Query 034617
Match_columns 89
No_of_seqs 65 out of 67
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 04:42:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034617.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034617hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13961 DUF4219: Domain of un 69.3 0.26 5.7E-06 26.6 -3.0 14 51-64 1-14 (27)
2 PF10847 DUF2656: Protein of u 57.9 21 0.00045 26.4 4.1 29 55-86 41-69 (132)
3 PF02664 LuxS: S-Ribosylhomocy 57.2 26 0.00057 26.2 4.6 32 53-88 81-112 (157)
4 COG1854 LuxS LuxS protein invo 51.5 34 0.00074 26.0 4.5 32 53-88 81-112 (161)
5 PRK02260 S-ribosylhomocysteina 48.3 39 0.00085 25.3 4.3 31 53-87 81-111 (158)
6 COG2166 sufE Cysteine desulfur 47.0 48 0.001 24.5 4.6 39 49-87 51-94 (144)
7 PF14581 SseB_C: SseB protein 43.7 60 0.0013 21.0 4.2 35 51-87 43-77 (108)
8 TIGR02778 ligD_pol DNA polymer 43.3 23 0.0005 27.9 2.6 19 65-83 11-29 (245)
9 cd00126 PAH Pancreatic Hormone 41.0 33 0.00073 20.1 2.4 18 64-81 6-23 (36)
10 PF08776 VASP_tetra: VASP tetr 38.7 38 0.00082 20.5 2.5 15 72-86 24-38 (40)
11 PF00159 Hormone_3: Pancreatic 35.5 45 0.00097 19.5 2.4 17 65-81 7-23 (36)
12 PF02902 Peptidase_C48: Ulp1 p 35.1 22 0.00047 24.3 1.2 22 47-68 84-107 (216)
13 smart00309 PAH Pancreatic horm 34.7 48 0.001 19.5 2.4 18 64-81 6-23 (36)
14 PF10547 P22_AR_N: P22_AR N-te 30.8 22 0.00047 25.2 0.6 33 55-87 75-107 (120)
15 PF00113 Enolase_C: Enolase, C 29.9 39 0.00085 26.9 2.0 17 69-85 132-148 (295)
16 PF13282 DUF4070: Domain of un 29.7 65 0.0014 22.9 2.9 24 61-86 24-48 (146)
17 KOG3852 Uncharacterized conser 27.9 49 0.0011 28.4 2.3 25 63-87 149-178 (426)
18 COG1935 Uncharacterized conser 25.3 22 0.00048 26.0 -0.1 19 2-20 22-40 (122)
19 PF03432 Relaxase: Relaxase/Mo 25.1 1.7E+02 0.0036 20.7 4.3 39 49-88 47-86 (242)
20 PF11342 DUF3144: Protein of u 25.0 5.3 0.00011 26.7 -3.2 40 48-87 28-70 (78)
21 cd06481 ACD_HspB9_like Alpha c 25.0 76 0.0016 20.4 2.3 17 52-68 1-18 (87)
22 PF03800 Nuf2: Nuf2 family; I 24.9 76 0.0016 21.8 2.5 20 69-88 35-54 (146)
23 TIGR02691 arsC_pI258_fam arsen 24.9 1E+02 0.0023 20.9 3.1 31 54-86 91-122 (129)
24 cd00954 NAL N-Acetylneuraminic 23.8 1.3E+02 0.0027 22.8 3.7 18 69-86 109-126 (288)
25 KOG0178 20S proteasome, regula 23.4 50 0.0011 26.7 1.5 29 61-89 175-203 (249)
26 PF06855 DUF1250: Protein of u 23.1 75 0.0016 18.5 1.9 18 64-81 10-27 (46)
27 PF08947 BPS: BPS (Between PH 22.9 47 0.001 21.0 1.0 18 60-77 8-31 (49)
28 COG3285 Predicted eukaryotic-t 22.6 73 0.0016 26.3 2.3 18 65-82 19-36 (299)
29 TIGR00683 nanA N-acetylneurami 22.0 1.4E+02 0.003 22.9 3.6 30 55-86 96-126 (290)
30 PF12785 VESA1_N: Variant eryt 21.8 57 0.0012 28.4 1.6 13 75-87 54-66 (462)
31 PRK09633 ligD ATP-dependent DN 21.4 85 0.0018 27.4 2.6 18 66-83 334-351 (610)
32 PF10410 DnaB_bind: DnaB-helic 21.3 77 0.0017 18.0 1.7 14 75-88 40-53 (59)
33 smart00252 SH2 Src homology 2 21.1 1.5E+02 0.0032 17.8 3.0 30 53-82 44-81 (84)
34 PF07105 DUF1367: Protein of u 20.8 78 0.0017 24.6 2.0 32 53-89 55-89 (196)
35 TIGR02776 NHEJ_ligase_prk DNA 20.6 92 0.002 26.9 2.6 18 66-83 291-308 (552)
No 1
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=69.30 E-value=0.26 Score=26.57 Aligned_cols=14 Identities=36% Similarity=0.983 Sum_probs=12.0
Q ss_pred ccCCCcceeEEEEe
Q 034617 51 LEGCDYKHWLVVME 64 (89)
Q Consensus 51 f~GcDy~HWLVvMd 64 (89)
|+|.+|.+|-+.|.
