Query 021167
Match_columns 316
No_of_seqs 132 out of 1827
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 08:07:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021167hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00145 DNA_methylase: C-5 cy 100.0 3.3E-54 7.1E-59 397.2 16.0 263 3-313 61-335 (335)
2 TIGR00675 dcm DNA-methyltransf 100.0 1.1E-53 2.5E-58 389.7 19.3 242 3-311 59-315 (315)
3 COG0270 Dcm Site-specific DNA 100.0 5.2E-53 1.1E-57 387.6 18.9 254 3-315 67-324 (328)
4 cd00315 Cyt_C5_DNA_methylase C 100.0 5.8E-52 1.3E-56 371.8 19.7 211 3-313 62-275 (275)
5 PRK10458 DNA cytosine methylas 100.0 3.9E-50 8.4E-55 379.2 22.1 259 3-314 169-455 (467)
6 KOG0919 C-5 cytosine-specific 100.0 1.1E-46 2.4E-51 315.5 8.5 257 2-312 68-337 (338)
7 PF13651 EcoRI_methylase: Aden 81.9 3.6 7.9E-05 37.5 5.8 53 3-78 135-191 (336)
8 COG4747 ACT domain-containing 56.9 17 0.00037 28.1 3.7 36 50-90 8-44 (142)
9 PF03078 ATHILA: ATHILA ORF-1 43.0 25 0.00053 34.0 3.2 44 260-303 138-184 (458)
10 TIGR03704 PrmC_rel_meth putati 36.5 1.5E+02 0.0032 26.1 7.1 73 3-81 153-238 (251)
11 PF11513 TA0956: Thermoplasma 31.8 62 0.0013 23.8 3.0 18 63-80 91-108 (110)
12 PRK13562 acetolactate synthase 29.6 86 0.0019 22.7 3.5 44 50-102 7-51 (84)
13 PF09535 Gmx_para_CXXCG: Prote 27.9 31 0.00067 29.9 1.2 41 11-53 45-88 (237)
14 TIGR02264 gmx_para_CXXCG Myxoc 26.9 34 0.00074 29.4 1.2 46 11-56 45-91 (237)
15 PRK08178 acetolactate synthase 26.4 62 0.0014 24.1 2.4 44 50-101 13-56 (96)
16 PHA01632 hypothetical protein 25.8 86 0.0019 20.7 2.6 43 48-90 17-63 (64)
17 PRK06737 acetolactate synthase 25.7 1.1E+02 0.0025 21.6 3.6 29 50-83 7-35 (76)
18 cd05784 DNA_polB_II_exo DEDDy 24.8 2.5E+02 0.0054 23.6 6.2 42 31-78 53-94 (193)
19 cd05776 DNA_polB_alpha_exo ina 24.7 1.1E+02 0.0023 26.7 4.0 39 31-75 84-122 (234)
20 cd05160 DEDDy_DNA_polB_exo DED 24.6 1.1E+02 0.0025 25.4 4.1 43 30-78 64-106 (199)
21 COG2098 Uncharacterized protei 23.9 80 0.0017 24.0 2.6 44 263-315 6-50 (116)
22 PF07530 PRE_C2HC: Associated 23.2 2E+02 0.0044 19.8 4.4 39 65-105 2-40 (68)
23 COG0391 Uncharacterized conser 22.9 2.9E+02 0.0062 25.5 6.5 84 3-98 189-278 (323)
24 PF05050 Methyltransf_21: Meth 22.7 44 0.00095 26.5 1.1 44 32-78 123-167 (167)
25 PF12017 Tnp_P_element: Transp 22.6 1.6E+02 0.0034 25.9 4.6 39 45-86 182-220 (236)
26 PRK00014 ribB 3,4-dihydroxy-2- 22.4 27 0.00058 30.4 -0.2 27 260-286 116-142 (230)
27 TIGR01764 excise DNA binding d 22.2 60 0.0013 19.7 1.5 16 264-279 1-16 (49)
28 PRK11152 ilvM acetolactate syn 21.6 92 0.002 22.0 2.4 29 50-83 8-36 (76)
29 PF12728 HTH_17: Helix-turn-he 20.8 64 0.0014 20.3 1.4 15 264-278 1-15 (51)
30 PF08624 CRC_subunit: Chromati 20.5 14 0.0003 29.5 -2.1 21 264-284 48-68 (139)
31 PF01842 ACT: ACT domain; Int 20.3 2.5E+02 0.0054 18.0 4.6 33 50-87 5-37 (66)
32 TIGR00537 hemK_rel_arch HemK-r 20.2 3.2E+02 0.0069 22.2 5.9 79 3-92 82-170 (179)
No 1
>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....
Probab=100.00 E-value=3.3e-54 Score=397.22 Aligned_cols=263 Identities=23% Similarity=0.359 Sum_probs=152.9
Q ss_pred cccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcCc---hHHHHHHHHHHcCCCeee
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFETS---DTHAKMIEILANSDYLTQ 79 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~---~~~~~i~~~l~~~GY~v~ 79 (316)
++|||+||||||+||.+|++++.+|+|+.||++++|+|+++ +|++|+||||+||+++ ..++.|++.|+++||.+.
T Consensus 61 ~~D~l~ggpPCQ~fS~ag~~~~~~d~r~~L~~~~~~~v~~~--~Pk~~~~ENV~~l~~~~~~~~~~~i~~~l~~lGY~v~ 138 (335)
T PF00145_consen 61 DVDLLIGGPPCQGFSIAGKRKGFDDPRNSLFFEFLRIVKEL--KPKYFLLENVPGLLSSKNGEVFKEILEELEELGYNVQ 138 (335)
T ss_dssp T-SEEEEE---TTTSTTSTHHCCCCHTTSHHHHHHHHHHHH--S-SEEEEEEEGGGGTGGGHHHHHHHHHHHHHTTEEEE
T ss_pred cceEEEeccCCceEeccccccccccccchhhHHHHHHHhhc--cceEEEecccceeeccccccccccccccccccceeeh
Confidence 58999999999999999998899999999999999999999 9999999999999998 479999999999999999
Q ss_pred EEEEccCCCCCCCCCcEEEEEEEeCCCCcccccccccccCCCCCcCCCCCccccccCCCCCCcccccCccCCchHHhhhh
Q 021167 80 EFILSPLQFGVPYSRPRYFCLAKRKPLSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDDSWDKLLESCDPVERFLEF 159 (316)
Q Consensus 80 ~~vlna~~yGvPQ~R~R~~iva~r~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 159 (316)
+.+|||++|||||+|+|+|+||+|++.....+.. .....+|.... . .....+.|+++.
T Consensus 139 ~~vlna~~yGvPQ~R~R~fivg~r~~~~~~~~~~-~~~~~~~~~~~----~-----------------~~~~~i~dl~~~ 196 (335)
T PF00145_consen 139 WRVLNAADYGVPQNRERVFIVGIRKDLPLPPPFP-IPKFDFPEPKD----P-----------------TVSDAIRDLPDE 196 (335)
T ss_dssp EEEEEGGGGTSSBE-EEEEEEEEEGGG--TSSCC-GTTEEC-SSCG----------------------SHHHHHGGGSTS
T ss_pred hccccHhhCCCCCceeeEEEEEECCCCCcccccc-ccccccccccc----c-----------------cceeeEeecccc
Confidence 9999999999999999999999999875331000 00011111100 0 000113333332
Q ss_pred cCCCCCccccccccccccccccccCccccchhhccccccccccCcHHHhhhcCccc-cccC---CCCCcccccccceeee
Q 021167 160 SNSGDQVNTETGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAM-DIVY---PDSKRCCCFTKSYYRY 235 (316)
Q Consensus 160 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~-d~~~---p~~~~~~~~~~~y~R~ 235 (316)
.... ........ ....... ..........+.... .+.. ............|++.
