Query 022801
Match_columns 292
No_of_seqs 75 out of 77
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 06:14:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022801.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022801hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06217 GAGA_bind: GAGA bindi 100.0 7E-123 2E-127 852.5 18.5 270 1-292 1-301 (301)
2 PF06217 GAGA_bind: GAGA bindi 78.2 6.5 0.00014 38.0 6.5 110 57-172 40-172 (301)
3 cd00374 RNase_T2 Ribonuclease 70.9 4.5 9.8E-05 33.9 3.1 30 256-285 60-92 (195)
4 cd06434 GT2_HAS Hyaluronan syn 41.8 7.3 0.00016 31.8 -0.4 16 208-223 220-235 (235)
5 KOG1642 Ribonuclease, T2 famil 39.6 27 0.00059 33.5 2.9 48 218-285 74-128 (263)
6 PF14799 FAM195: FAM195 family 34.8 16 0.00035 29.8 0.5 10 273-282 82-91 (99)
7 PLN02543 pfkB-type carbohydrat 33.3 2.2E+02 0.0048 28.9 8.3 25 250-274 194-219 (496)
8 PF08212 Lipocalin_2: Lipocali 32.5 34 0.00074 27.8 2.1 31 242-272 105-137 (143)
9 PF07120 DUF1376: Protein of u 30.7 29 0.00062 26.9 1.3 35 234-271 38-72 (88)
10 PF14359 DUF4406: Domain of un 30.3 32 0.00069 27.3 1.5 23 254-276 16-38 (92)
11 PF11752 DUF3309: Protein of u 28.0 16 0.00034 27.4 -0.5 15 9-26 23-37 (49)
12 PF00445 Ribonuclease_T2: Ribo 27.9 30 0.00065 29.2 1.1 28 258-285 65-95 (189)
13 COG0701 Predicted permeases [G 25.4 19 0.0004 34.7 -0.7 15 196-210 67-81 (317)
14 smart00419 HTH_CRP helix_turn_ 24.6 79 0.0017 20.2 2.4 18 251-268 20-37 (48)
15 PF03551 PadR: Transcriptional 23.3 89 0.0019 22.8 2.7 32 246-284 23-55 (75)
16 cd07377 WHTH_GntR Winged helix 23.0 88 0.0019 21.0 2.5 19 250-268 36-54 (66)
17 cd02116 ACT ACT domains are co 22.9 65 0.0014 18.8 1.6 19 253-271 9-27 (60)
18 COG3719 Rna Ribonuclease I [Tr 22.7 36 0.00078 32.4 0.7 58 229-286 87-146 (249)
19 PF12802 MarR_2: MarR family; 22.2 89 0.0019 21.3 2.4 18 251-268 33-50 (62)
20 COG3695 Predicted methylated D 21.9 32 0.0007 29.0 0.2 25 255-279 73-99 (103)
21 PF13342 Toprim_Crpt: C-termin 21.2 65 0.0014 24.3 1.6 19 244-262 9-27 (62)
22 PF03773 DUF318: Predicted per 21.1 23 0.00049 32.6 -0.9 14 197-210 58-71 (307)
23 PF01842 ACT: ACT domain; Int 20.7 60 0.0013 21.7 1.3 19 253-271 11-29 (66)
24 smart00345 HTH_GNTR helix_turn 20.6 1.1E+02 0.0023 20.1 2.5 19 250-268 31-49 (60)
No 1
>PF06217 GAGA_bind: GAGA binding protein-like family; InterPro: IPR010409 This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA []. It seems likely that the region which defines this family mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain.