T Consensus 1 l~g~NY~~W~~~M~ 14 (27)
T PF13961_consen 1 LDGTNYSTWKIRMK 14 (27)
T ss_pred CCccCHHHHHHHHH
Confidence 78999999988775
No 2
>PF10847 DUF2656: Protein of unknown function (DUF2656); InterPro: IPR020325 This entry contains uncharacterised proteins from the cpeY 3'-region. They have no known function, but are found in the phycobilisome.
Probab=57.87 E-value=21 Score=26.40 Aligned_cols=29 Identities=24% Similarity=0.454 Sum_probs=24.5
Q ss_pred CcceeEEEEeCCCCCCCHHHHHHHHHHHHHHh
Q 034617 55 DYKHWLVVMEAPKGYPPRDEIVNGYVKTLASA 86 (89)
Q Consensus 55 Dy~HWLVvMd~P~~~psr~emId~YvkTLAkV 86 (89)
+-.||||-++ ..-|++||-..-++++.+.
T Consensus 41 ~hPHW~v~i~---s~lsp~~~~~~~v~aw~~~ 69 (132)
T PF10847_consen 41 NHPHWMVEIE---SDLSPDEMAEELVRAWKQY 69 (132)
T ss_pred cCCceEEEec---ccCCHHHHHHHHHHHHHHH
Confidence 6789999999 6778899988888888764
No 3
>PF02664 LuxS: S-Ribosylhomocysteinase (LuxS); InterPro: IPR003815 In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. For example, enteric bacteria use quorum sensing to regulate several traits that allow them to establish and maintain infection in their host, including motility, biofilm formation, and virulence-specific genes []. The LuxS/AI-2 system is one of several quorum sensing mechanisms. AI-2 (autoinducer-2) is a signalling molecule that functions in interspecies communication by regulating niche-specific genes with diverse functions in various bacteria, often in response to population density. LuxS (S-ribosylhomocysteinase; 4.4.1.21 from EC) is an autoinducer-production protein that has a metabolic function as a component of the activated methyl cycle. LuxS converts S-ribosylhomocysteine to homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD); DPD can then spontaneously cyclise to active AI-2 [, ]. LuxS is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases []. ; GO: 0005506 iron ion binding, 0009372 quorum sensing; PDB: 1J6X_B 1VGX_A 1INN_B 1VJE_B 1J6V_A 1VH2_A 1J6W_B 1JOE_B 1J98_A 1IE0_A ....