T Consensus 197 ~~~~---~~~~~~~~--~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 254 (335)
T PF00145_consen 197 PSPK---DEDKYNFS--DRVIEDL-----------------NRIRNNTIKPGKGIPNKISRNRIDKIEDLKGPSRTYRRS 254 (335)
T ss_dssp CCEC---CCCCGBHS--HCHHCSH-----------------CCSHHHHHHHCCCCSTHEECTSTTTTCECTTTCTCCTTS
T ss_pred cccc---cccccccc--hhhhhhh-----------------ccccccccccccchhhhhhhhhccccccccccccccccc
Confidence 1000 00000000 0000000 000000000000000 0000 0000001112222222
Q ss_pred ecCCCce--eeeeccCCCCC---CccccCCCcccCCHHHHHHhCCCCCCcccCCCCCHHHHHHHhCCcccHHHHHHHHHH
Q 021167 236 VKGTGSL--LATVQPKNKGK---ASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQY 310 (316)
Q Consensus 236 ~~~~~s~--~~~~~~~~~~~---~~~ihp~~~R~LT~rE~arLqgFPd~f~f~~~~s~~~~~~qiGNAVp~~v~~~i~~~ 310 (316)
.++.... +.......... ...+||.+.|.||+|||||||||||+|.|.| +.+++|+||||||||+|+++|+++
T Consensus 255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~hp~~~R~LT~rE~aRLqgFPd~~~f~g--~~~~~~~qiGNAVpp~v~~~I~~~ 332 (335)
T PF00145_consen 255 GRGEKMPPQIPTTGSTGKNGHRFRPFIHPEQNRRLTPREAARLQGFPDDFKFPG--SKTQQYKQIGNAVPPPVAEAIAKA 332 (335)
T ss_dssp CTCC-BCCCCCSTSTTTTTHEHCCTEBTTSSSCB-BHHHHHHHTTSSTTS-S-S--SHHHHHHHHHCS--HHHHHHHHHH
T ss_pred cccccccccccccccccccCCccccccCCCCCCcCcHHHHHHhCCCCCceEccC--CHHHHhceECCCcCHHHHHHHHHH
Confidence 2211000 00000000011 1278999999999999999999999999999 888999999999999999999999
Q ss_pred HHh
Q 021167 311 LFA 313 (316)
Q Consensus 311 l~~ 313 (316)
|++
T Consensus 333 i~~ 335 (335)
T PF00145_consen 333 IKK 335 (335)
T ss_dssp HH-
T ss_pred hhC
Confidence 974
No 2
>TIGR00675 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.1e-53 Score=389.71 Aligned_cols=242 Identities=25% Similarity=0.379 Sum_probs=165.1
Q ss_pred cccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcCc---hHHHHHHHHHHcCCCeee
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFETS---DTHAKMIEILANSDYLTQ 79 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~---~~~~~i~~~l~~~GY~v~ 79 (316)
++|+|+||||||+||.+|++++.+|+|+.||++++|+|+++ +|++|+||||+|+++. ..++.|+..|+++||.+.
T Consensus 59 ~~dvl~gg~PCq~fS~ag~~~~~~d~r~~L~~~~~r~i~~~--~P~~~v~ENV~~l~~~~~~~~~~~i~~~l~~~GY~v~ 136 (315)
T TIGR00675 59 DFDILLGGFPCQPFSIAGKRKGFEDTRGTLFFEIVRILKEK--KPKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVY 136 (315)
T ss_pred CcCEEEecCCCcccchhcccCCCCCchhhHHHHHHHHHhhc--CCCEEEeeccHHHHhcccchHHHHHHHHHHhCCCEEE
Confidence 68999999999999999999888999999999999999999 9999999999999875 479999999999999999
Q ss_pred EEEEccCCCCCCCCCcEEEEEEEe-CCCCcccccccccccCCCCCcCCCCCccccccCCCCCCcccccCccCCchHHhhh
Q 021167 80 EFILSPLQFGVPYSRPRYFCLAKR-KPLSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDDSWDKLLESCDPVERFLE 158 (316)
Q Consensus 80 ~~vlna~~yGvPQ~R~R~~iva~r-~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~ 158 (316)
+.+|||++||+||+|+|+|+||+| ++... .+.+|.++. .. ....+.|+++
T Consensus 137 ~~~l~a~dyGvPQ~R~R~f~ia~r~~~~~~--------~~~~p~~~~--~~-------------------~~~~l~d~~~ 187 (315)
T TIGR00675 137 YKVLNAKDFGVPQNRERIYIVGFRDFDDKL--------NFEFPKPIY--VA-------------------KKKRIGDLLD 187 (315)
T ss_pred EEEEcHHHCCCCCCccEEEEEEEeCCCcCc--------CCCCCCCcc--cc-------------------cccchHHhcc
Confidence 999999999999999999999999 44221 234554421 00 0012555554
Q ss_pred hcCCCCCccccccccccccccccccCccccchhhccccccccccCcHHHhhhcCccccccCCCCCcccccccceeeeecC
Q 021167 159 FSNSGDQVNTETGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAMDIVYPDSKRCCCFTKSYYRYVKG 238 (316)
Q Consensus 159 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~d~~~p~~~~~~~~~~~y~R~~~~ 238 (316)
...... ....+. +. .++++.. ...++...+. .+. .+...|.|..++
T Consensus 188 ~~~~~~----~~~~~~------------~~--~~~~~~~----------~~~~~~~~~~-~~~-----~~~~~~~~~~~~ 233 (315)
T TIGR00675 188 LSVDLE----EKYYLS------------EE--KKNGLLL----------LLENMRKKEG-TGE-----QIGSFYNRESKS 233 (315)
T ss_pred cccCcC----CcEEeC------------HH--HHHHHHH----------Hhhccccccc-ccc-----ccceeeccCCcc
Confidence 221100 000000 00 0000000 0000001000 000 011122333333
Q ss_pred CCceeeeeccC---C--------CCCCccccCCCcccCCHHHHHHhCCCCCCcccCCCCCHHHHHHHhCCcccHHHHHHH
Q 021167 239 TGSLLATVQPK---N--------KGKASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPL 307 (316)
Q Consensus 239 ~~s~~~~~~~~---~--------~~~~~~ihp~~~R~LT~rE~arLqgFPd~f~f~~~~s~~~~~~qiGNAVp~~v~~~i 307 (316)
.++.+++.... . ......+||.+.|.||+||+||||||||+|+|.+ +.+++|+||||||||+++++|
T Consensus 234 ~~~~~i~~~~~~~~~~~~t~~~~~~~~~~~hp~~~R~lT~RE~aRLQ~FPd~f~f~~--s~~~~~~qiGNAVPp~la~~I 311 (315)
T TIGR00675 234 SIIRTLSARGYTFVKGGKSVLIVPHKSTVVHPGRIRRLTPRECARLQGFPDDFKFPV--SDSQLYKQAGNAVVVPVIEAI 311 (315)
T ss_pred ceeeeeeccccccCCCCcceeeccccceeccCCceeeCCHHHHHHHcCCCcccEeCC--CHHHHHhhhCCcccHHHHHHH
Confidence 33333322100 0 0011227999999999999999999999999998 999999999999999999999
Q ss_pred HHHH
Q 021167 308 LQYL 311 (316)
Q Consensus 308 ~~~l 311 (316)
|++|
T Consensus 312 ~~~i 315 (315)
T TIGR00675 312 AKQI 315 (315)
T ss_pred HhhC
Confidence 9875
No 3
>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.2e-53 Score=387.64 Aligned_cols=254 Identities=24% Similarity=0.369 Sum_probs=178.0
Q ss_pred cccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcCc--hHHHHHHHHHHcCCCeeeE
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFETS--DTHAKMIEILANSDYLTQE 80 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~--~~~~~i~~~l~~~GY~v~~ 80 (316)
++|+|+||||||+||.||++++.+|+|++||++++|+|.++ +|++||||||+||+++ +.++.|++.|+++||.+.+
T Consensus 67 ~~DvligGpPCQ~FS~aG~r~~~~D~R~~L~~~~~r~I~~~--~P~~fv~ENV~gl~~~~~~~~~~i~~~L~~~GY~~~~ 144 (328)
T COG0270 67 DVDVLIGGPPCQDFSIAGKRRGYDDPRGSLFLEFIRLIEQL--RPKFFVLENVKGLLSSKGQTFDEIKKELEELGYGVEF 144 (328)
T ss_pred CCCEEEeCCCCcchhhcCcccCCcCccceeeHHHHHHHHhh--CCCEEEEecCchHHhcCchHHHHHHHHHHHcCCcchH
Confidence 68999999999999999999999999999999999999999 9999999999999986 6899999999999999999
Q ss_pred EEEccCCCCCCCCCcEEEEEEEeCC-CCcccccccccccCCCCCcCCCCCccccccCCCCCCcccccCccCCchHHhhhh
Q 021167 81 FILSPLQFGVPYSRPRYFCLAKRKP-LSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDDSWDKLLESCDPVERFLEF 159 (316)
Q Consensus 81 ~vlna~~yGvPQ~R~R~~iva~r~~-~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 159 (316)
.+|||++|||||+|+|+|+||++++ ..+.. ..+.+.. .. . ...+.+.+..
