Query psy4005
Match_columns 202
No_of_seqs 104 out of 188
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 22:57:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4005hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3484|consensus 100.0 7E-47 1.5E-51 288.0 7.4 76 81-156 1-76 (91)
2 PF01111 CKS: Cyclin-dependent 100.0 1.7E-45 3.7E-50 269.8 6.3 70 85-154 1-70 (70)
3 PLN00010 cyclin-dependent kina 100.0 4.4E-45 9.6E-50 276.8 8.1 77 84-160 2-78 (86)
4 PTZ00453 cyclin-dependent kina 100.0 9.2E-44 2E-48 273.9 7.6 74 81-154 23-96 (96)
5 PLN00010 cyclin-dependent kina 90.7 0.16 3.6E-06 39.4 1.9 16 14-29 60-75 (86)
6 KOG3484|consensus 90.3 0.15 3.3E-06 39.9 1.4 13 14-26 62-74 (91)
7 PF01111 CKS: Cyclin-dependent 87.7 0.2 4.4E-06 37.4 0.5 12 14-25 58-69 (70)
8 PF13783 DUF4177: Domain of un 76.0 3.1 6.7E-05 28.6 2.8 52 96-152 1-61 (61)
9 COG0429 Predicted hydrolase of 37.7 15 0.00033 34.6 1.0 21 162-182 300-320 (345)
10 PF05972 APC_15aa: APC 15 resi 34.4 19 0.00041 20.6 0.6 13 84-96 4-16 (16)
11 TIGR02011 IscA iron-sulfur clu 33.6 30 0.00064 26.0 1.8 17 18-36 85-101 (105)
12 PRK09502 iscA iron-sulfur clus 32.3 32 0.0007 26.0 1.8 17 18-36 87-103 (107)
13 TIGR02150 IPP_isom_1 isopenten 28.3 89 0.0019 24.6 3.8 27 137-163 32-58 (158)
14 PRK03759 isopentenyl-diphospha 25.3 1E+02 0.0022 24.9 3.7 29 128-156 26-58 (184)
15 PF09355 Phage_Gp19: Phage pro 23.1 52 0.0011 26.1 1.6 21 114-134 88-108 (116)
16 PTZ00235 DNA polymerase epsilo 22.4 39 0.00085 31.1 0.8 49 14-62 233-291 (291)
17 PF07254 DUF1434: Protein of u 21.6 48 0.001 27.1 1.1 11 117-127 116-126 (132)
18 TIGR00049 Iron-sulfur cluster 21.0 72 0.0016 23.4 1.9 17 19-37 86-102 (105)
19 cd04697 Nudix_Hydrolase_38 Mem 20.6 1.8E+02 0.0039 21.6 3.9 21 136-156 4-24 (126)
20 PF13975 gag-asp_proteas: gag- 20.3 64 0.0014 22.6 1.4 18 116-133 31-48 (72)
21 cd03676 Nudix_hydrolase_3 Memb 20.2 1.4E+02 0.003 23.7 3.5 33 130-162 26-66 (180)
22 PF10738 Lpp-LpqN: Probable li 20.1 70 0.0015 27.0 1.8 42 126-167 33-85 (175)
No 1
>KOG3484|consensus
Probab=100.00 E-value=7e-47 Score=287.99 Aligned_cols=76 Identities=55% Similarity=0.926 Sum_probs=73.7
Q ss_pred CCCCCeeecCCcCCCceeEEEEEcChHHHhhCCCCCCCCHHHHhhhccccCCCeeEeeecCCCceeEEEecccccc
Q psy4005 81 MSADDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLPGNENWVKNRYETLV 156 (202)
Q Consensus 81 M~~~~I~YS~KY~DD~YEYRHViLPkel~K~VPK~rLLsE~EWR~LGIQQS~GW~HYmiHkPEPHILLFRRPl~~~ 156 (202)
|..++|+||+||.||+||||||+|||+++|+|||+|||||+|||+||||||+||+|||||.|||||||||||++..