Probab=57.23 E-value=26 Score=26.23 Aligned_cols=32 Identities=28% Similarity=0.534 Sum_probs=27.5
Q ss_pred CCCcceeEEEEeCCCCCCCHHHHHHHHHHHHHHhhC
Q 034617 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALG 88 (89)
Q Consensus 53 GcDy~HWLVvMd~P~~~psr~emId~YvkTLAkVLG 88 (89)
||..-+.|++. |.++.+++++...++|..|++
T Consensus 81 GCrTGFYli~~----g~~~~~~i~~l~~~~l~~i~~ 112 (157)
T PF02664_consen 81 GCRTGFYLILW----GDPSSEDIADLLKETLEFILE 112 (157)
T ss_dssp TTSSEEEEEEE----SS--HHHHHHHHHHHHHHHHT
T ss_pred ccccccEEEEe----CCCCHHHHHHHHHHHHHHHHh
Confidence 99999999997 457899999999999999885
No 4
>COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms]
Probab=51.55 E-value=34 Score=26.01 Aligned_cols=32 Identities=22% Similarity=0.562 Sum_probs=29.2
Q ss_pred CCCcceeEEEEeCCCCCCCHHHHHHHHHHHHHHhhC
Q 034617 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALG 88 (89)
Q Consensus 53 GcDy~HWLVvMd~P~~~psr~emId~YvkTLAkVLG 88 (89)
||..-+.|++. |.|+.+|++|....++..||+
T Consensus 81 GCrTGFYm~l~----G~~~~~~i~~~~~~~m~dvl~ 112 (161)
T COG1854 81 GCRTGFYMILI----GTPTSQDIADVLEATMKDVLK 112 (161)
T ss_pred ccccceEEEEE----CCCCHHHHHHHHHHHHHHHHc
Confidence 99999999998 567899999999999998886
No 5
>PRK02260 S-ribosylhomocysteinase; Provisional
Probab=48.30 E-value=39 Score=25.26 Aligned_cols=31 Identities=26% Similarity=0.672 Sum_probs=28.5
Q ss_pred CCCcceeEEEEeCCCCCCCHHHHHHHHHHHHHHhh
Q 034617 53 GCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASAL 87 (89)
Q Consensus 53 GcDy~HWLVvMd~P~~~psr~emId~YvkTLAkVL 87 (89)
||..-+.||+. |.++.+|+++...++|..|+
T Consensus 81 GCrTGFYli~~----g~~~~~~i~~l~~~~l~~i~ 111 (158)
T PRK02260 81 GCRTGFYLILI----GTPDEEDVADALKATLEDVL 111 (158)
T ss_pred ccccccEEEEe----CCCCHHHHHHHHHHHHHHHH
Confidence 99999999996 56889999999999999986
No 6
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=46.99 E-value=48 Score=24.48 Aligned_cols=39 Identities=28% Similarity=0.520 Sum_probs=32.8
Q ss_pred ccccCCCcceeEEEEeCCCC-----CCCHHHHHHHHHHHHHHhh
Q 034617 49 SLLEGCDYKHWLVVMEAPKG-----YPPRDEIVNGYVKTLASAL 87 (89)
Q Consensus 49 ~Lf~GcDy~HWLVvMd~P~~-----~psr~emId~YvkTLAkVL 87 (89)
-...||...-||+..-..++ ..|.+.||..++-+|..++
T Consensus 51 n~V~GC~S~vwL~~~~~~~~~~~F~gdSdA~ivrGL~aill~~~ 94 (144)
T COG2166 51 NPVPGCQSQVWLVTEQNDDGTLHFFGDSDARIVRGLLAILLAAY 94 (144)
T ss_pred cCCCccccceeEEEeecCCceEEEeccchhHHHHHHHHHHHHHH
Confidence 34679999999998877744 7899999999999987765
No 7
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=43.73 E-value=60 Score=21.03 Aligned_cols=35 Identities=11% Similarity=0.069 Sum_probs=24.1
Q ss_pred ccCCCcceeEEEEeCCCCCCCHHHHHHHHHHHHHHhh
Q 034617 51 LEGCDYKHWLVVMEAPKGYPPRDEIVNGYVKTLASAL 87 (89)
Q Consensus 51 f~GcDy~HWLVvMd~P~~~psr~emId~YvkTLAkVL 87 (89)
...++-.||+|+.|+.+ ...+++++.--+.+...+
T Consensus 43 ~~~~~~~~~li~vd~~~--~~~~~~~~~i~~~~~~~~ 77 (108)
T PF14581_consen 43 QDEDEQPSLLIGVDFDG--EDIEEIFQEIGRAARPYL 77 (108)
T ss_pred hccCCCceEEEEEeccC--hhHHHHHHHHHHHhhhcC
Confidence 34688899999999988 455566655555544443
No 8
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=43.33 E-value=23 Score=27.94 Aligned_cols=19 Identities=11% Similarity=0.092 Sum_probs=15.9
Q ss_pred CCCCCCCHHHHHHHHHHHH
Q 034617 65 APKGYPPRDEIVNGYVKTL 83 (89)
Q Consensus 65 ~P~~~psr~emId~YvkTL 83 (89)
||+...||.|.|+||.+.=
T Consensus 11 ~P~~g~TK~dl~~YY~~va 29 (245)
T TIGR02778 11 WPAEGITKLDLADYYAAVA 29 (245)
T ss_pred cCCCCCcHHHHHHHHHHHH
Confidence 4667899999999999863
No 9
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=41.03 E-value=33 Score=20.12 Aligned_cols=18 Identities=17% Similarity=0.195 Sum_probs=14.0
Q ss_pred eCCCCCCCHHHHHHHHHH
Q 034617 64 EAPKGYPPRDEIVNGYVK 81 (89)
Q Consensus 64 d~P~~~psr~emId~Yvk 81 (89)
