el~~c~~~~p~~y 76 (99)
T PF00101_consen 47 MWKLPMFGCTDPAQVLAELEACLAEHPGEY 76 (99)
T ss_dssp EESSEBTTBSSHHHHHHHHHHHHHHSTTSE
T ss_pred cCCCCCcCCCCHHHHHHHHHHHHHhCCCce
Confidence 455566667899999999999999754333
No 82
>PRK15327 type III secretion system needle complex protein PrgH; Provisional
Probab=20.35 E-value=3e+02 Score=24.73 Aligned_cols=57 Identities=18% Similarity=0.247 Sum_probs=41.1
Q ss_pred eeeeeeecccCCChHHHHHHHHHHhhhCCCceee---eCCEEEEEEeCC------------------CCCCcceEEEEEE
Q psy2660 63 RFTWSMKTTSSRDPNEIRAEIRKVLDANNCDYEQ---RERFLLLCVHGD------------------PNTDSLVQWEIEV 121 (149)
Q Consensus 63 k~~fsvsTTSsk~P~ei~~EI~rvL~~~~i~y~~---~~~y~l~C~~~d------------------~~~~~~v~fEmEV 121 (149)
.+.-+++.. .++.++++++=+.-|++.+|.|++ .+++.|. ..+. ..|+..|+|-++.
T Consensus 286 pya~~v~I~-~~s~~~l~~~Ae~GL~~~nv~yr~i~~~~~vtFi-I~~sL~D~~l~~l~~fv~~F~~~WG~~~IqFsI~L 363 (393)
T PRK15327 286 PYADSVNIT-LMDDVTAAGQAEAGLKQQALPYSRRDHKGSVTFV-IQGALDDGEIQRARQFVDSYYRTWGGRYVQFAIEL 363 (393)
T ss_pred CccceeEEE-EcCHHHHHHHHHhhHHhcCCceEEEecCCcEEEE-EcCCCCHHHHHHHHHHHHHHHHhhCccEEEEEEEe
Confidence 344444443 489999999999999999999998 3556554 3332 1456889999883
No 83
>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=20.24 E-value=44 Score=23.88 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=17.6
Q ss_pred hHHHHHHHHhhcCccccCCCCc
Q psy2660 18 PMMHTVCLVWANCKYYQGPMAM 39 (149)
Q Consensus 18 pl~h~v~LiW~~s~yY~~p~ri 39 (149)
-+.+-+.|||.||+-||.+...
T Consensus 66 ~f~~D~~lm~~Na~~yN~~~s~ 87 (103)
T cd05520 66 ELEADLNLMFENAKRYNVPNSR 87 (103)
T ss_pred HHHHHHHHHHHHHHHHCCCCCH
Confidence 3567788999999999987643
No 84
>PRK05111 acetylornithine deacetylase; Provisional
Probab=20.15 E-value=2e+02 Score=24.11 Aligned_cols=38 Identities=8% Similarity=0.156 Sum_probs=32.8
Q ss_pred CCCCCCCCeeEeeeeeeecccCCChHHHHHHHHHHhhh
Q psy2660 52 VNDDQVKPRSLRFTWSMKTTSSRDPNEIRAEIRKVLDA 89 (149)
Q Consensus 52 ~~~~~~kPR~lk~~fsvsTTSsk~P~ei~~EI~rvL~~ 89 (149)
+.....-|-...+.+++..+...+++++.++|++.+++
T Consensus 246 g~~~NvVP~~~~~~~diR~~p~~~~~~v~~~i~~~i~~ 283 (383)
T PRK05111 246 GDAPNRICGCCELHFDIRPLPGMTLEDLRGLLREALAP 283 (383)
T ss_pred CCcCcccCCceEEEEEEecCCCCCHHHHHHHHHHHHHH
Confidence 34455678889999999999999999999999999885
Done!