T Consensus 145 ~ilna~dyGvPQ~ReRvfiig~~~~~~~~~~--------~~~~~~~----~~------~-----------~~~~~~~i~~ 195 (328)
T COG0270 145 NILNAADYGVPQSRERVFIVGFRRDNIDLDP--------NVLPPLP----LG------R-----------KKTLKEALKN 195 (328)
T ss_pred heeeHHhcCCCCCccEEEEEEecCccccccc--------cccCccc----cc------c-----------ccchhhhhhh
Confidence 9999999999999999999999985 21111 0000000 00 0 0001111110
Q ss_pred cCCCCCcccc-ccccccccccccccCccccchhhccccccccccCcHHHhhhcCccccccCCCCCcccccccceeeeecC
Q 021167 160 SNSGDQVNTE-TGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAMDIVYPDSKRCCCFTKSYYRYVKG 238 (316)
Q Consensus 160 ~~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~d~~~p~~~~~~~~~~~y~R~~~~ 238 (316)
.......... .... ..+....+... .....+. ..+....... .... ....|.|+.++
T Consensus 196 ~~~~~~~~~~~~~~~--~~~~~~~~~~~------------~~~~~~~---~~~~~~~~~~-~~~~----~~~~~~rl~~~ 253 (328)
T COG0270 196 NDLPETDELYLSRDL--RNHEAKSLPKN------------KGERLPS---LRWGEALTLS-RRYK----GKGSYIRLHPD 253 (328)
T ss_pred ccCcchhhhhccccc--cccccccCchh------------hhccccc---cccccccccc-cccC----CCceeEeCCCC
Confidence 0000000000 0000 00000000000 0000000 0000000000 0000 15678999999
Q ss_pred CCceeeeeccCCCCCCccccCCCcccCCHHHHHHhCCCCCCcccCCCCCHHHHHHHhCCcccHHHHHHHHHHHHhhc
Q 021167 239 TGSLLATVQPKNKGKASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQYLFAQA 315 (316)
Q Consensus 239 ~~s~~~~~~~~~~~~~~~ihp~~~R~LT~rE~arLqgFPd~f~f~~~~s~~~~~~qiGNAVp~~v~~~i~~~l~~~~ 315 (316)
.+++|+.. ......+||.+.|.||+||+||||||||+|.|.| |.+++|+||||||||+++++||+.|++.+
T Consensus 254 ~~~~t~~~----~~~~~~~h~~~~r~lt~rE~arlq~fPd~~~~~g--s~~~~~~qiGnsVp~~l~~~ia~~i~~~l 324 (328)
T COG0270 254 KPAPTVRG----GGNERFIHPLEDRELTVREAARLQGFPDDFVFPG--SKTDQYRQIGNSVPPLLAEAIAKAILKKL 324 (328)
T ss_pred CCCceeec----CCCcccCCCCcCCCCCHHHHHHhcCCCCceEEec--cchhhhhhccCcCCHHHHHHHHHHHHHHh
Confidence 99999983 2457899999999999999999999999999999 99999999999999999999999998764
No 4
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=100.00 E-value=5.8e-52 Score=371.84 Aligned_cols=211 Identities=30% Similarity=0.494 Sum_probs=164.2
Q ss_pred cccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcC---chHHHHHHHHHHcCCCeee
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFET---SDTHAKMIEILANSDYLTQ 79 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~---~~~~~~i~~~l~~~GY~v~ 79 (316)
++|+|+||||||+||.+|++++.+|+|+.||++++++|+.+ +|++|+||||+|+++ +..++.|++.|+++||.+.
T Consensus 62 ~~D~l~~gpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~--~P~~~v~ENV~g~~~~~~~~~~~~i~~~l~~~GY~~~ 139 (275)
T cd00315 62 DIDLLTGGFPCQPFSIAGKRKGFEDTRGTLFFEIIRILKEK--KPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYNVY 139 (275)
T ss_pred CCCEEEeCCCChhhhHHhhcCCCCCchHHHHHHHHHHHHhc--CCCEEEEEcCcchhccCchHHHHHHHHHHHhCCcEEE
Confidence 68999999999999999998888999999999999999999 999999999999998 5689999999999999999
Q ss_pred EEEEccCCCCCCCCCcEEEEEEEeCCCCcccccccccccCCCCCcCCCCCccccccCCCCCCcccccCccCCchHHhhhh
Q 021167 80 EFILSPLQFGVPYSRPRYFCLAKRKPLSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDDSWDKLLESCDPVERFLEF 159 (316)
Q Consensus 80 ~~vlna~~yGvPQ~R~R~~iva~r~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 159 (316)
+.+|||++||+||+|+|+|+||++++....++. .+|.+.. +..+++|+|..
T Consensus 140 ~~~l~a~~~GvPQ~R~R~~~ia~~~~~~~~~~~------~~p~~~~-----------------------~~~t~~d~l~~ 190 (275)
T cd00315 140 WKLLNASDYGVPQNRERVFIIGIRKDLILNFFS------PFPKPSE-----------------------KKKTLKDILRI 190 (275)
T ss_pred EEEEEHHHcCCCCCCcEEEEEEEeCCCCccccc------cCCCCCC-----------------------CCCcHHHHHhh
Confidence 999999999999999999999999986433210 0111110 01125555521
Q ss_pred cCCCCCccccccccccccccccccCccccchhhccccccccccCcHHHhhhcCccccccCCCCCcccccccceeeeecCC
Q 021167 160 SNSGDQVNTETGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAMDIVYPDSKRCCCFTKSYYRYVKGT 239 (316)
Q Consensus 160 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~d~~~p~~~~~~~~~~~y~R~~~~~ 239 (316)
.. ++. .+.|++..|++ +.
T Consensus 191 ~~----------------------------------------------------------~~~-~~~ti~~~~~~---~~ 208 (275)
T cd00315 191 RD----------------------------------------------------------PDE-PSPTLTASYGK---GT 208 (275)
T ss_pred hc----------------------------------------------------------CCC-CccceecCCCC---Cc
Confidence 10 011 12334444433 11
Q ss_pred CceeeeeccCCCCCCccccCCCcccCCHHHHHHhCCCCCCcccCCCCCHHHHHHHhCCcccHHHHHHHHHHHHh
Q 021167 240 GSLLATVQPKNKGKASSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLLQYLFA 313 (316)
Q Consensus 240 ~s~~~~~~~~~~~~~~~ihp~~~R~LT~rE~arLqgFPd~f~f~~~~s~~~~~~qiGNAVp~~v~~~i~~~l~~ 313 (316)
+++.... .....||.+.|.||+||+||||||||+|.|.|. +.+++|+||||||||+++++|+++|.+
T Consensus 209 ~~~~~~~------~~~~~~~~~~R~lT~rE~arlqgFPd~f~f~g~-~~~~~~~qiGNAVp~~~~~~I~~~i~~ 275 (275)
T cd00315 209 GSVHPTA------PDMIGKESNIRRLTPRECARLQGFPDDFEFPGK-SVTQAYRQIGNSVPVPVAEAIAKAIKE 275 (275)
T ss_pred cccccCc------ccccccCCCCCCCCHHHHHHHcCCCCCcEEcCC-CHHHHHHhhcCCcCHHHHHHHHHHHhC
Confidence 1111110 011468899999999999999999999999986 799999999999999999999999864
No 5
>PRK10458 DNA cytosine methylase; Provisional
Probab=100.00 E-value=3.9e-50 Score=379.16 Aligned_cols=259 Identities=22% Similarity=0.322 Sum_probs=176.0
Q ss_pred cccEEEeCCCCcHHhhccCCC--------CC-CCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcCch---HHHHHHHH
Q 021167 3 GAHAWLLSPPCQPYTRQGLQK--------QS-SDARAFSFLKILELIPHTVKPPHMLFVENVVGFETSD---THAKMIEI 70 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~--------~~-~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~~---~~~~i~~~ 70 (316)
++|||+||||||+||.||+++ +. +|+|++||++++|+|+++ +|++||||||+||++++ +|+.|++.
