Query 029063
Match_columns 199
No_of_seqs 174 out of 289
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:53:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029063.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029063hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2567 Uncharacterized conser 100.0 1.6E-33 3.6E-38 232.3 7.7 92 1-92 53-144 (179)
2 PRK04015 DNA/RNA-binding prote 99.2 2E-11 4.2E-16 92.9 6.4 55 1-63 37-91 (91)
3 COG1581 Ssh10b Archaeal DNA-bi 99.2 5.8E-11 1.2E-15 89.7 6.5 55 1-63 37-91 (91)
4 TIGR00285 DNA-binding protein 99.2 7.8E-11 1.7E-15 89.0 6.4 54 1-62 34-87 (87)
5 PF01918 Alba: Alba; InterPro 98.6 3.4E-08 7.3E-13 70.0 3.4 31 1-31 38-69 (70)
6 PF12328 Rpp20: Rpp20 subunit 97.6 0.00015 3.3E-09 59.2 5.7 57 1-58 69-143 (144)
7 KOG0921 Dosage compensation co 96.3 0.017 3.6E-07 59.6 8.7 9 145-153 1235-1243(1282)
8 KOG0921 Dosage compensation co 96.0 0.043 9.4E-07 56.7 9.5 21 144-164 1226-1247(1282)
9 KOG3973 Uncharacterized conser 90.1 2.7 6E-05 39.7 9.7 9 10-18 264-272 (465)
10 KOG3262 H/ACA small nucleolar 77.6 15 0.00032 32.0 7.9 10 53-62 103-112 (215)
11 PF05918 API5: Apoptosis inhib 70.4 1.4 3E-05 43.4 0.0 10 58-67 457-466 (556)
12 KOG2748 Uncharacterized conser 55.2 7.2 0.00016 36.6 1.7 39 8-46 9-51 (369)
13 TIGR01543 proheadase_HK97 phag 47.8 89 0.0019 25.1 6.8 58 5-67 77-134 (145)
14 PF04586 Peptidase_U35: Caudov 46.6 1E+02 0.0023 24.7 7.1 59 6-68 89-147 (162)
15 KOG2945 Predicted RNA-binding 45.6 22 0.00048 33.5 3.3 14 55-68 288-301 (365)
16 PF03759 PRONE: PRONE (Plant-s 37.0 8.7 0.00019 36.0 -0.7 27 7-34 298-324 (365)
17 cd08982 GH43_3 Glycosyl hydrol 35.3 53 0.0012 29.1 4.0 38 50-87 248-288 (295)
18 PF05655 AvrD: Pseudomonas avi 35.2 65 0.0014 29.7 4.6 37 4-41 72-109 (311)
19 COG2065 PyrR Pyrimidine operon 26.9 1.4E+02 0.0031 25.6 4.9 72 4-77 11-86 (179)
20 KOG3428 Small nuclear ribonucl 26.3 38 0.00082 26.9 1.3 15 49-63 34-48 (109)
21 cd00133 PTS_IIB PTS_IIB: subun 24.7 1.5E+02 0.0033 19.6 4.0 31 4-34 9-39 (84)
No 1
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-33 Score=232.31 Aligned_cols=92 Identities=51% Similarity=0.770 Sum_probs=88.2
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCCCCCCCCCCCCCCCCcCC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDTSSTGYQPPLPADQ 80 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~elD~ss~GYQ~P~p~~~ 80 (199)
||+||+|+|+||||||||+++|||+|.|.+++|+|+|+|++|||++|+++||||+|+|+||++|||++++|||+|.|...
T Consensus 53 ~Grai~KTVscaEilKrRipgLhQ~t~l~~~sv~d~W~p~~eGl~pl~vtRhVp~l~IlLS~deL~~~~~GyQ~P~~~p~ 132 (179)
T KOG2567|consen 53 SGRAIVKTVSCAEILKRRIPGLHQVTRLRYTSVEDVWEPTEEGLEPLEVTRHVPMLHILLSLDELDPTSPGYQPPNPQPH 132 (179)
T ss_pred CCcceeeeeeHHHHHhhhCcchhhhceeeeeehhhcccccccCccceEEeeccceEEEEEecccCCCCCCCccCCCCCCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999888
Q ss_pred CCCCCccccCCC
Q 029063 81 VKPWNEFEDEGE 92 (199)
Q Consensus 81 vk~~~E~e~~~~ 92 (199)
.+.+...++++.