+.|++..|+||+..+|-+
T Consensus 6 ~~Pg~~a~~eel~~Y~~~ 23 (36)
T cd00126 6 ENPGDDASPEELRQYLAA 23 (36)
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 346678899999988765
No 10
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=38.69 E-value=38 Score=20.54 Aligned_cols=15 Identities=20% Similarity=0.457 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHh
Q 034617 72 RDEIVNGYVKTLASA 86 (89)
Q Consensus 72 r~emId~YvkTLAkV 86 (89)
|+|+||+..+-|.++
T Consensus 24 K~EIIeA~~~eL~r~ 38 (40)
T PF08776_consen 24 KEEIIEAIRQELSRR 38 (40)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcc
Confidence 789999999888764
No 11
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=35.55 E-value=45 Score=19.52 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=13.2
Q ss_pred CCCCCCCHHHHHHHHHH
Q 034617 65 APKGYPPRDEIVNGYVK 81 (89)
Q Consensus 65 ~P~~~psr~emId~Yvk 81 (89)
.|++..|.||+.+||.+
T Consensus 7 ~P~~~aspeel~~Y~~~ 23 (36)
T PF00159_consen 7 RPGDFASPEELAQYYAA 23 (36)
T ss_dssp SSSTTSSHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHH
Confidence 35568899999888765
No 12
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=35.12 E-value=22 Score=24.34 Aligned_cols=22 Identities=27% Similarity=0.422 Sum_probs=17.0
Q ss_pred CCccccCCC-ccee-EEEEeCCCC
Q 034617 47 LPSLLEGCD-YKHW-LVVMEAPKG 68 (89)
Q Consensus 47 ~~~Lf~GcD-y~HW-LVvMd~P~~ 68 (89)
.-+++|=|. .+|| ++++|.|.+
T Consensus 84 ~~i~iPin~~~~HW~l~vi~~~~~ 107 (216)
T PF02902_consen 84 DYIFIPININNNHWVLLVIDLPKK 107 (216)
T ss_dssp SEEEEEEEETTTEEEEEEEETTTT
T ss_pred CEEEEEEechhhccceeEEccccc
Confidence 347788888 9999 567888873
No 13
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=34.71 E-value=48 Score=19.48 Aligned_cols=18 Identities=11% Similarity=0.172 Sum_probs=13.8
Q ss_pred eCCCCCCCHHHHHHHHHH
Q 034617 64 EAPKGYPPRDEIVNGYVK 81 (89)
Q Consensus 64 d~P~~~psr~emId~Yvk 81 (89)
+.|++..|.||+..+|.+
T Consensus 6 ~~Pg~~a~~e~l~~Y~~~ 23 (36)
T smart00309 6 ERPGDDASPEDLRQYLAA 23 (36)
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 347778999998887754
No 14
>PF10547 P22_AR_N: P22_AR N-terminal domain; InterPro: IPR018875 The antirepressor protein, ANT, prevents the prophage p22 c2 repressor protein from binding to its operators; it also inhibits the action of other prophage repressor proteins, including those of phages lambda and 434. The synthesis of antirepressor is negatively regulated by the protein products of the two other immi genes, mnt and arc.
Probab=30.82 E-value=22 Score=25.17 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=28.5
Q ss_pred CcceeEEEEeCCCCCCCHHHHHHHHHHHHHHhh
Q 034617 55 DYKHWLVVMEAPKGYPPRDEIVNGYVKTLASAL 87 (89)
Q Consensus 55 Dy~HWLVvMd~P~~~psr~emId~YvkTLAkVL 87 (89)
.-+-||..+|.=+.+|.-.|.|-.|-+-|++||
T Consensus 75 ~L~~WL~~I~p~kV~pelr~kvi~YQ~Ec~~vL 107 (120)
T PF10547_consen 75 KLPGWLFTINPNKVKPELREKVIAYQEECDDVL 107 (120)
T ss_pred HHHHHHhhCChhhcCHHHHHHHHHHHHHHHHHH
Confidence 345699999887778999999999999999998
No 15
>PF00113 Enolase_C: Enolase, C-terminal TIM barrel domain; InterPro: IPR020810 Enolase (2-phospho-D-glycerate hydrolase) is an essential glycolytic enzyme that catalyses the interconversion of 2-phosphoglycerate and phosphoenolpyruvate [, ]. In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer []. The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown [] to be evolutionary related to enolase. Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.; GO: 0000287 magnesium ion binding, 0004634 phosphopyruvate hydratase activity, 0006096 glycolysis, 0000015 phosphopyruvate hydratase complex; PDB: 2FYM_D 3H8A_C 1E9I_D 3TQP_B 2PU1_A 1OEP_A 2PA6_A 1PDY_A 1PDZ_A 3UJ2_E ....