T Consensus 169 ~~DvL~gGpPCQ~FS~AG~~k~~~~gr~~g~~~d~rg~Lf~~~~rii~~~--kPk~fvlENV~gl~s~~~g~~f~~i~~~ 246 (467)
T PRK10458 169 DHDVLLAGFPCQPFSLAGVSKKNSLGRAHGFECETQGTLFFDVARIIDAK--RPAIFVLENVKNLKSHDKGKTFRIIMQT 246 (467)
T ss_pred CCCEEEEcCCCCccchhcccccccccccccccCCccccHHHHHHHHHHHh--CCCEEEEeCcHhhhcccccHHHHHHHHH
Confidence 689999999999999999754 22 378999999999999999 99999999999999764 89999999
Q ss_pred HHcCCCeee---------EEEEccCCCCCCCCCcEEEEEEEeCCCCcccccccccccCCCCCcCCCCCccccccCCCCCC
Q 021167 71 LANSDYLTQ---------EFILSPLQFGVPYSRPRYFCLAKRKPLSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDD 141 (316)
Q Consensus 71 l~~~GY~v~---------~~vlna~~yGvPQ~R~R~~iva~r~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 141 (316)
|+++||.+. +.||||++| |||+|+|+|+||+|++..+.. .|.+|..... .+
T Consensus 247 L~~lGY~v~~~~~~g~~~~~vlna~~f-VPQ~R~RvfiVg~r~~~~~~~------~f~~~~~~~~---~p---------- 306 (467)
T PRK10458 247 LDELGYDVADAEDNGPDDPKIIDGKHF-LPQHRERIVLVGFRRDLNLKA------DFTLRDISEC---YP---------- 306 (467)
T ss_pred HHHcCCeEEeccccCcccceEeehhhC-CCccCcEEEEEEEeCCccccc------Cccccccccc---CC----------
Confidence 999999995 689999999 999999999999999864321 1222221100 00
Q ss_pred cccccCccCCchHHhhhhcCCCCCccccccccccccccccccCccccchhhccccccccccCcHHHhhhcCccccccCCC
Q 021167 142 SWDKLLESCDPVERFLEFSNSGDQVNTETGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAMDIVYPD 221 (316)
Q Consensus 142 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~d~~~p~ 221 (316)
...+++.++|+.... +++.+. ...+.. + ..+.. ....+..|..++++.|.
T Consensus 307 ------~~~~~l~diL~~~~~------~ky~ls--~~~~~~---------l------~~~~~-k~~~~g~g~~~~i~~~~ 356 (467)
T PRK10458 307 ------AQRPTLAELLDPVVD------AKYILT--PVLWKY---------L------YRYAK-KHQAKGNGFGYGLVYPN 356 (467)
T ss_pred ------CCCCCHHHhcCCCCC------cceeeC--HHHHHH---------H------HHHHh-hccccCCCcceeeeecC
Confidence 001237777764211 111110 000000 0 00000 00011224456666665
Q ss_pred CCcccccccceeeeecCCCceeeeec-cCCCCCCccccC----CCcccCCHHHHHHhCCC--CCCcccCCCCCHHHHHHH
Q 021167 222 SKRCCCFTKSYYRYVKGTGSLLATVQ-PKNKGKASSLKE----QHLRYFTPREVANLHSF--PGDFQFPHHLSLRQRYAL 294 (316)
Q Consensus 222 ~~~~~~~~~~y~R~~~~~~s~~~~~~-~~~~~~~~~ihp----~~~R~LT~rE~arLqgF--Pd~f~f~~~~s~~~~~~q 294 (316)
...+.|.|.++ |+.++....++... ....+...+.|| ...|+|||||||||||| ||+|.|...+|.+++|+|
T Consensus 357 ~~~~~~~t~~~-ry~k~gs~~~i~~~~~~~~~~~~~~~~~~~~~~~RrLTprE~aRLqGF~~pd~~~F~~~vSdtq~Ykq 435 (467)
T PRK10458 357 NPQSVTRTLSA-RYYKDGSEILIDRGWDMALGEKDFDDPENQQHRPRRLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQ 435 (467)
T ss_pred CCCCccccccc-ccccCCCceeeecccccccccccccccccccCCcccCCHHHHHHhCCCCCCccccccCCCCHHHHHHH
Confidence 55555666554 77676333333322 111222334445 35899999999999999 567777666799999999
Q ss_pred hCCcccHHHHHHHHHHHHhh
Q 021167 295 LGNSLSIAVVAPLLQYLFAQ 314 (316)
Q Consensus 295 iGNAVp~~v~~~i~~~l~~~ 314 (316)
+||||+|+|+++||+.|.+.
T Consensus 436 ~GNSV~Vpvv~aIa~~L~~~ 455 (467)
T PRK10458 436 FGNSVVVPVFAAVAKLLEPK 455 (467)
T ss_pred hCCcccHHHHHHHHHHHHHH
Confidence 99999999999999998753
No 6
>KOG0919 consensus C-5 cytosine-specific DNA methylase [Transcription]
Probab=100.00 E-value=1.1e-46 Score=315.46 Aligned_cols=257 Identities=40% Similarity=0.686 Sum_probs=207.5
Q ss_pred CcccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcCchHHHHHHHHHHcCCCeeeEE
Q 021167 2 YGAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFETSDTHAKMIEILANSDYLTQEF 81 (316)
Q Consensus 2 ~~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~ 81 (316)
+++|+|.+|||||+|++.|.+++..|+|+..|.|++.++-++..-|+|++||||+||..+++-+..++.|+++||+..+.
T Consensus 68 l~~~m~lMSPpCQPfTRiG~q~D~~D~Rs~aflhil~~lP~~q~LPeYIL~ENVkGFE~S~ar~~~i~~lencGf~~~Ef 147 (338)
T KOG0919|consen 68 LQANMLLMSPPCQPFTRIGLQRDTEDKRSDAFLHILGLLPECQELPEYILMENVKGFESSQARNQFIESLENCGFHWREF 147 (338)
T ss_pred cccceEeeCCCCCchhhhcccccccCchhHHHHHHHhhhhhhhhhhHHHHHhhcccchhhhHHHHHHHHHHhcCchhhhe
Confidence 57899999999999999999999999999999999999988855599999999999999999999999999999999999
Q ss_pred EEccCCCCCCCCCcEEEEEEEeCCCCcccccccccccCCCCCcCCCCCccccccCCCCCCcccccCccCCchHHhhhhcC
Q 021167 82 ILSPLQFGVPYSRPRYFCLAKRKPLSFRCQLLNNQLLRSPSPLLGNDDMTVITKHDQPDDSWDKLLESCDPVERFLEFSN 161 (316)
Q Consensus 82 vlna~~yGvPQ~R~R~~iva~r~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 161 (316)
+|...+||+|.+|-|+|+||... .+|++ ++...|+ .... .++. + .+ ....+-++|+++.+.