Probab=100.00 E-value=7e-123 Score=852.46 Aligned_cols=270 Identities=57% Similarity=0.990 Sum_probs=234.2
Q ss_pred CCcCcCCCcCcccccCC--CCCCccccccCCCCCCCCCCCCCCCCCCCCc-eecCCCCCCCCCcCCCCCCccccc-cccc
Q 022801 1 MDDDALNMRNWGYYEPS--FKGHLGLQLMSTMPMVDRDTKPFLPGRDPNI-MIGANGAFHPRDCVVSEASIPMNY-MRDS 76 (292)
Q Consensus 1 MDD~~lniRNWGyyEp~--~kg~LGLQLMSs~p~~drdtKpfl~~r~~~l-m~~~ng~~h~Rd~gv~e~~~pM~y-~rd~ 76 (292)
||||+...||||||||. +|+||||||||+ |+|||+++ ++.++ |.+.+++||+|| |+| +||+
T Consensus 1 MDddg~~~R~wg~ye~~~s~K~hLGLqlMs~--maERDaai----~er~~al~ekk~a~aeRD---------ma~~qRD~ 65 (301)
T PF06217_consen 1 MDDDGSLERNWGYYEPQNSMKGHLGLQLMSI--MAERDAAI----RERNLALSEKKAAFAERD---------MAYLQRDA 65 (301)
T ss_pred CCCccccccCcccccccccccccccceeecc--ccccCccc----ccccchhccccccccchh---------hhhhhhhh
Confidence 89654444999999997 799999999999 56999999 56665 789999999997 999 8899
Q ss_pred cccc-------cc-cccccCCCCCC--------CCcccCCCcccccccc-----CCCCCCCccccCCCCCCCCCCCCCcc
Q 022801 77 WISQ-------RD-KFLNMLPSNPT--------FGVLPETSGAHSLQML-----QPPPNMSRDDRLAPDRVAPDRIVPKV 135 (292)
Q Consensus 77 Wi~q-------re-Kfln~~p~n~~--------y~~~pets~a~~mQm~-----q~~p~~~k~e~~~~~~~~p~~~p~~~ 135 (292)
||+| || +|+++++.|++ |+++|+|+.+|++|++ ++++....++.+ ....++.
T Consensus 66 aiaern~ai~ERd~a~a~l~~~~~~~n~~~p~~~~~~~~tk~~~~~q~~~~~~~~~~~~~~~~~~~-------~~~~~i~ 138 (301)
T PF06217_consen 66 AIAERNNAIMERDNAIAALQPRNNNGNHHCPPGCGILPGTKHIHHMQQHHHPQLQPPPYSTREMHN-------IDAPPIS 138 (301)
T ss_pred hhccchhhcccchhhhhhccccCCCccccCCCCCcccCCCccCCCcccccccccCCCCCCcccccc-------ccccccc
Confidence 9999 45 99999998774 8999999999999994 332333333321 0122333
Q ss_pred cCCccccCCCCccccCCCCCCCCCCCCCCCC----CCCCCCCcc--ccccCcccccceeccceecccCCCCccceeecCC
Q 022801 136 EEPVVKTEGAPVKKRQGGGASKMPKAKKPKK----PKDNNGTAV--QRVKPAKKSMDVVINGIDMDISGIPIPVCSCTGA 209 (292)
Q Consensus 136 e~~~v~~~~~~~KKr~~~~~~k~pKaKKpKK----Pkd~~~~~~--~R~k~~~k~~~~~in~i~~d~s~~P~PvCsCTG~ 209 (292)
++..+.+..++.||+++++++|++|+||+|| ++++.+.++ +|+|.+||++||+||||+||+|+||||||||||+
T Consensus 139 ~~~~~~~~~~~~k~~~~~~~~k~~k~~k~kk~~~~~~~~~~~~~~~~~~k~~~k~~dl~in~i~~D~s~mP~PvCSCTG~ 218 (301)
T PF06217_consen 139 TAPPESKKSKPPKKRKRPKSPKSPKPKKPKKKPSVPNRNVNPPGSDQRSKPEKKNQDLVINGINFDESTMPIPVCSCTGV 218 (301)
T ss_pred cCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhhccccccccccccccccccccccceeeccCCCCCcccccCCC
Confidence 4455556667888999999999999999998 444554443 8999999999999999999999999999999999
Q ss_pred CcceeeccCCcccccccccccccccCCCCCCCCCccccccccChHHHHHHHHHHHhcccCCCCCccchhhhhhcCCccee
Q 022801 210 PQQCYRWGCGGWQSACCTTNVSMYPLPMSTKRRGARIAGRKMSQGAFKKVLEKLAAEGYNFANPIDLRTHWARHGTNKFV 289 (292)