T Consensus 133 p~~~~~~p~~~~ 144 (179)
T KOG2567|consen 133 PRSQPRHPYSPR 144 (179)
T ss_pred CCCcccCCcccc
Confidence 888888877653
No 2
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.23 E-value=2e-11 Score=92.91 Aligned_cols=55 Identities=36% Similarity=0.431 Sum_probs=41.6
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKK 63 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~ 63 (199)
||+||+|||+||||||+||-.. .++..++|..+-...++| .+++||+|+|+|+++
T Consensus 37 ~G~aIskAV~vaEilk~r~~~~---v~v~~I~i~se~i~~~~g-----~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 37 RGRAISKAVDVAEIVRNRFLPD---VEIKEIKIGTEEVTSEDG-----RESNVSTIEIVLEKK 91 (91)
T ss_pred eccccchhhhHHHHHHHhccCC---eEEEEEEeccEEeecCCC-----cEEEEEEEEEEEecC
Confidence 6999999999999999999433 446666665443333444 678999999999874
No 3
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=99.17 E-value=5.8e-11 Score=89.72 Aligned_cols=55 Identities=40% Similarity=0.526 Sum_probs=45.6
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKK 63 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~ 63 (199)
.|+||||||++|||||+|| |+ ..+|+.++|.++-...++| .+++||+|+|+|.+.
T Consensus 37 RGraIskAVDvaeivRnrf--~p-~v~ik~Iki~se~~~~~~g-----r~~~VS~IeI~L~k~ 91 (91)
T COG1581 37 RGRAISKAVDVAEIVRNRF--IP-DVQIKDIKIGTEELEGEDG-----RTRNVSTIEIVLAKK 91 (91)
T ss_pred cchhhHhhHhHHHHHHHhc--CC-CceEEEEEecceeeecCCC-----ceeeEEEEEEEEecC
Confidence 3899999999999999999 77 5688888887665555554 578999999999873
No 4
>TIGR00285 DNA-binding protein Alba. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
Probab=99.16 E-value=7.8e-11 Score=88.97 Aligned_cols=54 Identities=33% Similarity=0.383 Sum_probs=43.5
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSK 62 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk 62 (199)
||+||||||+||||||+||...+ ++..++|..+-.+.++| .+++||+|+|+|++
T Consensus 34 rG~aIskAVdvaeiik~r~~~~v---~v~~I~i~te~~~~~~G-----~~~~VStIEI~l~~ 87 (87)
T TIGR00285 34 RGRAISRAVDVAEIVRNRFIPDI---KIKKIKIGTEEIKSEQG-----REVNVSTIEIVLAK 87 (87)
T ss_pred ecchhhhHHHHHHHHHHhccCCc---eEEEEEeccEEeecCCC-----ceeeEEEEEEEEeC
Confidence 79999999999999999994433 57777776665556665 77889999999975
No 5
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function. The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
Probab=98.61 E-value=3.4e-08 Score=70.03 Aligned_cols=31 Identities=48% Similarity=0.713 Sum_probs=28.0
Q ss_pred CchhhHHHHHHHHHHHHhhc-CCccceeeEEE
Q 029063 1 MGRAINKTVMIAELIKRRIA-GLHQNTSIGST 31 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~-gLhQ~t~i~~~ 31 (199)
||+||+|||+||||||+++. +|||++.+.++
T Consensus 38 ~G~aI~kaI~vaei~K~~~~~~~~qv~~~t~t 69 (70)
T PF01918_consen 38 RGKAISKAISVAEILKRRFGEGLYQVNKITST 69 (70)
T ss_dssp ECCHHHHHHHHHHHHHHHTSTTTEEEEEEEEE
T ss_pred EcHHHHHHHHHHHHHHHhhcCCCEEEEEEecc
Confidence 68999999999999999994 89999988764