T Consensus 148 iLsPtqfniPNsR~Ryy~iArl~-~~F~~--~G~~s~d--~~~q-Fsei-----a-------qk-~g~Vk~i~d~lE~~~ 208 (338)
T KOG0919|consen 148 ILSPTQFNIPNSRYRYYCIARLG-ADFPF--AGGKSWD--EMPQ-FSEI-----A-------QK-QGLVKQIADILEENV 208 (338)
T ss_pred eccccccCCCCcchheeehhhhC-CCCCC--CCCcccc--cccc-hHHH-----H-------Hh-cchHHHHHHHHHhcC
Confidence 99999999999999999999765 22221 1211111 0000 0000 0 00 000123566776432
Q ss_pred CCCCccccccccccccccccccCccccchhhccccccccccCcHHHhhhcCccccccCCCCCcccccccceeeeecCCCc
Q 021167 162 SGDQVNTETGFLSTGTAAVDDFGAAEETVEVDRCVSIDHFLVPLSLIERWGSAMDIVYPDSKRCCCFTKSYYRYVKGTGS 241 (316)
Q Consensus 162 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~d~~~p~~~~~~~~~~~y~R~~~~~~s 241 (316)
+ |..|++|+..+.+|+-.+|++.|.+.+|.|+|++|+++..|+||
T Consensus 209 d-----------------------------------~s~ylvp~~vL~k~~l~~DIv~P~~srs~CFTkGYthy~eGtGS 253 (338)
T KOG0919|consen 209 D-----------------------------------PSDYLVPDDVLTKRVLVMDIVHPAQSRSMCFTKGYTHYTEGTGS 253 (338)
T ss_pred C-----------------------------------HHHccCCHHHHHHhHhheeecccccccceEeecCccceeecchH
Confidence 2 35689999999999999999999999999999999999999999
Q ss_pred eeeeeccCCCC-----CC--------ccccCCCcccCCHHHHHHhCCCCCCcccCCCCCHHHHHHHhCCcccHHHHHHHH
Q 021167 242 LLATVQPKNKG-----KA--------SSLKEQHLRYFTPREVANLHSFPGDFQFPHHLSLRQRYALLGNSLSIAVVAPLL 308 (316)
Q Consensus 242 ~~~~~~~~~~~-----~~--------~~ihp~~~R~LT~rE~arLqgFPd~f~f~~~~s~~~~~~qiGNAVp~~v~~~i~ 308 (316)
++.+....+.. .. ..+|--+.|++|+||.|||||||.+|.|+.+++.+++|+++|||+.|.|+..+.
T Consensus 254 ilq~~~~i~~eN~~~s~~~~~~~~~~~~l~~l~LRYFTprEvArLmgFPe~fefp~~~T~kq~YRLLGNSiNVkVV~~LI 333 (338)
T KOG0919|consen 254 ILQLVKEIDTENQDASKSEKILQQRLDLLHQLRLRYFTPREVARLMGFPENFEFPPETTNKQKYRLLGNSINVKVVGELI 333 (338)
T ss_pred HHHHHhhhcccchhHHHHHHHHHHHHHHHHHHHhhccCHHHHHHHcCCCcccCCCcchhHHHHHHHhcCcccceeHHHHH
Confidence 88764421111 11 456778999999999999999999999999999999999999999999999988
Q ss_pred HHHH
Q 021167 309 QYLF 312 (316)
Q Consensus 309 ~~l~ 312 (316)
+-|.
T Consensus 334 klL~ 337 (338)
T KOG0919|consen 334 KLLT 337 (338)
T ss_pred HHhc
Confidence 7764
No 7
>PF13651 EcoRI_methylase: Adenine-specific methyltransferase EcoRI
Probab=81.92 E-value=3.6 Score=37.48 Aligned_cols=53 Identities=15% Similarity=0.321 Sum_probs=40.7
Q ss_pred cccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcCchHHHHHHHHHHc----CCCee
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFETSDTHAKMIEILAN----SDYLT 78 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~~~~~~i~~~l~~----~GY~v 78 (316)
++|||+--|| || ||.+|++++-+. .=+|+|+-|.-.+ ++..|...+++ +||..
T Consensus 135 eADIVVTNPP---FS--------------LFrEyv~~Li~~--~KkFlIIGN~Nai----TYkeiFplik~nk~WlG~~~ 191 (336)
T PF13651_consen 135 EADIVVTNPP---FS--------------LFREYVAQLIEY--DKKFLIIGNINAI----TYKEIFPLIKENKIWLGYTF 191 (336)
T ss_pred cCCEEEeCCC---cH--------------HHHHHHHHHHHh--CCCEEEEeccccc----cHHHHHHHHhcCcEEecccc
Confidence 4677777777 44 999999999988 7899999999777 45556566654 57765
No 8
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=56.89 E-value=17 Score=28.06 Aligned_cols=36 Identities=28% Similarity=0.406 Sum_probs=29.5
Q ss_pred EEEcchhhhcCchHHHHHHHHHHcCCCeeeEE-EEccCCCCC
Q 021167 50 LFVENVVGFETSDTHAKMIEILANSDYLTQEF-ILSPLQFGV 90 (316)
Q Consensus 50 ~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~-vlna~~yGv 90 (316)
+++||-||=+ ....+.|.+.|-.+... +-|+.+||+
T Consensus 8 vFlENk~GRL-----~~~~~~L~eagINiRA~tiAdt~dFGI 44 (142)
T COG4747 8 VFLENKPGRL-----ASVANKLKEAGINIRAFTIADTGDFGI 44 (142)
T ss_pred EEecCCcchH-----HHHHHHHHHcCCceEEEEeccccCcce
Confidence 6799999974 56678899999888654 669999997
No 9
>PF03078 ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 ATHILA is a group of Arabidopsis thaliana retrotransposons [] belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons[, ]. The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown.
Probab=43.05 E-value=25 Score=33.97 Aligned_cols=44 Identities=11% Similarity=0.224 Sum_probs=32.6
Q ss_pred CCcccCCHHHHHHhCCCCCCcccCCCC---CHHHHHHHhCCcccHHH
Q 021167 260 QHLRYFTPREVANLHSFPGDFQFPHHL---SLRQRYALLGNSLSIAV 303 (316)
Q Consensus 260 ~~~R~LT~rE~arLqgFPd~f~f~~~~---s~~~~~~qiGNAVp~~v 303 (316)
...=.||+.+.+++.|||......... -...-|..||+++|-..
T Consensus 138 ~~~y~lsi~~L~~i~GF~~~~~i~~~~~~~el~~~W~~ig~~~p~~~ 184 (458)
T PF03078_consen 138 GVEYSLSIKHLERIFGFPSGDEIKPDFDPEELNDFWATIGGGKPFNS 184 (458)
T ss_pred ceeeeeeHHHHHHHhCCCCccccCCCCCchHHHHHHHHhcCCCcccc
Confidence 344568999999999999976653322 34678999999976544
No 10
>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.
Probab=36.45 E-value=1.5e+02 Score=26.07 Aligned_cols=73 Identities=15% Similarity=0.209 Sum_probs=40.2
Q ss_pred cccEEEeCCCCcHHhhccCCCC---CCCcchh---------hHHHHHHHhhhhcCCCc-EEEEcchhhhcCchHHHHHHH
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQ---SSDARAF---------SFLKILELIPHTVKPPH-MLFVENVVGFETSDTHAKMIE 69 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~---~~d~r~~---------L~~~~~~~i~~~~~~P~-~~~~ENV~~~~~~~~~~~i~~ 69 (316)
.+|+++..|||.+.+..+.... ..+++.. ++..+++-+..+. +|. .++||-= ..-...+++
T Consensus 153 ~fDlVv~NPPy~~~~~~~~~~~e~~~~ep~~al~gg~dgl~~~~~i~~~a~~~L-~~gG~l~l~~~-----~~~~~~v~~ 226 (251)
T TIGR03704 153 RVDILAANAPYVPTDAIALMPPEARDHEPRVALDGGADGLDVLRRVAAGAPDWL-APGGHLLVETS-----ERQAPLAVE 226 (251)
T ss_pred CEeEEEECCCCCCchhhhcCCHHHHhCCCHHHhcCCCcHHHHHHHHHHHHHHhc-CCCCEEEEEEC-----cchHHHHHH
Confidence 4799999999998765432110 1222222 2445554333332 563 4455521 123467888
Q ss_pred HHHcCCCeeeEE
Q 021167 70 ILANSDYLTQEF 81 (316)
Q Consensus 70 ~l~~~GY~v~~~ 81 (316)
.|++.|+.....