Q Consensus 210 ~qqCYrWG~GGWQSaCCTt~iS~yPLP~~~~rrgaRi~GRKMS~gaf~klL~rLa~eg~~ls~piDLk~~WAkHGTNk~v 289 (292)
|||||||||||||||||||+||||||||+||||||||||||||+|||+|||+|||+||||||+|||||+|||||||||||
T Consensus 219 pqqCYrWG~GGWQSaCCTT~iSmYPLPm~~nkRgaRi~GRKMS~gAF~KlL~rLAaEGydls~PiDLK~hWAKHGTNryv 298 (301)
T PF06217_consen 219 PQQCYRWGNGGWQSACCTTTISMYPLPMSPNKRGARIGGRKMSGGAFKKLLERLAAEGYDLSNPIDLKDHWAKHGTNRYV 298 (301)
T ss_pred CccccccCCCccccccccccccccccCCCCCCCccccccccccHHHHHHHHHHHHhcccccCCccchHHHHHhcCCcceE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeC
Q 022801 290 TIR 292 (292)
Q Consensus 290 tik 292 (292)
|||
T Consensus 299 TIk 301 (301)
T PF06217_consen 299 TIK 301 (301)
T ss_pred ecC
Confidence 998
No 2
>PF06217 GAGA_bind: GAGA binding protein-like family; InterPro: IPR010409 This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA []. It seems likely that the region which defines this family mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain.
Probab=78.17 E-value=6.5 Score=38.00 Aligned_cols=110 Identities=23% Similarity=0.323 Sum_probs=55.9
Q ss_pred CCCCcCCCCCCcccccccccccccccccccc-----CCCCCCC-Cccc-CC-------------CccccccccCCCCCCC
Q 022801 57 HPRDCVVSEASIPMNYMRDSWISQRDKFLNM-----LPSNPTF-GVLP-ET-------------SGAHSLQMLQPPPNMS 116 (292)
Q Consensus 57 h~Rd~gv~e~~~pM~y~rd~Wi~qreKfln~-----~p~n~~y-~~~p-et-------------s~a~~mQm~q~~p~~~ 116 (292)
+.|+-.++|.--.+ .-||.=|-|||..++- ++-...| .+++ |+ ++++++|++|+.+.+.
T Consensus 40 ~er~~al~ekk~a~-aeRDma~~qRD~aiaern~ai~ERd~a~a~l~~~~~~~n~~~p~~~~~~~~tk~~~~~q~~~~~~ 118 (301)
T PF06217_consen 40 RERNLALSEKKAAF-AERDMAYLQRDAAIAERNNAIMERDNAIAALQPRNNNGNHHCPPGCGILPGTKHIHHMQQHHHPQ 118 (301)
T ss_pred ccccchhccccccc-cchhhhhhhhhhhhccchhhcccchhhhhhccccCCCccccCCCCCcccCCCccCCCcccccccc
Confidence 44554455542222 3467666688866654 2222223 3443 22 3466777777744432
Q ss_pred ccccCCCCCCCCCCCCCcccCCcccc---CCCCccccCCCCCCCCCCCCCCCCCCCCCC
Q 022801 117 RDDRLAPDRVAPDRIVPKVEEPVVKT---EGAPVKKRQGGGASKMPKAKKPKKPKDNNG 172 (292)
Q Consensus 117 k~e~~~~~~~~p~~~p~~~e~~~v~~---~~~~~KKr~~~~~~k~pKaKKpKKPkd~~~ 172 (292)
..+.. .+.......++..++. +....|+.++...++.||.+|+||+|..+.
T Consensus 119 ~~~~~-----~~~~~~~~~~~~~i~~~~~~~~~~~~~k~~~~~~~~k~~k~~k~kk~~~ 172 (301)
T PF06217_consen 119 LQPPP-----YSTREMHNIDAPPISTAPPESKKSKPPKKRKRPKSPKSPKPKKPKKKPS 172 (301)
T ss_pred cCCCC-----CCccccccccccccccCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 22210 0011112222223222 234455566667889999999999888765
No 3
>cd00374 RNase_T2 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen.