T Consensus 1 ~~~~qi~YS~kY~Dd~fEYRHV~Lpk~~~K~vPk~rllsE~EWR~lGvqQS~GW~hYmiH~PEpHIlLFrRp~~~~ 76 (91)
T KOG3484|consen 1 MFMDQIYYSDKYFDDEFEYRHVMLPKEVAKLVPKNRLLSETEWRGLGVQQSLGWVHYMIHAPEPHILLFRRPLNYA 76 (91)
T ss_pred CCccceecccccccccceeEEeecCHHHHhhCCccccccHHHHhhhCccccCCeeEEEecCCCceEEEEecccchH
Confidence 5679999999999999999999999999999999999999999999999999999999999999999999999775
No 2
>PF01111 CKS: Cyclin-dependent kinase regulatory subunit; InterPro: IPR000789 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 []. In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division []. The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded beta-barrel structure []. Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs []. Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation [, ].; GO: 0016538 cyclin-dependent protein kinase regulator activity, 0007049 cell cycle; PDB: 1CKS_C 3QY2_B 1QB3_C 1SCE_B 1PUC_A 1DKS_B 2AST_C 1BUH_B 1DKT_B 2ASS_C.
Probab=100.00 E-value=1.7e-45 Score=269.79 Aligned_cols=70 Identities=56% Similarity=0.992 Sum_probs=55.8
Q ss_pred CeeecCCcCCCceeEEEEEcChHHHhhCCCCCCCCHHHHhhhccccCCCeeEeeecCCCceeEEEecccc
Q psy4005 85 DIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLPGNENWVKNRYET 154 (202)
Q Consensus 85 ~I~YS~KY~DD~YEYRHViLPkel~K~VPK~rLLsE~EWR~LGIQQS~GW~HYmiHkPEPHILLFRRPl~ 154 (202)
+|+||+||+||+||||||||||+++|++|+++||||+|||+||||||+||+|||+|+|||||||||||+|
T Consensus 1 ~I~YS~kY~Dd~yeYRhViLpk~~~k~vp~~~llsE~EWR~LGIqqS~GW~Hy~~h~pephiLlFrRp~n 70 (70)
T PF01111_consen 1 QIYYSDKYYDDEYEYRHVILPKEIAKLVPKDRLLSEEEWRGLGIQQSPGWEHYMIHKPEPHILLFRRPLN 70 (70)
T ss_dssp G-EEE--EEBSSEEEEEEE--HHHHGTS-CCS---HHHHHHTT--S-TT-EEECETTSSTTEEEEEEECT
T ss_pred CccccccccCCceEEEEEECCHHHHhhCccCcccCHHHHHhhCCccCCCcEEEEEeCCCCcEEEEecCCC
Confidence 5899999999999999999999999999999999999999999999999999999999999999999986
No 3
>PLN00010 cyclin-dependent kinases regulatory subunit; Provisional
Probab=100.00 E-value=4.4e-45 Score=276.75 Aligned_cols=77 Identities=47% Similarity=0.881 Sum_probs=73.6
Q ss_pred CCeeecCCcCCCceeEEEEEcChHHHhhCCCCCCCCHHHHhhhccccCCCeeEeeecCCCceeEEEecccccccCCC
Q psy4005 84 DDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLPGNENWVKNRYETLVRLRG 160 (202)
Q Consensus 84 ~~I~YS~KY~DD~YEYRHViLPkel~K~VPK~rLLsE~EWR~LGIQQS~GW~HYmiHkPEPHILLFRRPl~~~~l~g 160 (202)
++|+||+||+||+||||||||||+++|+||+++||||+|||+||||||+||+|||+|+|||||||||||++..+..|
T Consensus 2 ~~I~YS~kY~Dd~yeYRhViLPk~~~k~ipk~~LL~E~EWR~LGIqqS~GW~Hy~~h~pEphILlFrRp~~~~~~~~ 78 (86)
T PLN00010 2 GQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQE 78 (86)
T ss_pred CccEeCCceeCCCcEEEEEEeCHHHHHhCCcCcccCHHHHHHhccccCCCcEEeeecCCCceEEEEEccCCCCCccc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999998876443
No 4
>PTZ00453 cyclin-dependent kinase; Provisional