T Consensus 227 ~l~~~g~~~~~~ 238 (251)
T TIGR03704 227 AFARAGLIARVA 238 (251)
T ss_pred HHHHCCCCceee
Confidence 888888765433
No 11
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=31.80 E-value=62 Score=23.76 Aligned_cols=18 Identities=11% Similarity=0.261 Sum_probs=14.5
Q ss_pred HHHHHHHHHHcCCCeeeE
Q 021167 63 THAKMIEILANSDYLTQE 80 (316)
Q Consensus 63 ~~~~i~~~l~~~GY~v~~ 80 (316)
..+.+++.+++.||++..
T Consensus 91 ~i~ei~kkykd~GykvE~ 108 (110)
T PF11513_consen 91 SIEEIVKKYKDSGYKVEI 108 (110)
T ss_dssp HHHHHHHHHHCCS-EEEE
T ss_pred HHHHHHHHhhcCCceeec
Confidence 468899999999999865
No 12
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=29.62 E-value=86 Score=22.73 Aligned_cols=44 Identities=14% Similarity=0.127 Sum_probs=30.9
Q ss_pred EEEcchhhhcCchHHHHHHHHHHcCCCeeeEEEEcc-CCCCCCCCCcEEEEEEE
Q 021167 50 LFVENVVGFETSDTHAKMIEILANSDYLTQEFILSP-LQFGVPYSRPRYFCLAK 102 (316)
Q Consensus 50 ~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~vlna-~~yGvPQ~R~R~~iva~ 102 (316)
++.||.+|.+ ..+...|...||.+..--+.. .+-|+ .|+-++..
T Consensus 7 vlVeN~~GVL-----~Rit~lFsRRg~NI~SLtvg~Te~~~i----SRmtivv~ 51 (84)
T PRK13562 7 LQVADQVSTL-----NRITSAFVRLQYNIDTLHVTHSEQPGI----SNMEIQVD 51 (84)
T ss_pred EEEECCCCHH-----HHHHHHHhccCcCeeeEEecccCCCCc----eEEEEEEe
Confidence 5789999986 678889999999986554433 23333 36666654
No 13
>PF09535 Gmx_para_CXXCG: Protein of unknown function (Gmx_para_CXXCG); InterPro: IPR011750 This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=27.92 E-value=31 Score=29.91 Aligned_cols=41 Identities=20% Similarity=0.201 Sum_probs=32.9
Q ss_pred CCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCC---cEEEEc
Q 021167 11 PPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPP---HMLFVE 53 (316)
Q Consensus 11 pPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P---~~~~~E 53 (316)
-||.+.|..-.++..+++|-.-|.+|.|+.+.+ +| ....+|
T Consensus 45 YP~VDLS~lper~~~~~prp~~~eEf~RLrelV--RP~~Ppga~l~ 88 (237)
T PF09535_consen 45 YPCVDLSSLPERKELEEPRPEPFEEFSRLRELV--RPLAPPGAPLE 88 (237)
T ss_pred ccccccccCcchHhhcCCCCCCHHHHHHHHHHh--cccCCCCCcCC
Confidence 599999988877778899988999999999988 54 444444
No 14
>TIGR02264 gmx_para_CXXCG Myxococcus xanthus double-CXXCG motif paralogous family. This family consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=26.86 E-value=34 Score=29.36 Aligned_cols=46 Identities=17% Similarity=0.169 Sum_probs=35.4
Q ss_pred CCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhc-CCCcEEEEcchh
Q 021167 11 PPCQPYTRQGLQKQSSDARAFSFLKILELIPHTV-KPPHMLFVENVV 56 (316)
Q Consensus 11 pPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~-~~P~~~~~ENV~ 56 (316)
-||.+.|..-.++..+++|..-|.+|.|+=+.+. .-|....+|-=.
T Consensus 45 YPcVDLs~lper~~~~~prp~~~eefsrLRelvRP~aPpgA~LePGt 91 (237)
T TIGR02264 45 YPCVDLSSLPERKLLEEPRPEPFEEFSRLREQVRPLAPPGALLEPGT 91 (237)
T ss_pred ccccchhhchhhHhhccCCCCCHHHHHHHHHHhcccCCCCccCCCCC
Confidence 4999999988777789999989999998877772 135667776543
No 15
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=26.39 E-value=62 Score=24.08 Aligned_cols=44 Identities=18% Similarity=0.209 Sum_probs=29.4
Q ss_pred EEEcchhhhcCchHHHHHHHHHHcCCCeeeEEEEccCCCCCCCCCcEEEEEE
Q 021167 50 LFVENVVGFETSDTHAKMIEILANSDYLTQEFILSPLQFGVPYSRPRYFCLA 101 (316)
Q Consensus 50 ~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~vlna~~yGvPQ~R~R~~iva 101 (316)
++.||.+|++ ..+...|..-||.+.-. .++.-+.|. =.|+.++.
T Consensus 13 vlv~N~pGVL-----~RIaglFsRRgyNIeSL--tvg~te~~~-iSRmtivv 56 (96)
T PRK08178 13 LTVRNHPGVM-----SHVCGLFARRAFNVEGI--LCLPIQDGD-KSRIWLLV 56 (96)
T ss_pred EEEECCcCHH-----HHHHHHHhcCCcCeeeE--EEeecCCCC-ceEEEEEE
Confidence 5789999986 67888999999998544 333333443 13455544
No 16
>PHA01632 hypothetical protein
Probab=25.77 E-value=86 Score=20.68 Aligned_cols=43 Identities=21% Similarity=0.217 Sum_probs=27.0
Q ss_pred cEEEEcchhhhcCch----HHHHHHHHHHcCCCeeeEEEEccCCCCC
Q 021167 48 HMLFVENVVGFETSD----THAKMIEILANSDYLTQEFILSPLQFGV 90 (316)
Q Consensus 48 ~~~~~ENV~~~~~~~----~~~~i~~~l~~~GY~v~~~vlna~~yGv 90 (316)
-|+++|.||.--+.. +...|+..+.+|==+-...++|+...|+
T Consensus 17 iyilieqvp~kpteeelrkvlpkilkdyanmie~gk~ki~ds~ewgi 63 (64)
T PHA01632 17 IYILIEQVPQKPTEEELRKVLPKILKDYANMIENGKIKILDSKEWGI 63 (64)
T ss_pred EEEehhhcCCCCCHHHHHHHHHHHHHHHHHHHhcCceEEeccccccc
Confidence 468899998775542 4444544444332233567899998885
No 17
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=25.66 E-value=1.1e+02 Score=21.57 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=23.8
Q ss_pred EEEcchhhhcCchHHHHHHHHHHcCCCeeeEEEE
Q 021167 50 LFVENVVGFETSDTHAKMIEILANSDYLTQEFIL 83 (316)
Q Consensus 50 ~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~vl 83 (316)
++.||.+|.+ ..+...|...||.+..--+
T Consensus 7 i~v~n~pGVL-----~Ri~~lf~rRgfNI~Sl~v 35 (76)
T PRK06737 7 LVIHNDPSVL-----LRISGIFARRGYYISSLNL 35 (76)
T ss_pred EEEecCCCHH-----HHHHHHHhccCcceEEEEe
Confidence 5789999985 7889999999999875443
No 18
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=24.78 E-value=2.5e+02 Score=23.62 Aligned_cols=42 Identities=12% Similarity=0.153 Sum_probs=37.2
Q ss_pred hhHHHHHHHhhhhcCCCcEEEEcchhhhcCchHHHHHHHHHHcCCCee
Q 021167 31 FSFLKILELIPHTVKPPHMLFVENVVGFETSDTHAKMIEILANSDYLT 78 (316)
Q Consensus 31 ~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~~~~~~i~~~l~~~GY~v 78 (316)
.|...|+.++... .|.+++==|+.+| .+..|.+.++.+|...