Probab=29.91 E-value=39 Score=26.92 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.6
Q ss_pred CCCHHHHHHHHHHHHHH
Q 034617 69 YPPRDEIVNGYVKTLAS 85 (89)
Q Consensus 69 ~psr~emId~YvkTLAk 85 (89)
.-|.+||||+|.+.+.+
T Consensus 132 ~~s~delid~y~~li~~ 148 (295)
T PF00113_consen 132 YKSSDELIDYYKDLIKK 148 (295)
T ss_dssp EEEHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHh
Confidence 46999999999998765
No 16
>PF13282 DUF4070: Domain of unknown function (DUF4070)
Probab=29.69 E-value=65 Score=22.89 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=19.9
Q ss_pred EEEeC-CCCCCCHHHHHHHHHHHHHHh
Q 034617 61 VVMEA-PKGYPPRDEIVNGYVKTLASA 86 (89)
Q Consensus 61 VvMd~-P~~~psr~emId~YvkTLAkV 86 (89)
..||| | +-+.||+++-|.+.+.+.
T Consensus 24 ~~~NFiP--~m~~e~L~~gy~~~~~~l 48 (146)
T PF13282_consen 24 SSTNFIP--KMPREELADGYRRLMWRL 48 (146)
T ss_pred ccccccc--CCCHHHHHHHHHHHHHHH
Confidence 45788 6 489999999999998764
No 17
>KOG3852 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.87 E-value=49 Score=28.37 Aligned_cols=25 Identities=20% Similarity=0.384 Sum_probs=21.4
Q ss_pred EeC-CCC----CCCHHHHHHHHHHHHHHhh
Q 034617 63 MEA-PKG----YPPRDEIVNGYVKTLASAL 87 (89)
Q Consensus 63 Md~-P~~----~psr~emId~YvkTLAkVL 87 (89)
.|| |+| |.|++-|-|+|||.|-||-
T Consensus 149 ldflP~~v~keKisp~tlKdaYvqKlvKVc 178 (426)
T KOG3852|consen 149 LDFLPEGVNKEKISPLTLKDAYVQKLVKVC 178 (426)
T ss_pred HHhCcccccccccChhHHHHHHHHHHHHhc
Confidence 466 776 7899999999999999984
No 18
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=25.30 E-value=22 Score=25.99 Aligned_cols=19 Identities=26% Similarity=0.380 Sum_probs=16.1
Q ss_pred chhhhhccccchhHHHHHh
Q 034617 2 LRNIILRCPLNLTAAIYRR 20 (89)
Q Consensus 2 ~~~~~~r~pl~ltaa~~~~ 20 (89)
+|.|.||++.|+.++.+..
T Consensus 22 ~rTieiRsa~N~~tv~rl~ 40 (122)
T COG1935 22 IRTIEIRSARNLLTVLRLH 40 (122)
T ss_pred ceEEEEEcccchHHhhcCC
Confidence 5788999999999988654
No 19
>PF03432 Relaxase: Relaxase/Mobilisation nuclease domain ; InterPro: IPR005094 Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing trans-esterification [].
Probab=25.14 E-value=1.7e+02 Score=20.70 Aligned_cols=39 Identities=10% Similarity=0.199 Sum_probs=27.6
Q ss_pred ccccCC-CcceeEEEEeCCCCCCCHHHHHHHHHHHHHHhhC
Q 034617 49 SLLEGC-DYKHWLVVMEAPKGYPPRDEIVNGYVKTLASALG 88 (89)
Q Consensus 49 ~Lf~Gc-Dy~HWLVvMd~P~~~psr~emId~YvkTLAkVLG 88 (89)
.+++-+ ....|-+++-||++.+|+++|.+. ++.+++-+|
T Consensus 47 ~~~~~~~~~~~~h~i~Sf~~~e~~~e~~~~~-~~~~~~~~~ 86 (242)
T PF03432_consen 47 ALNKKVNKRPVYHIIISFPPDELTPEQAHEI-AREFAEEMG 86 (242)
T ss_pred HHcccccCceEEEEeccCCccccCHHHHHHH-HHHHHHHcC
Confidence 567777 788999999997777888666554 444544444
No 20
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=25.03 E-value=5.3 Score=26.66 Aligned_cols=40 Identities=8% Similarity=0.208 Sum_probs=33.7
Q ss_pred CccccCCCcceeEEEEeCCCC---CCCHHHHHHHHHHHHHHhh
Q 034617 48 PSLLEGCDYKHWLVVMEAPKG---YPPRDEIVNGYVKTLASAL 87 (89)
Q Consensus 48 ~~Lf~GcDy~HWLVvMd~P~~---~psr~emId~YvkTLAkVL 87 (89)
.+||..-.|+=|...-.++.+ ...|+++||+|++-..+-|
T Consensus 28 allyAaARfnAf~~a~~~~~~~~~~~~ke~~i~~f~~qy~~mL 70 (78)
T PF11342_consen 28 ALLYAAARFNAFVAASSFESKADMAAEKEEAIDYFTEQYRKML 70 (78)
T ss_pred HHHHHHHHHHHHHHHHccCcHHHHHHhHHHHHHHHHHHHHHHH
Confidence 467888889999998888864 7899999999998877655
No 21
>cd06481 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9 interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone.