No 6
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=97.57 E-value=0.00015 Score=59.25 Aligned_cols=57 Identities=30% Similarity=0.421 Sum_probs=36.9
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCC------------------CCCCCCceeeeeeEEEE
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLE------------------EGLLPLETTRHVSMITI 58 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~e------------------EGL~~le~tR~Vs~I~I 58 (199)
||+||.||+.||--|++.- ++.=.+...++.+.|..++.+ +..++...+|+||+|+|
T Consensus 69 tGkAIeKal~la~~Fq~~~-~~~V~V~TgTV~vvDdi~~~e~~~~~~~~~~~~~~~~~~~~~~~esR~R~vS~VEv 143 (144)
T PF12328_consen 69 TGKAIEKALSLALWFQRKK-GYKVEVRTGTVEVVDDIVEDEDEDEDEEESEEREDDDDDEDEEPESRTRWVSMVEV 143 (144)
T ss_dssp EGGGHHHHHHHHHHHHHTT----EEEEEEEEEEEEE-----------------------------EEEEEEEEEEE
T ss_pred ccHHHHHHHHHHHHHhhcC-CeEEEEEeceEEEEEEEeeccccccccccccccccCccccccCccceEEeeEEEEE
Confidence 8999999999999998775 454456677777777776542 33456668999999998
No 7
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.33 E-value=0.017 Score=59.63 Aligned_cols=9 Identities=44% Similarity=0.549 Sum_probs=3.3
Q ss_pred CCCCCCCCC
Q 029063 145 FRGRGWGYG 153 (199)
Q Consensus 145 ~~G~g~Gy~ 153 (199)
|++-++|||
T Consensus 1235 frnnggGdy 1243 (1282)
T KOG0921|consen 1235 FRNNGGGDY 1243 (1282)
T ss_pred cccCCCCCC
Confidence 333333433
No 8
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=95.96 E-value=0.043 Score=56.72 Aligned_cols=21 Identities=29% Similarity=0.642 Sum_probs=9.8
Q ss_pred CCCCCCC-CCCCCCCCCCCCCC
Q 029063 144 SFRGRGW-GYGSQSGGYYDYGE 164 (199)
Q Consensus 144 g~~G~g~-Gy~~~~~~~~~~~~ 164 (199)
||+|..+ ||-+..+++|.++.
T Consensus 1226 GyrGvsrgGfrnnggGdyrnpg 1247 (1282)
T KOG0921|consen 1226 GYRGVSRGGFRNNGGGDYRNPG 1247 (1282)
T ss_pred CCccccCCccccCCCCCCCCCC
Confidence 4444444 35444455554433
No 9
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=90.10 E-value=2.7 Score=39.69 Aligned_cols=9 Identities=33% Similarity=0.497 Sum_probs=3.6
Q ss_pred HHHHHHHHh
Q 029063 10 MIAELIKRR 18 (199)
Q Consensus 10 ~vAEIlKrR 18 (199)
+||-+|-.|
T Consensus 264 dvahLLaAr 272 (465)
T KOG3973|consen 264 DVAHLLAAR 272 (465)
T ss_pred HHHHHHHhh
Confidence 344444333
No 10
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=77.55 E-value=15 Score=32.04 Aligned_cols=10 Identities=20% Similarity=0.062 Sum_probs=6.2
Q ss_pred eeEEEEEccC
Q 029063 53 VSMITITLSK 62 (199)
Q Consensus 53 Vs~I~ItLSk 62 (199)
-..++|+||.
T Consensus 103 d~~fsIK~~d 112 (215)
T KOG3262|consen 103 DVHFSIKPSD 112 (215)
T ss_pred ccEEEEecCC
Confidence 3456777765
No 11
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=70.44 E-value=1.4 Score=43.37 Aligned_cols=10 Identities=50% Similarity=0.484 Sum_probs=1.5
Q ss_pred EEccCCCCCC
Q 029063 58 ITLSKKDLDT 67 (199)
Q Consensus 58 ItLSk~elD~ 67 (199)
|+||=++...