Probab=70.95 E-value=4.5 Score=33.87 Aligned_cols=30 Identities=23% Similarity=0.414 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcccCCCCC--ccchhh-hhhcCC
Q 022801 256 FKKVLEKLAAEGYNFANP--IDLRTH-WARHGT 285 (292)
Q Consensus 256 f~klL~rLa~eg~~ls~p--iDLk~~-WAkHGT 285 (292)
...|+..|...=-||..+ -+|-.| |.||||
T Consensus 60 ~~~l~~~l~~~w~~~~~~~~~~fw~hEW~KHGT 92 (195)
T cd00374 60 DSDLLDELNKYWPDLMPGKDSSFWKHEWNKHGT 92 (195)
T ss_pred cHHHHHHHHhhCcccCCCCCchHHHHHHhcCce
Confidence 346777787777777766 556544 899998
No 4
>cd06434 GT2_HAS Hyaluronan synthases catalyze polymerization of hyaluronan. Hyaluronan synthases (HASs) are bi-functional glycosyltransferases that catalyze polymerization of hyaluronan. HASs transfer both GlcUA and GlcNAc in beta-(1,3) and beta-(1,4) linkages, respectively to the hyaluronan chain using UDP-GlcNAc and UDP-GlcUA as substrates. HA is made as a free glycan, not attached to a protein or lipid. HASs do not need a primer for HA synthesis; they initiate HA biosynthesis de novo with only UDP-GlcNAc, UDP-GlcUA, and Mg2+. Hyaluronan (HA) is a linear heteropolysaccharide composed of (1-3)-linked beta-D-GlcUA-beta-D-GlcNAc disaccharide repeats. It can be found in vertebrates and a few microbes and is typically on the cell surface or in the extracellular space, but is also found inside mammalian cells. Hyaluronan has several physiochemical and biological functions such as space filling, lubrication, and providing a hydrated matrix through which cells can migrate.
Probab=41.80 E-value=7.3 Score=31.83 Aligned_cols=16 Identities=31% Similarity=0.665 Sum_probs=13.5
Q ss_pred CCCcceeeccCCcccc
Q 022801 208 GAPQQCYRWGCGGWQS 223 (292)
Q Consensus 208 G~~qqCYrWG~GGWQS 223 (292)
...+|++||..|+|+|
T Consensus 220 ~~~~q~~Rw~~~~~~~ 235 (235)
T cd06434 220 KFLKQQLRWSRSNWRS 235 (235)
T ss_pred HHHHHhhhhhhcccCC
Confidence 3457899999999987
No 5
>KOG1642 consensus Ribonuclease, T2 family [RNA processing and modification]
Probab=39.58 E-value=27 Score=33.52 Aligned_cols=48 Identities=21% Similarity=0.550 Sum_probs=35.1
Q ss_pred CCcccccccccccccccCCCCCCCCCccccccccChHHHHHHHHHHHhcccCCCCCcc-------chhhhhhcCC
Q 022801 218 CGGWQSACCTTNVSMYPLPMSTKRRGARIAGRKMSQGAFKKVLEKLAAEGYNFANPID-------LRTHWARHGT 285 (292)
Q Consensus 218 ~GGWQSaCCTt~iS~yPLP~~~~rrgaRi~GRKMS~gaf~klL~rLa~eg~~ls~piD-------Lk~~WAkHGT 285 (292)
.|+|++-|=-+ +| .--..++-|+.+|..|==||+-|-- -|--|.||||
T Consensus 74 ~G~~P~~Cn~s---------------~~-----Fd~~~isdl~~~L~~~Wp~L~~~s~n~g~~~fW~HEweKHGT 128 (263)
T KOG1642|consen 74 HGSWPQNCNRS---------------SQ-----FDDSKISDLEDSLEKEWPDLYCPSPNGGHESFWKHEWEKHGT 128 (263)
T ss_pred CCCCcccCCCc---------------cc-----CChHHccchhhhHHhhccccccCCCCCccchhhhhhhhccCc
Confidence 68999877433 22 3345577899999999889988874 2445899999
No 6
>PF14799 FAM195: FAM195 family