T Consensus 53 ~lL~~f~~~i~~~--dPDvi~g~N~~~F----D~~yl~~R~~~~~i~~ 94 (193)
T cd05784 53 SLLLALIAWFAQY--DPDIIIGWNVINF----DLRLLQRRAEAHGLPL 94 (193)
T ss_pred HHHHHHHHHHHhh--CCCEEEECCCcCc----CHHHHHHHHHHhCCCc
Confidence 5999999999999 8999999999999 7899999998876553
No 19
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=24.67 E-value=1.1e+02 Score=26.65 Aligned_cols=39 Identities=13% Similarity=0.207 Sum_probs=35.8
Q ss_pred hhHHHHHHHhhhhcCCCcEEEEcchhhhcCchHHHHHHHHHHcCC
Q 021167 31 FSFLKILELIPHTVKPPHMLFVENVVGFETSDTHAKMIEILANSD 75 (316)
Q Consensus 31 ~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~~~~~~i~~~l~~~G 75 (316)
.|...|+.+|..+ -|++++==|+.|| .+..+++.++.+|
T Consensus 84 ~LL~~f~~~i~~~--DPDiivG~Ni~~f----dl~~L~~R~~~l~ 122 (234)
T cd05776 84 ALLNFFLAKLQKI--DPDVLVGHDLEGF----DLDVLLSRIQELK 122 (234)
T ss_pred HHHHHHHHHHhhc--CCCEEEeeccCCC----CHHHHHHHHHHhC
Confidence 6999999999999 8999999999999 7899999998765
No 20
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=24.63 E-value=1.1e+02 Score=25.42 Aligned_cols=43 Identities=12% Similarity=0.127 Sum_probs=37.9
Q ss_pred hhhHHHHHHHhhhhcCCCcEEEEcchhhhcCchHHHHHHHHHHcCCCee
Q 021167 30 AFSFLKILELIPHTVKPPHMLFVENVVGFETSDTHAKMIEILANSDYLT 78 (316)
Q Consensus 30 ~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~~~~~~~i~~~l~~~GY~v 78 (316)
..|...|+++++.. .|.+++==|+.+| .+..|.+.+..+|...
T Consensus 64 ~~lL~~f~~~i~~~--dpdiivg~N~~~F----D~~~L~~R~~~~~~~~ 106 (199)
T cd05160 64 KELLKRFFDIIREY--DPDILTGYNIDDF----DLPYLLKRAEALGIKL 106 (199)
T ss_pred HHHHHHHHHHHHhc--CCCEEEEeccCCC----cHHHHHHHHHHhCCCc
Confidence 36899999999999 8999999999999 7899999998877654
No 21
>COG2098 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.94 E-value=80 Score=24.01 Aligned_cols=44 Identities=23% Similarity=0.266 Sum_probs=34.2
Q ss_pred ccCCHHHHHHhCCCCCCcccCCCCCHHHHHHH-hCCcccHHHHHHHHHHHHhhc
Q 021167 263 RYFTPREVANLHSFPGDFQFPHHLSLRQRYAL-LGNSLSIAVVAPLLQYLFAQA 315 (316)
Q Consensus 263 R~LT~rE~arLqgFPd~f~f~~~~s~~~~~~q-iGNAVp~~v~~~i~~~l~~~~ 315 (316)
-.||.||-| .|.++++....|+| +|--|++--+..|.++|-+++
T Consensus 6 ~~~tdrerA---------iFEaGIklGalyHqf~GtPvs~~~a~~le~aI~esi 50 (116)
T COG2098 6 KKLTDRERA---------IFEAGIKLGALYHQFVGTPVSPGTAESLEKAIEESI 50 (116)
T ss_pred cccCHHHHH---------HHHcccchhhhhhhhcCCcCCccchHHHHHHHHHHH
Confidence 357888877 36677888899887 788898888888888887653
No 22
>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth. These proteins are possibly involved in RNA binding or single strand DNA binding.
Probab=23.22 E-value=2e+02 Score=19.76 Aligned_cols=39 Identities=10% Similarity=-0.012 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCCeeeEEEEccCCCCCCCCCcEEEEEEEeCC
Q 021167 65 AKMIEILANSDYLTQEFILSPLQFGVPYSRPRYFCLAKRKP 105 (316)
Q Consensus 65 ~~i~~~l~~~GY~v~~~vlna~~yGvPQ~R~R~~iva~r~~ 105 (316)
+.|.++|++.||.+. .+.|... +.-....++|.|-....
T Consensus 2 ~~I~~~L~~~G~~v~-~i~~~~~-~~~k~pl~mf~veL~p~ 40 (68)
T PF07530_consen 2 EEIKEELKDQGHPVR-NIHNMHS-RNTKKPLNMFFVELEPK 40 (68)
T ss_pred HHHHHHHHHcCCceE-EEEcccc-CCCCCCceEEEEeeccC
Confidence 578999999999986 4444422 22222236776665443
No 23
>COG0391 Uncharacterized conserved protein [Function unknown]
Probab=22.88 E-value=2.9e+02 Score=25.51 Aligned_cols=84 Identities=17% Similarity=0.104 Sum_probs=53.7
Q ss_pred cccEEEeCCCCcHHhhccCCCCCCCcchhhHHHHHHHhhhhcCCCcEEEEcchhhhcC----chHHHHHHHHHHc-CCCe
Q 021167 3 GAHAWLLSPPCQPYTRQGLQKQSSDARAFSFLKILELIPHTVKPPHMLFVENVVGFET----SDTHAKMIEILAN-SDYL 77 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~~~P~~~~~ENV~~~~~----~~~~~~i~~~l~~-~GY~ 77 (316)
++|+++-| |=..|+..+... |.-++.+.+.+. .-+++..+||-+-.. .-.++.-+..+.+ +|=.
T Consensus 189 ~AD~IviG-PgSl~TSIlP~L--------llp~I~eaLr~~--~ap~i~v~n~~~~~g~~t~~~~~~d~i~~i~~~~g~~ 257 (323)
T COG0391 189 EADLIVIG-PGSLFTSILPIL--------LLPGIAEALRET--VAPIVYVCNLMTQAGKETDGLSVEDHIAALAQHYGAF 257 (323)
T ss_pred hCCEEEEc-CCccHhhhchhh--------chhHHHHHHHhC--CCCEEEeccCCCCCCcccccccHHHHHHHHHHHhCcc
Confidence 67999999 668888888753 566777888777 667778999944322 2233333333332 3422
Q ss_pred -eeEEEEccCCCCCCCCCcEEE
Q 021167 78 -TQEFILSPLQFGVPYSRPRYF 98 (316)
Q Consensus 78 -v~~~vlna~~yGvPQ~R~R~~ 98 (316)
++..++|..+....... |+|
T Consensus 258 ~iD~vivd~~~~~~~~~~-~~~ 278 (323)
T COG0391 258 VIDAVIVDNDDVEDEDLI-RYV 278 (323)
T ss_pred cCcEEEECCCCccHHHHH-HHh
Confidence 78889999888443333 444
No 24
>PF05050 Methyltransf_21: Methyltransferase FkbM domain; InterPro: IPR007744 This entry contains proteins of unknown function.; PDB: 2PY6_A.
Probab=22.66 E-value=44 Score=26.53 Aligned_cols=44 Identities=16% Similarity=0.301 Sum_probs=11.7
Q ss_pred hHHHHHHHhhhhcCCCcEEEEcchhhh-cCchHHHHHHHHHHcCCCee
Q 021167 32 SFLKILELIPHTVKPPHMLFVENVVGF-ETSDTHAKMIEILANSDYLT 78 (316)
Q Consensus 32 L~~~~~~~i~~~~~~P~~~~~ENV~~~-~~~~~~~~i~~~l~~~GY~v 78 (316)
++....++++.. +|.++ +|--... .....+..+++.|++.||.+
T Consensus 123 vL~g~~~~l~~~--~~~~i-~E~~~~~~~~~~~~~~i~~~L~~~Gy~~ 167 (167)
T PF05050_consen 123 VLKGARELLKKC--RPKVI-VEIHHNHYGRQESFREILDFLRDHGYRL 167 (167)
T ss_dssp HHHTTHHHHHHH----EEE-EE--S-----------------------
T ss_pred HhhCCcccHhHc--CcEEE-EEEcCCccccccccccccccccccccCC
Confidence 344455667767 79988 9944332 12246788899999999974
No 25
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=22.62 E-value=1.6e+02 Score=25.91 Aligned_cols=39 Identities=18% Similarity=0.136 Sum_probs=31.4
Q ss_pred CCCcEEEEcchhhhcCchHHHHHHHHHHcCCCeeeEEEEccC
Q 021167 45 KPPHMLFVENVVGFETSDTHAKMIEILANSDYLTQEFILSPL 86 (316)
Q Consensus 45 ~~P~~~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~vlna~ 86 (316)
++|-+|.|. .-++...+..|+..|.+.||.|-..+-|..