Probab=100.00 E-value=9.2e-44 Score=273.91 Aligned_cols=74 Identities=54% Similarity=0.936 Sum_probs=71.3
Q ss_pred CCCCCeeecCCcCCCceeEEEEEcChHHHhhCCCCCCCCHHHHhhhccccCCCeeEeeecCCCceeEEEecccc
Q psy4005 81 MSADDIRYSDKYEDDNYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLPGNENWVKNRYET 154 (202)
Q Consensus 81 M~~~~I~YS~KY~DD~YEYRHViLPkel~K~VPK~rLLsE~EWR~LGIQQS~GW~HYmiHkPEPHILLFRRPl~ 154 (202)
+..++|+||+||+||+||||||||||+++|+||+++||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus 23 ~~~~~I~YS~kY~DD~yEYRHViLPk~~~k~ipk~~LL~E~EWR~LGIqqS~GW~HY~~h~pEphILLFRRp~t 96 (96)
T PTZ00453 23 KLQSKILYSDKYYDDEYEYRHVILPKDFARLVPRSRLMSESEWRQLGVQQSVGWRHYMIHKPEPHVLLFKRPKT 96 (96)
T ss_pred hccccceeCCceeCCCcEEEEEEeCHHHHHhCCCCccccHHHHHHhhhccCCCcEEeeecCCCCcEEEEecCCC
Confidence 34679999999999999999999999999999999999999999999999999999999999999999999974
No 5
>PLN00010 cyclin-dependent kinases regulatory subunit; Provisional
Probab=90.73 E-value=0.16 Score=39.43 Aligned_cols=16 Identities=50% Similarity=0.918 Sum_probs=13.3
Q ss_pred ecceEEeeeCCCCCCC
Q psy4005 14 LEPHVLLFRRPKQPTP 29 (202)
Q Consensus 14 ~~~~~~~~~~~~~~~~ 29 (202)
-|||+||||||..-.+
T Consensus 60 pEphILlFrRp~~~~~ 75 (86)
T PLN00010 60 PEPHIMLFRRPLNYQQ 75 (86)
T ss_pred CCceEEEEEccCCCCC
Confidence 4999999999987554
No 6
>KOG3484|consensus
Probab=90.25 E-value=0.15 Score=39.91 Aligned_cols=13 Identities=69% Similarity=1.244 Sum_probs=11.2
Q ss_pred ecceEEeeeCCCC
Q psy4005 14 LEPHVLLFRRPKQ 26 (202)
Q Consensus 14 ~~~~~~~~~~~~~ 26 (202)
-|||+||||||+.
T Consensus 62 PEpHIlLFrRp~~ 74 (91)
T KOG3484|consen 62 PEPHILLFRRPLN 74 (91)
T ss_pred CCceEEEEecccc
Confidence 3899999999874
No 7
>PF01111 CKS: Cyclin-dependent kinase regulatory subunit; InterPro: IPR000789 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 []. In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division []. The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded beta-barrel structure []. Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs []. Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation [, ].; GO: 0016538 cyclin-dependent protein kinase regulator activity, 0007049 cell cycle; PDB: 1CKS_C 3QY2_B 1QB3_C 1SCE_B 1PUC_A 1DKS_B 2AST_C 1BUH_B 1DKT_B 2ASS_C.
Probab=87.68 E-value=0.2 Score=37.41 Aligned_cols=12 Identities=75% Similarity=1.328 Sum_probs=10.8
Q ss_pred ecceEEeeeCCC
Q psy4005 14 LEPHVLLFRRPK 25 (202)
Q Consensus 14 ~~~~~~~~~~~~ 25 (202)
-|||+||||||+
T Consensus 58 pephiLlFrRp~ 69 (70)
T PF01111_consen 58 PEPHILLFRRPL 69 (70)
T ss_dssp SSTTEEEEEEEC
T ss_pred CCCcEEEEecCC
Confidence 489999999996
No 8
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=75.96 E-value=3.1 Score=28.62 Aligned_cols=52 Identities=17% Similarity=0.227 Sum_probs=34.4
Q ss_pred ceeEEEEEcChHHHhhCCCCCCCCHHHHhhhccccCCCeeEeeecCC---------CceeEEEecc