Probab=34.76 E-value=16 Score=29.82 Aligned_cols=10 Identities=40% Similarity=1.099 Sum_probs=5.3
Q ss_pred Cccchhhhhh
Q 022801 273 PIDLRTHWAR 282 (292)
Q Consensus 273 piDLk~~WAk 282 (292)
|+||-++|+|
T Consensus 82 PfDLE~wW~~ 91 (99)
T PF14799_consen 82 PFDLEEWWGQ 91 (99)
T ss_pred ccCHHHHHHH
Confidence 5555555554
No 7
>PLN02543 pfkB-type carbohydrate kinase family protein
Probab=33.33 E-value=2.2e+02 Score=28.89 Aligned_cols=25 Identities=12% Similarity=0.162 Sum_probs=18.5
Q ss_pred ccChHHH-HHHHHHHHhcccCCCCCc
Q 022801 250 KMSQGAF-KKVLEKLAAEGYNFANPI 274 (292)
Q Consensus 250 KMS~gaf-~klL~rLa~eg~~ls~pi 274 (292)
+.....| ..|++.|..+|.|.+.-+
T Consensus 194 ~VGdD~fG~~l~~~L~~~GVDts~v~ 219 (496)
T PLN02543 194 KVGDDDFGEELVLMMNKERVQTRAVK 219 (496)
T ss_pred EeCCCHHHHHHHHHHHHcCCcccceE
Confidence 4555666 456789999999987644
No 8
>PF08212 Lipocalin_2: Lipocalin-like domain; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 3EBW_B 1QWD_A 2ACO_A 3MBT_A.
Probab=32.53 E-value=34 Score=27.83 Aligned_cols=31 Identities=19% Similarity=0.500 Sum_probs=20.8
Q ss_pred CCcccccc--ccChHHHHHHHHHHHhcccCCCC
Q 022801 242 RGARIAGR--KMSQGAFKKVLEKLAAEGYNFAN 272 (292)
Q Consensus 242 rgaRi~GR--KMS~gaf~klL~rLa~eg~~ls~ 272 (292)
...-|=.| .||...+.++|+++++.|||.+.
T Consensus 105 ~~~WILsR~p~~~~~~~~~~~~~~~~~G~d~~~ 137 (143)
T PF08212_consen 105 EYLWILSRTPQLSEETYAEILDRAKQQGYDVSK 137 (143)
T ss_dssp CEEEEEESSSS--HHHHHHHHHHHHHTT--GGG
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHHHHcCCCHHH
Confidence 34445444 47889999999999999999874
No 9
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=30.72 E-value=29 Score=26.88 Aligned_cols=35 Identities=37% Similarity=0.563 Sum_probs=28.2
Q ss_pred cCCCCCCCCCccccccccChHHHHHHHHHHHhcccCCC
Q 022801 234 PLPMSTKRRGARIAGRKMSQGAFKKVLEKLAAEGYNFA 271 (292)
Q Consensus 234 PLP~~~~rrgaRi~GRKMS~gaf~klL~rLa~eg~~ls 271 (292)
|||- -.++=||++| +|...|.++++-|.++++.+.
T Consensus 38 plp~-d~~~Lar~~~--~s~~~~~~a~~~ll~~f~~~~ 72 (88)
T PF07120_consen 38 PLPD-DDKRLARICG--CSTKEWRKALDFLLREFFRLE 72 (88)
T ss_pred CCCC-CHHHHHHHHC--cCHHHHHHHHHHHHHhCCCCC
Confidence 7884 4455789987 799999999999999998443
No 10
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=30.29 E-value=32 Score=27.30 Aligned_cols=23 Identities=39% Similarity=0.736 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhcccCCCCCccc
Q 022801 254 GAFKKVLEKLAAEGYNFANPIDL 276 (292)
Q Consensus 254 gaf~klL~rLa~eg~~ls~piDL 276 (292)
.+|.+.-.+|.++||..-||+.+
T Consensus 16 ~~f~~~a~~L~~~G~~vvnPa~~ 38 (92)
T PF14359_consen 16 PAFNAAAKRLRAKGYEVVNPAEL 38 (92)
T ss_pred HHHHHHHHHHHHCCCEEeCchhh
Confidence 68999999999999999999998
No 11
>PF11752 DUF3309: Protein of unknown function (DUF3309); InterPro: IPR021738 This family is conserved in bacteria but its function is not known.