Probab=24.96 E-value=76 Score=20.38 Aligned_cols=17 Identities=18% Similarity=0.157 Sum_probs=13.9
Q ss_pred cCCCc-ceeEEEEeCCCC
Q 034617 52 EGCDY-KHWLVVMEAPKG 68 (89)
Q Consensus 52 ~GcDy-~HWLVvMd~P~~ 68 (89)
+|||- ++|.|.||-|+-
T Consensus 1 ~~~~~~d~~~v~~dlpG~ 18 (87)
T cd06481 1 EGKDGKEGFSLKLDVRGF 18 (87)
T ss_pred CCCCccceEEEEEECCCC
Confidence 47875 589999999975
No 22
>PF03800 Nuf2: Nuf2 family; InterPro: IPR005549 Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Q9C953 from SWISSPROT. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.; GO: 0007067 mitosis, 0000775 chromosome, centromeric region; PDB: 2VE7_D 3IZ0_D.
Probab=24.88 E-value=76 Score=21.76 Aligned_cols=20 Identities=25% Similarity=0.363 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHHHHHHHhhC
Q 034617 69 YPPRDEIVNGYVKTLASALG 88 (89)
Q Consensus 69 ~psr~emId~YvkTLAkVLG 88 (89)
+|+++-+...|.+.|..++|
T Consensus 35 kPt~e~v~~ly~~~L~~~~g 54 (146)
T PF03800_consen 35 KPTPEFVQKLYERFLETFLG 54 (146)
T ss_dssp G--HHHHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHHHHC
Confidence 89999999999999999887
No 23
>TIGR02691 arsC_pI258_fam arsenate reductase (thioredoxin). This family describes the well-studied thioredoxin-dependent arsenate reductase of Staphylococcus aureaus plasmid pI258 and other mechanistically similar arsenate reductases. The mechanism involves an intramolecular disulfide bond cascade, and aligned members of this family have four absolutely conserved Cys residues. This group of arsenate reductases belongs to the low-molecular weight protein-tyrosine phosphatase family (pfam01451), as does a group of glutathione/glutaredoxin type arsenate reductases (TIGR02689). At least two other, non-homologous groups of arsenate reductases involved in arsenical resistance are also known. This enzyme reduces arsenate to arsenite, which may be more toxic but which is more easily exported.
Probab=24.86 E-value=1e+02 Score=20.87 Aligned_cols=31 Identities=13% Similarity=0.260 Sum_probs=23.1
Q ss_pred CCcceeEEEEeCCCC-CCCHHHHHHHHHHHHHHh
Q 034617 54 CDYKHWLVVMEAPKG-YPPRDEIVNGYVKTLASA 86 (89)
Q Consensus 54 cDy~HWLVvMd~P~~-~psr~emId~YvkTLAkV 86 (89)
-.+.||- ++-|.+ ..|.+|..+.|.++..+.