Q psy4005 96 NYIYRHVMLPPDLAKQVPKTHLMTETEWRNLGVQQSPGWIHYMLHLP---------GNENWVKNRY 152 (202)
Q Consensus 96 ~YEYRHViLPkel~K~VPK~rLLsE~EWR~LGIQQS~GW~HYmiHkP---------EPHILLFRRP 152 (202)
.|||+.|.++......++... -|++...+| ..||+=-.+..+ +..+|+|+|+
T Consensus 1 ~~EYk~v~~~~~~~~~~~~~~--~~~~Ln~~g---~eGWeLV~~~~~~~~~~~g~~~~~~~ifkRe 61 (61)
T PF13783_consen 1 KWEYKVVEVPTGGFFGIDPED--LEEILNEYG---KEGWELVSIIPPFEPGGYGGTEGYVLIFKRE 61 (61)
T ss_pred CcceEEEEEecccccCCCHHH--HHHHHHHHH---hCCcEEEEEEcCCcccCCCCcceEEEEEEcC
Confidence 489999998875443322211 145566666 569987777666 2578999986
No 9
>COG0429 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]
Probab=37.71 E-value=15 Score=34.61 Aligned_cols=21 Identities=38% Similarity=0.534 Sum_probs=18.7
Q ss_pred cCCcccccccccCCccceeee
Q psy4005 162 RDFSVLSQQDKQGGHVGYARL 182 (202)
Q Consensus 162 ~dp~~~~~q~~q~~~~~~~~~ 182 (202)
..|.|+-++.+-||||||--=
T Consensus 300 ~np~v~l~~t~~GGHvGfl~~ 320 (345)
T COG0429 300 LNPNVLLQLTEHGGHVGFLGG 320 (345)
T ss_pred CCCceEEEeecCCceEEeccC
Confidence 789999999999999999653
No 10
>PF05972 APC_15aa: APC 15 residue motif; InterPro: IPR009240 The 15 aa repeat is found in the APC protein family. It is involved in binding beta-catenin [] along with the IPR009223 from INTERPRO repeats. Many human cancer mutations map to the region around these motifs, and may be involved in disrupting their binding of beta-catenin.; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1JPP_C.
Probab=34.44 E-value=19 Score=20.60 Aligned_cols=13 Identities=38% Similarity=0.698 Sum_probs=6.4
Q ss_pred CCeeecCCcCCCc
Q psy4005 84 DDIRYSDKYEDDN 96 (202)
Q Consensus 84 ~~I~YS~KY~DD~ 96 (202)
.+|.||.||..++
T Consensus 4 qP~dyS~kY~e~~ 16 (16)
T PF05972_consen 4 QPIDYSLKYSEEQ 16 (16)
T ss_dssp ----CCCCTTT--
T ss_pred cccchhhhccccC
Confidence 3588999998763
No 11
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=33.59 E-value=30 Score=26.02 Aligned_cols=17 Identities=29% Similarity=0.835 Sum_probs=12.2
Q ss_pred EEeeeCCCCCCCcccccCC
Q psy4005 18 VLLFRRPKQPTPTSCSCGN 36 (202)
Q Consensus 18 ~~~~~~~~~~~~~~~~~gn 36 (202)
-+.|..|. .+.+|+||+
T Consensus 85 ~F~~~nPn--a~~~CgCg~ 101 (105)
T TIGR02011 85 GFKFTNPN--VKDECGCGE 101 (105)
T ss_pred eEEEECCC--CCccCCCCC
Confidence 35666766 468999994
No 12
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=32.27 E-value=32 Score=25.98 Aligned_cols=17 Identities=29% Similarity=0.806 Sum_probs=12.6
Q ss_pred EEeeeCCCCCCCcccccCC
Q psy4005 18 VLLFRRPKQPTPTSCSCGN 36 (202)
Q Consensus 18 ~~~~~~~~~~~~~~~~~gn 36 (202)
-+.|..|.. ..+|+||+
T Consensus 87 ~F~f~NPna--~~~CgCG~ 103 (107)
T PRK09502 87 GFKFTNPNV--KDECGCGE 103 (107)
T ss_pred eEEEECCCC--CCccCCCC
Confidence 456777765 57999995
No 13
>TIGR02150 IPP_isom_1 isopentenyl-diphosphate delta-isomerase, type 1. This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate.