Probab=28.05 E-value=16 Score=27.36 Aligned_cols=15 Identities=60% Similarity=1.143 Sum_probs=11.2
Q ss_pred cCcccccCCCCCCccccc
Q 022801 9 RNWGYYEPSFKGHLGLQL 26 (292)
Q Consensus 9 RNWGyyEp~~kg~LGLQL 26 (292)
|+||||-. |-||+-|
T Consensus 23 r~wGy~Ps---G~lG~il 37 (49)
T PF11752_consen 23 RGWGYGPS---GGLGLIL 37 (49)
T ss_pred CCCCcCCc---cHHHHHH
Confidence 89999964 7777654
No 12
>PF00445 Ribonuclease_T2: Ribonuclease T2 family; InterPro: IPR001568 The fungal ribonucleases T2 from Aspergillus oryzae, M from Aspergillus saitoi and Rh from Rhizopus niveus are structurally and functionally related 30 Kd glycoproteins [] that cleave the 3'-5' internucleotide linkage of RNA via a nucleotide 2',3'-cyclic phosphate intermediate (3.1.27.1 from EC). Two histidines residues have been shown [, ] to be involved in the catalytic mechanism of RNase T2 and Rh. These residues and the region around them are highly conserved in a number of other RNAses that have been found to be evolutionary related to these fungal enzymes.; GO: 0003723 RNA binding, 0033897 ribonuclease T2 activity; PDB: 1IOO_A 3D3Z_A 1UCG_B 1UCC_A 1J1F_A 1V9H_A 1UCD_A 1J1G_A 1UCA_A 1BK7_A ....
Probab=27.91 E-value=30 Score=29.19 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=19.5
Q ss_pred HHHHHHHhcccCCCCCc--cchhh-hhhcCC
Q 022801 258 KVLEKLAAEGYNFANPI--DLRTH-WARHGT 285 (292)
Q Consensus 258 klL~rLa~eg~~ls~pi--DLk~~-WAkHGT 285 (292)
.++.+|...=-+|..+- +|-.| |.||||
T Consensus 65 ~~~~~L~~~Wp~~~~~~~~~fw~hEW~KHGt 95 (189)
T PF00445_consen 65 ELKSELDKYWPDLKNSNSESFWKHEWEKHGT 95 (189)
T ss_dssp GGHHHHHHHSTBSSSSHHHHHHHHHHHHTGG
T ss_pred HHhhhhhhhhhhhccchhhhhHHhcceeeeE
Confidence 56667777666776664 66544 999998
No 13
>COG0701 Predicted permeases [General function prediction only]
Probab=25.36 E-value=19 Score=34.71 Aligned_cols=15 Identities=47% Similarity=1.196 Sum_probs=12.0
Q ss_pred cCCCCccceeecCCC
Q 022801 196 ISGIPIPVCSCTGAP 210 (292)
Q Consensus 196 ~s~~P~PvCsCTG~~ 210 (292)
..+++-|+|||+-+|
T Consensus 67 l~G~~~p~CsC~~vP 81 (317)
T COG0701 67 LLGLLLPVCSCGAVP 81 (317)
T ss_pred HHcccchhhhcccHH
Confidence 458889999998754
No 14
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=24.57 E-value=79 Score=20.23 Aligned_cols=18 Identities=22% Similarity=0.560 Sum_probs=16.5
Q ss_pred cChHHHHHHHHHHHhccc
Q 022801 251 MSQGAFKKVLEKLAAEGY 268 (292)
Q Consensus 251 MS~gaf~klL~rLa~eg~ 268 (292)
+|.....+.|.+|.++|+
T Consensus 20 ~s~~tv~~~l~~L~~~g~ 37 (48)
T smart00419 20 LTRETVSRTLKRLEKEGL 37 (48)
T ss_pred CCHHHHHHHHHHHHHCCC
Confidence 588899999999999997
No 15