T Consensus 457 itlSWk~~~~ 466 (556)
T PF05918_consen 457 ITLSWKEAKK 466 (556)
T ss_dssp ---TTS----
T ss_pred cceeeeeccc
Confidence 5555444433
No 12
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics]
Probab=55.18 E-value=7.2 Score=36.60 Aligned_cols=39 Identities=36% Similarity=0.481 Sum_probs=25.3
Q ss_pred HHHHHH-HHHHhhc-CC--ccceeeEEEeccceeeeCCCCCCC
Q 029063 8 TVMIAE-LIKRRIA-GL--HQNTSIGSTDITDMWEPLEEGLLP 46 (199)
Q Consensus 8 AV~vAE-IlKrRi~-gL--hQ~t~i~~~~i~d~wEP~eEGL~~ 46 (199)
-|..|| |||+||. |- +-+.+.++.....+|||.++-||+
T Consensus 9 ~VfAaEsIlkkRirKGrvEYlVKWkGWs~kyNTWEPEENILDp 51 (369)
T KOG2748|consen 9 RVFAAESILKKRIRKGRVEYLVKWKGWSQKYNTWEPEENILDP 51 (369)
T ss_pred hHHHHHHHHHHHhhccceEEEEEecccccccCccCccccccCH
Confidence 455565 7788873 32 223344455668899999987765
No 13
>TIGR01543 proheadase_HK97 phage prohead protease, HK97 family. This model describes the prohead protease of HK97 and related phage. It is generally encoded next to the gene for the capsid protein that it processes, and in some cases may be fused to it. This family does not show similarity to the prohead protease of phage T4 (see pfam03420).
Probab=47.76 E-value=89 Score=25.12 Aligned_cols=58 Identities=17% Similarity=0.259 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCCCCCC
Q 029063 5 INKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDT 67 (199)
Q Consensus 5 IsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~elD~ 67 (199)
.++|-.+.+.||+.. |.+ .+|.+....+.|+..+++ .+-+...+-..+|.|...|.++
T Consensus 77 ~~~~~~~~~~ik~G~--i~g-~SiGF~~~~~~~~~~~~~--~~r~i~~~~L~EVS~V~~PA~~ 134 (145)
T TIGR01543 77 TPDAADVYALVKAGD--VSG-MSFGFRVIKDVWDDREEG--DVISLLEAALYEVSVTTFPAYP 134 (145)
T ss_pred ChhHHHHHHHHHCCC--Cce-eeEEEEECcceeeecCCC--ceEEEEEeEEEEEeecCcCCCC
Confidence 456777888888766 666 478888777788766543 1222223445566655555443
No 14
>PF04586 Peptidase_U35: Caudovirus prohead protease; InterPro: IPR006433 This entry represents the prohead protease from bacteriophage HK97 and related phages []. It is generally encoded next to the gene for the capsid protein that it processes, and in some cases may be fused to it. This entry includes putative prophage sequences, and putative components of Gene Transfer Agents (GTA) [], such as ORFg4 (RCAP_rcc01686) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].
Probab=46.58 E-value=1e+02 Score=24.74 Aligned_cols=59 Identities=17% Similarity=0.249 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCCCCCCC
Q 029063 6 NKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDTS 68 (199)
Q Consensus 6 sKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~elD~s 68 (199)
..+-.+.+.||..+ |.+ .+|....+.++|+..+++.... ....+...+|-|...|.++.