T Consensus 91 ~~~~~w~--i~DP~~~~g~~~~~~~~~~~~~~~I 122 (129)
T TIGR02691 91 VKREHWG--LDDPARAEGTEEEKWAVFRRVRDEI 122 (129)
T ss_pred CeEEECC--CCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 3456993 355666 679999999999988764
No 24
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=23.83 E-value=1.3e+02 Score=22.79 Aligned_cols=18 Identities=28% Similarity=0.246 Sum_probs=15.5
Q ss_pred CCCHHHHHHHHHHHHHHh
Q 034617 69 YPPRDEIVNGYVKTLASA 86 (89)
Q Consensus 69 ~psr~emId~YvkTLAkV 86 (89)
++|.+|++++|.+.+..+
T Consensus 109 ~~~~~~i~~~~~~v~~a~ 126 (288)
T cd00954 109 KFSFEEIKDYYREIIAAA 126 (288)
T ss_pred CCCHHHHHHHHHHHHHhc
Confidence 789999999999887654
No 25
>KOG0178 consensus 20S proteasome, regulatory subunit alpha type PSMA4/PRE9 [Posttranslational modification, protein turnover, chaperones]
Probab=23.45 E-value=50 Score=26.69 Aligned_cols=29 Identities=14% Similarity=0.036 Sum_probs=24.9
Q ss_pred EEEeCCCCCCCHHHHHHHHHHHHHHhhCC
Q 034617 61 VVMEAPKGYPPRDEIVNGYVKTLASALGW 89 (89)
Q Consensus 61 VvMd~P~~~psr~emId~YvkTLAkVLGs 89 (89)
..+|++.+..+.+|.++--+|.|.|-+++
T Consensus 175 Lkqdykdd~~~~~eA~~laikvL~kt~d~ 203 (249)
T KOG0178|consen 175 LKQDYKDDENDLEEAKALAIKVLSKTLDS 203 (249)
T ss_pred HHhhhccccccHHHHHHHHHHHHHhhccc
Confidence 46788888779999999999999998764
No 26
>PF06855 DUF1250: Protein of unknown function (DUF1250); InterPro: IPR023089 This entry represents the YozE-like domain found in a group of proteins of unknown function.; PDB: 2KVS_A 2FJ6_A 2O6K_B.
Probab=23.05 E-value=75 Score=18.55 Aligned_cols=18 Identities=28% Similarity=0.143 Sum_probs=13.2
Q ss_pred eCCCCCCCHHHHHHHHHH
Q 034617 64 EAPKGYPPRDEIVNGYVK 81 (89)
Q Consensus 64 d~P~~~psr~emId~Yvk 81 (89)
+||++.-+.+|+.+|...
T Consensus 10 ~FPK~~~~~~eI~~Yle~ 27 (46)
T PF06855_consen 10 SFPKQETDFDEISSYLES 27 (46)
T ss_dssp TS-TT-SSHHHHHHHHHC
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 589998899999888654
No 27
>PF08947 BPS: BPS (Between PH and SH2) ; InterPro: IPR015042 The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor []. ; PDB: 2AUH_B.
Probab=22.90 E-value=47 Score=20.99 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=10.0
Q ss_pred EEEEeCCCC------CCCHHHHHH
Q 034617 60 LVVMEAPKG------YPPRDEIVN 77 (89)
Q Consensus 60 LVvMd~P~~------~psr~emId 77 (89)
||.|||-+. .|..++.|+
T Consensus 8 lVaMDFsG~~GRvIenP~EA~s~a 31 (49)
T PF08947_consen 8 LVAMDFSGQTGRVIENPKEAQSAA 31 (49)
T ss_dssp -EEEE-SSSS--B---HHHHHHHH
T ss_pred eEEeeecCCcccccCCHHHHHHHH
Confidence 799999762 455555554
No 28
>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]
Probab=22.65 E-value=73 Score=26.27 Aligned_cols=18 Identities=17% Similarity=0.292 Sum_probs=14.8
Q ss_pred CCCCCCCHHHHHHHHHHH
Q 034617 65 APKGYPPRDEIVNGYVKT 82 (89)
Q Consensus 65 ~P~~~psr~emId~YvkT 82 (89)
||+..+||+++++||.+.
T Consensus 19 ~p~~~~TK~dla~Yya~V 36 (299)
T COG3285 19 FPKTGITKEDLARYYAAV 36 (299)
T ss_pred cccCCcCHHHHHHHHHHH
Confidence 355679999999999874
No 29
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=21.97 E-value=1.4e+02 Score=22.86 Aligned_cols=30 Identities=23% Similarity=0.144 Sum_probs=20.4
Q ss_pred CcceeEEEEeCCCC-CCCHHHHHHHHHHHHHHh
Q 034617 55 DYKHWLVVMEAPKG-YPPRDEIVNGYVKTLASA 86 (89)
Q Consensus 55 Dy~HWLVvMd~P~~-~psr~emId~YvkTLAkV 86 (89)
.....++. .|-- .+|.+||+++|.+.+++.