T Consensus 182 KQpi~~~f~---t~m~~~~l~~iI~~l~~~g~~VvAivsD~g 220 (236)
T PF12017_consen 182 KQPIYFDFD---TSMDADILKNIIEKLHEIGYNVVAIVSDMG 220 (236)
T ss_pred CccEEEEec---CcCCHHHHHHHHHHHHHCCCEEEEEECCCC
Confidence 479999883 234567889999999999999988887764
No 26
>PRK00014 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=22.37 E-value=27 Score=30.44 Aligned_cols=27 Identities=26% Similarity=0.181 Sum_probs=24.3
Q ss_pred CCcccCCHHHHHHhCCCCCCcccCCCC
Q 021167 260 QHLRYFTPREVANLHSFPGDFQFPHHL 286 (316)
Q Consensus 260 ~~~R~LT~rE~arLqgFPd~f~f~~~~ 286 (316)
..+|..|+|+++--.++|+||.-||.+
T Consensus 116 A~DRa~Tir~La~~~~~~~DF~rPGHV 142 (230)
T PRK00014 116 AVDRVTTIRAAIAPGARSGDVVSPGHV 142 (230)
T ss_pred HHHHHHHHHHHhCCCCCHHHcCCCCcc
Confidence 477999999999999999999999853
No 27
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=22.20 E-value=60 Score=19.72 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=13.3
Q ss_pred cCCHHHHHHhCCCCCC
Q 021167 264 YFTPREVANLHSFPGD 279 (316)
Q Consensus 264 ~LT~rE~arLqgFPd~ 279 (316)
+||+.|+|.+.|.+..
T Consensus 1 ~lt~~e~a~~lgis~~ 16 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKD 16 (49)
T ss_pred CCCHHHHHHHHCCCHH
Confidence 4799999999988753
No 28
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=21.57 E-value=92 Score=22.03 Aligned_cols=29 Identities=0% Similarity=0.064 Sum_probs=23.4
Q ss_pred EEEcchhhhcCchHHHHHHHHHHcCCCeeeEEEE
Q 021167 50 LFVENVVGFETSDTHAKMIEILANSDYLTQEFIL 83 (316)
Q Consensus 50 ~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~vl 83 (316)
++++|-+|.+ ..+...|..-||.+..--+
T Consensus 8 i~v~n~pGVL-----~Ri~~lf~rRGfnI~sl~v 36 (76)
T PRK11152 8 IKARFRPEVL-----ERVLRVVRHRGFQVCSMNM 36 (76)
T ss_pred EEEECCccHH-----HHHHHHHhcCCeeeeeEEe
Confidence 5789999985 7899999999999865433
No 29
>PF12728 HTH_17: Helix-turn-helix domain
Probab=20.82 E-value=64 Score=20.27 Aligned_cols=15 Identities=33% Similarity=0.514 Sum_probs=12.8
Q ss_pred cCCHHHHHHhCCCCC
Q 021167 264 YFTPREVANLHSFPG 278 (316)
Q Consensus 264 ~LT~rE~arLqgFPd 278 (316)
+||+.|+|.+.|.+.
T Consensus 1 ~lt~~e~a~~l~is~ 15 (51)
T PF12728_consen 1 YLTVKEAAELLGISR 15 (51)
T ss_pred CCCHHHHHHHHCcCH
Confidence 489999999998875
No 30
>PF08624 CRC_subunit: Chromatin remodelling complex Rsc7/Swp82 subunit; InterPro: IPR013933 This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast) P32832 from SWISSPROT and its paralogue P43554 from SWISSPROT have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively [].
Probab=20.55 E-value=14 Score=29.48 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=17.1
Q ss_pred cCCHHHHHHhCCCCCCcccCC
Q 021167 264 YFTPREVANLHSFPGDFQFPH 284 (316)
Q Consensus 264 ~LT~rE~arLqgFPd~f~f~~ 284 (316)
+.=..|+||+.||-|+|.|..
T Consensus 48 ymL~td~ar~lg~rDs~~ff~ 68 (139)
T PF08624_consen 48 YMLSTDPARCLGFRDSYLFFR 68 (139)
T ss_pred EEEeHHHHHHhccccHHHHHH
Confidence 344789999999999998764
No 31
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=20.33 E-value=2.5e+02 Score=17.98 Aligned_cols=33 Identities=24% Similarity=0.238 Sum_probs=25.6
Q ss_pred EEEcchhhhcCchHHHHHHHHHHcCCCeeeEEEEccCC
Q 021167 50 LFVENVVGFETSDTHAKMIEILANSDYLTQEFILSPLQ 87 (316)
Q Consensus 50 ~~~ENV~~~~~~~~~~~i~~~l~~~GY~v~~~vlna~~ 87 (316)
+.++|.||++ ..+.+.|.+.|+.+.........
T Consensus 5 v~~~drpG~l-----~~v~~~la~~~inI~~~~~~~~~ 37 (66)
T PF01842_consen 5 VIVPDRPGIL-----ADVTEILADHGINIDSISQSSDK 37 (66)
T ss_dssp EEEETSTTHH-----HHHHHHHHHTTEEEEEEEEEEES
T ss_pred EEcCCCCCHH-----HHHHHHHHHcCCCHHHeEEEecC
Confidence 5788999984 78899999999988766555443
No 32
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=20.18 E-value=3.2e+02 Score=22.18 Aligned_cols=79 Identities=14% Similarity=0.275 Sum_probs=40.8
Q ss_pred cccEEEeCCCCcHHhhccCCC--------CCCCcchhhHHHHHHHhhhhcCCC--cEEEEcchhhhcCchHHHHHHHHHH
Q 021167 3 GAHAWLLSPPCQPYTRQGLQK--------QSSDARAFSFLKILELIPHTVKPP--HMLFVENVVGFETSDTHAKMIEILA 72 (316)
Q Consensus 3 ~~Dil~ggpPCq~fS~ag~~~--------~~~d~r~~L~~~~~~~i~~~~~~P--~~~~~ENV~~~~~~~~~~~i~~~l~ 72 (316)
..|+++.+||+...+..-... +..+.+ .++..+++.+..+. +| .+++.++-.. ....+++.|+
T Consensus 82 ~fD~Vi~n~p~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~L-k~gG~~~~~~~~~~-----~~~~~~~~l~ 154 (179)
T TIGR00537 82 KFDVILFNPPYLPLEDDLRRGDWLDVAIDGGKDGR-KVIDRFLDELPEIL-KEGGRVQLIQSSLN-----GEPDTFDKLD 154 (179)
T ss_pred cccEEEECCCCCCCcchhcccchhhhhhhcCCchH-HHHHHHHHhHHHhh-CCCCEEEEEEeccC-----ChHHHHHHHH
Confidence 369999999996443211110 011111 23555665443332 55 4444442211 1467788889
Q ss_pred cCCCeeeEEEEccCCCCCCC
Q 021167 73 NSDYLTQEFILSPLQFGVPY 92 (316)
Q Consensus 73 ~~GY~v~~~vlna~~yGvPQ 92 (316)
+.||.+. + .+.||.|-
T Consensus 155 ~~gf~~~--~--~~~~~~~~ 170 (179)
T TIGR00537 155 ERGFRYE--I--VAERGLFF 170 (179)
T ss_pred hCCCeEE--E--EEEeecCc
Confidence 9998653 2 23555553
Done!