T Consensus 89 ~~~~~~~~~vk~G~--l~~-~SiGf~~~~~~~~~~~~g~~~~-~i~~~~l~EvSlV~~PA~~~ 147 (162)
T PF04586_consen 89 PEGRDVYALVKDGT--LRG-LSIGFRVLEDEWDERDDGRPVR-IITEAELYEVSLVPVPANPN 147 (162)
T ss_pred HHHHHHHHHHHCCC--Cce-EeEEEEEeccEeeecCCccceE-EEEEEEEEEEEECccCCCCC
Confidence 44556677777654 544 6899888899998887543333 33345577777777666654
No 15
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=45.63 E-value=22 Score=33.48 Aligned_cols=14 Identities=21% Similarity=0.256 Sum_probs=6.1
Q ss_pred EEEEEccCCCCCCC
Q 029063 55 MITITLSKKDLDTS 68 (199)
Q Consensus 55 ~I~ItLSk~elD~s 68 (199)
+|.|+-+++..+.+
T Consensus 288 ~~v~~~~k~~e~~~ 301 (365)
T KOG2945|consen 288 TVVLHSSKDREEKS 301 (365)
T ss_pred ceeeeccccccchh
Confidence 34444445444443
No 16
>PF03759 PRONE: PRONE (Plant-specific Rop nucleotide exchanger); InterPro: IPR005512 In plants, the small GTP-binding proteins called Rops work as signalling switches that control growth, development and plant responses to various environmental stimuli. Rop proteins (Rho of plants, Rac-like and atRac in Arabidopsis thaliana (Mouse-ear cress)) belong to the Rho family of Ras-related GTP-binding proteins that turn on signalling pathways by switching from a GDP-bound inactive to a GTP-bound active conformation. Activation depends on guanine nucleotide exchange factors (GEFs) that catalyse the otherwise slow GDP dissociation for subsequent GTP binding. The plant-specific RopGEFs represent a unique family of exchange factor that display no homology to any known RhoGEFs from animals and fungi. They comprise a highly conserved catalytic domain termed PRONE (plant-specific Rop nucleotide exchanger) with exclusive substrate specificity for members of the Rop family. The PRONE domain has been shown to be necessary and sufficient to promote nucleotide release from Rop [, , ]. The PRONE domain can be divided into three highly conserved subdomains separated by two short stretches of variable amino acid residues [, ]. It is approximately 370 residues in length and displays an almost all alpha-helical structure except for a beta-turn that protrudes from the main body of the molecule. The overall structure of the PRONE domain can be divided into two subdomains, the first one including helices alpha1-5 and alpha13, the second alpha6-12 [].; GO: 0005089 Rho guanyl-nucleotide exchange factor activity; PDB: 2NTX_B 2NTY_B 2WBL_A.
Probab=37.01 E-value=8.7 Score=36.01 Aligned_cols=27 Identities=30% Similarity=0.441 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhcCCccceeeEEEecc
Q 029063 7 KTVMIAELIKRRIAGLHQNTSIGSTDIT 34 (199)
Q Consensus 7 KAV~vAEIlKrRi~gLhQ~t~i~~~~i~ 34 (199)
+|=++--+||+|||+|.| |.|...+|+
T Consensus 298 RAEtlL~~LK~RfPgl~Q-T~LD~~KIQ 324 (365)
T PF03759_consen 298 RAETLLLCLKQRFPGLPQ-TSLDISKIQ 324 (365)
T ss_dssp HHHHHHHHHHHHSTT-----HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCc-hHHHHHHHH
Confidence 455555689999999999 555554443
No 17
>cd08982 GH43_3 Glycosyl hydrolase family 43. This glycosyl hydrolase family 43 (GH43) includes enzymes with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially e
Probab=35.29 E-value=53 Score=29.09 Aligned_cols=38 Identities=16% Similarity=0.345 Sum_probs=25.9
Q ss_pred eeeeeEEEEEccCC---CCCCCCCCCCCCCCcCCCCCCCcc
Q 029063 50 TRHVSMITITLSKK---DLDTSSTGYQPPLPADQVKPWNEF 87 (199)
Q Consensus 50 tR~Vs~I~ItLSk~---elD~ss~GYQ~P~p~~~vk~~~E~ 87 (199)
.|++-+..|+-..+ .++..-..||.|||.+++||+.+.
T Consensus 248 ~R~~~i~pv~~~~dG~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 (295)
T cd08982 248 ERRIGLFPAFFDEDGVLYCNTAFGDYPMILPDKKIDPPEDL 288 (295)
T ss_pred CceeEEEEEEECCCCcEEEcccCCcCcccCCCCCCcccccc
Confidence 35554445655433 235556799999999999998654
No 18
>PF05655 AvrD: Pseudomonas avirulence D protein (AvrD); InterPro: IPR008799 This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae [].