Probab=28.26 E-value=89 Score=24.62 Aligned_cols=27 Identities=11% Similarity=0.074 Sum_probs=19.6
Q ss_pred eeecCCCceeEEEecccccccCCCccC
Q psy4005 137 YMLHLPGNENWVKNRYETLVRLRGKRD 163 (202)
Q Consensus 137 YmiHkPEPHILLFRRPl~~~~l~g~~d 163 (202)
-.+...+.+|||-||..+....+|.-|
T Consensus 32 v~v~~~~g~vLl~kR~~~k~~~PG~W~ 58 (158)
T TIGR02150 32 VFLFNEEGQLLLQRRALSKITWPGVWT 58 (158)
T ss_pred EEEEcCCCeEEEEeccCCCcCCCCCcc
Confidence 457788899999999876555555444
No 14
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=25.29 E-value=1e+02 Score=24.89 Aligned_cols=29 Identities=14% Similarity=0.029 Sum_probs=19.8
Q ss_pred cccCCCeeEee----ecCCCceeEEEecccccc
Q psy4005 128 VQQSPGWIHYM----LHLPGNENWVKNRYETLV 156 (202)
Q Consensus 128 IQQS~GW~HYm----iHkPEPHILLFRRPl~~~ 156 (202)
+++..|..|.. +..++-+|||-||+.+..
T Consensus 26 ~~~~~~~~h~av~v~i~~~~g~vLL~rR~~~~~ 58 (184)
T PRK03759 26 AHTADTPLHLAFSCYLFDADGRLLVTRRALSKK 58 (184)
T ss_pred HHhcCCCeeeEEEEEEEcCCCeEEEEEccCCCC
Confidence 34455655655 667788999999976544
No 15
>PF09355 Phage_Gp19: Phage protein Gp19/Gp15/Gp42; InterPro: IPR018963 This entry is represented by Mycobacteriophage D29, Gp19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.14 E-value=52 Score=26.06 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=16.6
Q ss_pred CCCCCCHHHHhhhccccCCCe
Q psy4005 114 KTHLMTETEWRNLGVQQSPGW 134 (202)
Q Consensus 114 K~rLLsE~EWR~LGIQQS~GW 134 (202)
.+-.++.+||+.||+...+-+
T Consensus 88 G~L~i~~~E~~~LGl~~~r~g 108 (116)
T PF09355_consen 88 GGLYITDSELARLGLSRQRYG 108 (116)
T ss_pred CCEEECHHHHHHhCcccCcce
Confidence 345799999999999886543
No 16
>PTZ00235 DNA polymerase epsilon subunit B; Provisional
Probab=22.39 E-value=39 Score=31.08 Aligned_cols=49 Identities=14% Similarity=0.269 Sum_probs=37.3
Q ss_pred ecceEEeeeCC-CCC-------CCcccccCC--CccccchhhhhHHHhhhhcCCCcccc
Q psy4005 14 LEPHVLLFRRP-KQP-------TPTSCSCGN--NSVQEESAYGKFEFCRAAAAPSLIPV 62 (202)
Q Consensus 14 ~~~~~~~~~~~-~~~-------~~~~~~~gn--~sv~~ds~Y~~~e~~~~~~kp~f~PV 62 (202)
=-|+.++.-.. -++ +.+.|.|-| ||..++..+..|.-++..++.-+.||
T Consensus 233 PlPd~ivL~D~s~~~~~~~~~~~~~~~~~~Np~gsF~~~~sF~~Y~~~~~~~~~~~~~~ 291 (291)
T PTZ00235 233 PLPHFICVCDNSCNSFISYASEDTSDCIISNSDMSFTRKKTFTVYSALHHEAKRYVVPL 291 (291)
T ss_pred CCCCEEEEecCCCCccceeecccCCceEEECCCCccCCCceEEEEehhcceeheeeccC
Confidence 35777666555 455 778999999 59999988888888888888766664
No 17
>PF07254 DUF1434: Protein of unknown function (DUF1434); InterPro: IPR009883 This family consists of several hypothetical bacterial proteins of around 135 residues in length. Members of this family all appear to be Enterobacterial proteins. The function of this family is unknown.
Probab=21.56 E-value=48 Score=27.07 Aligned_cols=11 Identities=45% Similarity=0.999 Sum_probs=9.6
Q ss_pred CCCHHHHhhhc
Q psy4005 117 LMTETEWRNLG 127 (202)
Q Consensus 117 LLsE~EWR~LG 127 (202)
=|+|+|||.|.