T Consensus 96 Gad~v~v~--~P~y~~~~~~~i~~yf~~v~~~~ 126 (290)
T TIGR00683 96 GYDCLSAV--TPFYYKFSFPEIKHYYDTIIAET 126 (290)
T ss_pred CCCEEEEe--CCcCCCCCHHHHHHHHHHHHhhC
Confidence 33444442 3544 889999999999887653
No 30
>PF12785 VESA1_N: Variant erythrocyte surface antigen-1; InterPro: IPR024751 This entry represents variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair [].
Probab=21.83 E-value=57 Score=28.39 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHhh
Q 034617 75 IVNGYVKTLASAL 87 (89)
Q Consensus 75 mId~YvkTLAkVL 87 (89)
+|++||.-|||||
T Consensus 54 vvrtyidqlaqvL 66 (462)
T PF12785_consen 54 VVRTYIDQLAQVL 66 (462)
T ss_pred eHHHHHHHHHHHH
Confidence 5889999999997
No 31
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=21.36 E-value=85 Score=27.43 Aligned_cols=18 Identities=11% Similarity=0.010 Sum_probs=15.1
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 034617 66 PKGYPPRDEIVNGYVKTL 83 (89)
Q Consensus 66 P~~~psr~emId~YvkTL 83 (89)
|+...||.|.++||.++=
T Consensus 334 p~~g~tK~dl~~Yy~~va 351 (610)
T PRK09633 334 PKIHKTKADYLLYLQEVS 351 (610)
T ss_pred CCCCCCHHHHHHHHHHHH
Confidence 556789999999999864
No 32
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=21.27 E-value=77 Score=18.02 Aligned_cols=14 Identities=36% Similarity=0.522 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHhhC
Q 034617 75 IVNGYVKTLASALG 88 (89)
Q Consensus 75 mId~YvkTLAkVLG 88 (89)
.-+.|++.||+.+|
T Consensus 40 ~r~~y~~~la~~~~ 53 (59)
T PF10410_consen 40 ERELYIRELAERLG 53 (59)
T ss_dssp HHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHhC
Confidence 35778888888776
No 33
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=21.06 E-value=1.5e+02 Score=17.78 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=22.0
Q ss_pred CCCcceeEEEEeCCC--------CCCCHHHHHHHHHHH
Q 034617 53 GCDYKHWLVVMEAPK--------GYPPRDEIVNGYVKT 82 (89)
Q Consensus 53 GcDy~HWLVvMd~P~--------~~psr~emId~YvkT 82 (89)
.....|.+|..+..+ .-+|-.|+|++|.+.
T Consensus 44 ~~~~~h~~I~~~~~~~~~l~~~~~F~sl~eLI~~y~~~ 81 (84)
T smart00252 44 KGKVKHYRIRRNEDGKFYLDGGRKFPSLVELVEHYQKN 81 (84)
T ss_pred CCEEEEEEEEECCCCcEEECCCCccCCHHHHHHHHhhC
Confidence 456778888766532 258999999999864
No 34
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=20.81 E-value=78 Score=24.57 Aligned_cols=32 Identities=34% Similarity=0.582 Sum_probs=24.2
Q ss_pred CCCcceeEEEEeCCCC-CCCH--HHHHHHHHHHHHHhhCC
Q 034617 53 GCDYKHWLVVMEAPKG-YPPR--DEIVNGYVKTLASALGW 89 (89)
Q Consensus 53 GcDy~HWLVvMd~P~~-~psr--~emId~YvkTLAkVLGs 89 (89)
-+-|+||- |.| ..|+ ..+|..|+|-||...|+
T Consensus 55 ~lgFeyW~-----P~gg~is~~E~~lv~g~v~~la~~~g~ 89 (196)
T PF07105_consen 55 NLGFEYWE-----PTGGTISPAERKLVRGFVKFLASYAGS 89 (196)
T ss_pred HHHHHHcc-----CCCCccCHHHHHHHHHHHHHHHHHhCC
Confidence 45689993 766 5554 45899999999998774
No 35
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=20.61 E-value=92 Score=26.89 Aligned_cols=18 Identities=17% Similarity=0.119 Sum_probs=14.9
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 034617 66 PKGYPPRDEIVNGYVKTL 83 (89)
Q Consensus 66 P~~~psr~emId~YvkTL 83 (89)
|....||.|.++||.+.=
T Consensus 291 p~~g~tK~dl~~Yy~~va 308 (552)
T TIGR02776 291 PKEGITKLDLAVYYAEVG 308 (552)
T ss_pred CCCCCCHHHHHHHHHHHH
Confidence 555789999999998863
Done!