Probab=35.19 E-value=65 Score=29.73 Aligned_cols=37 Identities=32% Similarity=0.362 Sum_probs=28.2
Q ss_pred hhHHHHHHHH-HHHHhhcCCccceeeEEEeccceeeeCC
Q 029063 4 AINKTVMIAE-LIKRRIAGLHQNTSIGSTDITDMWEPLE 41 (199)
Q Consensus 4 AIsKAV~vAE-IlKrRi~gLhQ~t~i~~~~i~d~wEP~e 41 (199)
||.-|+.|+| ++++.+.+|-+ ..|..+.|..--+|.|
T Consensus 72 ai~la~~l~e~~~~~~~~~~~~-~~i~~~~IkAG~~P~E 109 (311)
T PF05655_consen 72 AIVLAAQLAEDFYLREFCGLER-MWIRKFSIKAGSEPVE 109 (311)
T ss_pred HHHHHHHHHHHHHHhhhccccc-eeEEEEEEecCCChhh
Confidence 6788999999 99999887763 5677777766556644
No 19
>COG2065 PyrR Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=26.92 E-value=1.4e+02 Score=25.59 Aligned_cols=72 Identities=29% Similarity=0.342 Sum_probs=34.6
Q ss_pred hhHHHHH-HHHHHHHhhcCCccceeeEEEeccceeee--CCCCCCCCc-eeeeeeEEEEEccCCCCCCCCCCCCCCCC
Q 029063 4 AINKTVM-IAELIKRRIAGLHQNTSIGSTDITDMWEP--LEEGLLPLE-TTRHVSMITITLSKKDLDTSSTGYQPPLP 77 (199)
Q Consensus 4 AIsKAV~-vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP--~eEGL~~le-~tR~Vs~I~ItLSk~elD~ss~GYQ~P~p 77 (199)
+|.+|++ +|--|.-|.++|.++.-++-.. --.|.. +.+.|..++ ....+-.|.|||-.+.+....+ .+++..
T Consensus 11 ~i~RtitRia~eIiErnk~~~~~vlvGIkt-rGv~lA~rl~~~i~~~Eg~~vp~g~lDIt~yRDDl~~~~~-~~p~~~ 86 (179)
T COG2065 11 AIRRTITRIAHEIIERNKGLDNLVLVGIKT-RGVPLAERLAERIEELEGIEVPVGELDITLYRDDLTQKGP-LRPQAK 86 (179)
T ss_pred HHHHHHHHHHHHHHHHhCCCCceEEEeEec-CCHHHHHHHHHHHHHHhCCCCCeeeEEeEEeechhhhcCc-cCCccc
Confidence 5677777 5555555666787655444331 111100 000011111 2222456778888887765543 344333
No 20
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=26.27 E-value=38 Score=26.88 Aligned_cols=15 Identities=7% Similarity=0.195 Sum_probs=8.4
Q ss_pred eeeeeeEEEEEccCC
Q 029063 49 TTRHVSMITITLSKK 63 (199)
Q Consensus 49 ~tR~Vs~I~ItLSk~ 63 (199)
..-++-|+.++++-+
T Consensus 34 ~~Mn~~l~~v~~t~~ 48 (109)
T KOG3428|consen 34 VQMNTHLKHVKMTVK 48 (109)
T ss_pred hhheeEEEEEEEecC
Confidence 344455666666654
No 21
>cd00133 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby r
Probab=24.70 E-value=1.5e+02 Score=19.64 Aligned_cols=31 Identities=16% Similarity=0.325 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHHHhhcCCccceeeEEEecc
Q 029063 4 AINKTVMIAELIKRRIAGLHQNTSIGSTDIT 34 (199)
Q Consensus 4 AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~ 34 (199)
.+..+..+++-||+.|+.+.....+...++.
T Consensus 9 G~~~s~~l~~~l~~~~~~~~~~~~~~~~~~~ 39 (84)
T cd00133 9 GIGSSSMLAEKLEKAAKELGIEVKVEAQGLS 39 (84)
T ss_pred cHhHHHHHHHHHHHHHHHCCCeEEEEEcccc
Confidence 3456677888888888766665555444443
Done!