T Consensus 116 sm~~~ewR~Lr 126 (132)
T PF07254_consen 116 SMSDEEWRHLR 126 (132)
T ss_pred CCCHHHHHHHH
Confidence 58999999885
No 18
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=21.05 E-value=72 Score=23.38 Aligned_cols=17 Identities=29% Similarity=0.931 Sum_probs=11.8
Q ss_pred EeeeCCCCCCCcccccCCC
Q psy4005 19 LLFRRPKQPTPTSCSCGNN 37 (202)
Q Consensus 19 ~~~~~~~~~~~~~~~~gn~ 37 (202)
+.|..|.+ +.+|+||..
T Consensus 86 f~i~nPn~--~~~c~cg~s 102 (105)
T TIGR00049 86 FTFTNPNA--KGTCGCGKS 102 (105)
T ss_pred EEEECCCC--CccCCCCcC
Confidence 45566664 688999964
No 19
>cd04697 Nudix_Hydrolase_38 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=20.57 E-value=1.8e+02 Score=21.56 Aligned_cols=21 Identities=14% Similarity=-0.047 Sum_probs=15.8
Q ss_pred EeeecCCCceeEEEecccccc
Q psy4005 136 HYMLHLPGNENWVKNRYETLV 156 (202)
Q Consensus 136 HYmiHkPEPHILLFRRPl~~~ 156 (202)
+-.++.+..+|||-||..+..
T Consensus 4 ~v~i~~~~~~iLl~~R~~~~~ 24 (126)
T cd04697 4 YIFVFNSEGKLCVHKRTLTKD 24 (126)
T ss_pred EEEEEcCCCeEEEEECCCCCC
Confidence 456778888999988876544
No 20
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=20.35 E-value=64 Score=22.57 Aligned_cols=18 Identities=17% Similarity=0.326 Sum_probs=15.5
Q ss_pred CCCCHHHHhhhccccCCC
Q psy4005 116 HLMTETEWRNLGVQQSPG 133 (202)
Q Consensus 116 rLLsE~EWR~LGIQQS~G 133 (202)
-||+++.|+.||++.++.
T Consensus 31 ~fis~~~a~rLgl~~~~~ 48 (72)
T PF13975_consen 31 NFISESLAKRLGLPLEKP 48 (72)
T ss_pred eecCHHHHHHhCCCcccC
Confidence 599999999999987653
No 21
>cd03676 Nudix_hydrolase_3 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate spe
Probab=20.19 E-value=1.4e+02 Score=23.74 Aligned_cols=33 Identities=21% Similarity=0.280 Sum_probs=23.9
Q ss_pred cCCCeeEeeec------CCC--ceeEEEecccccccCCCcc
Q psy4005 130 QSPGWIHYMLH------LPG--NENWVKNRYETLVRLRGKR 162 (202)
Q Consensus 130 QS~GW~HYmiH------kPE--PHILLFRRPl~~~~l~g~~ 162 (202)
...|..|..+| +.+ .++||-||..+..--+|.-
T Consensus 26 ~~~g~~h~~v~~~~~~~~~~~~~~l~lqrRs~~K~~~Pg~w 66 (180)
T cd03676 26 RLFGLVTYGVHLNGYVRDEDGGLRIWIPRRSPTKATWPGML 66 (180)
T ss_pred ccCCceEEEEEEEEEEEcCCCCeEEEEEeccCCCCCCCCce
Confidence 35789999888 554 8999999998765333333
No 22
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=20.13 E-value=70 Score=27.01 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=27.8
Q ss_pred hccccCCCeeEeeecCCCceeEE--Eeccc---------ccccCCCccCCccc
Q psy4005 126 LGVQQSPGWIHYMLHLPGNENWV--KNRYE---------TLVRLRGKRDFSVL 167 (202)
Q Consensus 126 LGIQQS~GW~HYmiHkPEPHILL--FRRPl---------~~~~l~g~~dp~~~ 167 (202)
+-|.+-+||+++.--.+++--++ .+... ....|+|..||+-+
T Consensus 33 v~lP~P~GW~~~~~~~~~~a~~vi~~~~~~~~~~Pnavv~V~kL~G~~Dp~e~ 85 (175)
T PF10738_consen 33 VSLPTPPGWEPAPDPNPPWAYAVIVDPQADGGFPPNAVVTVSKLTGDFDPAEA 85 (175)
T ss_pred EeccCCcCcccCCCCCCCceEEEEEeccccCCCCCceEEEEEeccCCCCHHHH
Confidence 56889999999876666553333 33311 12278999999765
Done!