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=23.31 E-value=89 Score=22.78 Aligned_cols=32 Identities=31% Similarity=0.716 Sum_probs=24.9
Q ss_pred ccc-cccChHHHHHHHHHHHhcccCCCCCccchhhhhhcC
Q 022801 246 IAG-RKMSQGAFKKVLEKLAAEGYNFANPIDLRTHWARHG 284 (292)
Q Consensus 246 i~G-RKMS~gaf~klL~rLa~eg~~ls~piDLk~~WAkHG 284 (292)
+.| -+.|.|.+..+|.+|..+|+ +...|...+
T Consensus 23 ~~~~~~i~~g~lY~~L~~Le~~gl-------i~~~~~~~~ 55 (75)
T PF03551_consen 23 TGGFWKISPGSLYPALKRLEEEGL-------IESRWEEEG 55 (75)
T ss_dssp STTTEETTHHHHHHHHHHHHHTTS-------EEEEEEEET
T ss_pred hCCCcccChhHHHHHHHHHHhCCC-------EEEeeeccC
Confidence 344 68899999999999999997 455566543
No 16
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=22.98 E-value=88 Score=20.96 Aligned_cols=19 Identities=32% Similarity=0.527 Sum_probs=17.1
Q ss_pred ccChHHHHHHHHHHHhccc
Q 022801 250 KMSQGAFKKVLEKLAAEGY 268 (292)
Q Consensus 250 KMS~gaf~klL~rLa~eg~ 268 (292)
.+|-.+..++|.+|+.+|+
T Consensus 36 ~is~~~v~~~l~~L~~~G~ 54 (66)
T cd07377 36 GVSRTTVREALRELEAEGL 54 (66)
T ss_pred CCCHHHHHHHHHHHHHCCC
Confidence 4678899999999999998
No 17
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=22.92 E-value=65 Score=18.85 Aligned_cols=19 Identities=42% Similarity=0.590 Sum_probs=16.6
Q ss_pred hHHHHHHHHHHHhcccCCC
Q 022801 253 QGAFKKVLEKLAAEGYNFA 271 (292)
Q Consensus 253 ~gaf~klL~rLa~eg~~ls 271 (292)
.|.|.++++-|+.+|.++.
T Consensus 9 ~~~l~~i~~~l~~~~~~i~ 27 (60)
T cd02116 9 PGLLAKVLSVLAEAGINIT 27 (60)
T ss_pred CchHHHHHHHHHHCCCcEE
Confidence 4789999999999998864
No 18
>COG3719 Rna Ribonuclease I [Translation, ribosomal structure and biogenesis]
Probab=22.69 E-value=36 Score=32.44 Aligned_cols=58 Identities=22% Similarity=0.343 Sum_probs=26.5
Q ss_pred ccccccC-CCCCCCCCccccccccChHHHHHHHHHHHhcccCCCCCccc-hhhhhhcCCc
Q 022801 229 NVSMYPL-PMSTKRRGARIAGRKMSQGAFKKVLEKLAAEGYNFANPIDL-RTHWARHGTN 286 (292)
Q Consensus 229 ~iS~yPL-P~~~~rrgaRi~GRKMS~gaf~klL~rLa~eg~~ls~piDL-k~~WAkHGTN 286 (292)
...++=| |++++.|++|.-=|-+-+.--..|=+.++++=.++.--.-| +--|+||||=
T Consensus 87 gftVHGLWPqn~~~~~~~~~pr~cr~~~~~~lP~v~~~~l~~vmPg~~L~~heW~KHGtC 146 (249)
T COG3719 87 GFTVHGLWPQNENGRAVRDYPRFCRGRPWPRLPEVIASQLLDVMPGAGLERHEWRKHGTC 146 (249)
T ss_pred ceEEeccCCCCCCCcccccChhhhcCCCcccCCHHHHHHHhhcCCchhhhhhhHHhcCcc
Confidence 3455554 77777766663333222212222222222211112111113 4559999994
No 19
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=22.23 E-value=89 Score=21.26 Aligned_cols=18 Identities=17% Similarity=0.562 Sum_probs=15.6
Q ss_pred cChHHHHHHHHHHHhccc
Q 022801 251 MSQGAFKKVLEKLAAEGY 268 (292)
Q Consensus 251 MS~gaf~klL~rLa~eg~ 268 (292)
+|.++.+++|.+|.+.||
T Consensus 33 ~~~~~vs~~v~~L~~~Gl 50 (62)
T PF12802_consen 33 ISKSTVSRIVKRLEKKGL 50 (62)
T ss_dssp S-HHHHHHHHHHHHHTTS
T ss_pred cCHHHHHHHHHHHHHCCC
Confidence 678899999999999997
No 20
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=21.88 E-value=32 Score=29.04 Aligned_cols=25 Identities=36% Similarity=0.450 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhcccCCCC--Cccchhh
Q 022801 255 AFKKVLEKLAAEGYNFAN--PIDLRTH 279 (292)
Q Consensus 255 af~klL~rLa~eg~~ls~--piDLk~~ 279 (292)
.+..-.+.|-+||..|+. =|||++|
T Consensus 73 ~~~~Q~~lL~aEGv~~~~~g~i~L~~~ 99 (103)
T COG3695 73 DKQRQRELLLAEGVEFSDTGRIDLERY 99 (103)
T ss_pred cHHHHHHHHHHcCceeccCceeeHHHH
Confidence 577788999999999987 6889887
No 21
>PF13342 Toprim_Crpt: C-terminal repeat of topoisomerase
Probab=21.15 E-value=65 Score=24.25 Aligned_cols=19 Identities=42% Similarity=0.698 Sum_probs=16.3
Q ss_pred ccccccccChHHHHHHHHH
Q 022801 244 ARIAGRKMSQGAFKKVLEK 262 (292)
Q Consensus 244 aRi~GRKMS~gaf~klL~r 262 (292)
..|+||++|....++||++
T Consensus 9 k~i~gk~lt~~~~~~Ll~~ 27 (62)
T PF13342_consen 9 KTIAGKKLTDEEVKELLEK 27 (62)
T ss_pred cEEcCCCCCHHHHHHHHHc
Confidence 4599999999999998853
No 22
>PF03773 DUF318: Predicted permease; InterPro: IPR005524 This family of predicted integral membrane proteins.
Probab=21.15 E-value=23 Score=32.64 Aligned_cols=14 Identities=50% Similarity=1.130 Sum_probs=10.7
Q ss_pred CCCCccceeecCCC
Q 022801 197 SGIPIPVCSCTGAP 210 (292)
Q Consensus 197 s~~P~PvCsCTG~~ 210 (292)
.+++.|+|+|..+|
T Consensus 58 ~G~~~p~C~c~~~P 71 (307)
T PF03773_consen 58 LGALLPVCSCGAVP 71 (307)
T ss_pred HHhccCCCcccHHH
Confidence 47888899887654
No 23
>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=20.70 E-value=60 Score=21.71 Aligned_cols=19 Identities=37% Similarity=0.496 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHHhcccCCC
Q 022801 253 QGAFKKVLEKLAAEGYNFA 271 (292)
Q Consensus 253 ~gaf~klL~rLa~eg~~ls 271 (292)
-|++.++++-|+..|+|+.
T Consensus 11 pG~l~~v~~~la~~~inI~ 29 (66)
T PF01842_consen 11 PGILADVTEILADHGINID 29 (66)
T ss_dssp TTHHHHHHHHHHHTTEEEE
T ss_pred CCHHHHHHHHHHHcCCCHH
Confidence 4789999999999999875
No 24
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.62 E-value=1.1e+02 Score=20.14 Aligned_cols=19 Identities=32% Similarity=0.550 Sum_probs=16.9
Q ss_pred ccChHHHHHHHHHHHhccc
Q 022801 250 KMSQGAFKKVLEKLAAEGY 268 (292)
Q Consensus 250 KMS~gaf~klL~rLa~eg~ 268 (292)
.+|...-.+.|.+|..+|+
T Consensus 31 ~vs~~tv~~~l~~L~~~g~ 49 (60)
T smart00345 31 GVSRTTVREALSRLEAEGL 49 (60)
T ss_pred CCCHHHHHHHHHHHHHCCC
Confidence 4688899999999999997
Done!