Query 042002
Match_columns 143
No_of_seqs 104 out of 337
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 12:59:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042002hhsearch_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 2.4E-45 5.2E-50 276.2 11.4 142 1-142 1-142 (179)
2 PRK04015 DNA/RNA-binding prote 99.9 2.8E-22 6.2E-27 139.1 11.5 90 16-115 2-91 (91)
3 TIGR00285 DNA-binding protein 99.9 2.4E-21 5.3E-26 133.2 11.5 87 18-114 1-87 (87)
4 COG1581 Ssh10b Archaeal DNA-bi 99.9 3E-21 6.6E-26 132.0 11.8 88 16-114 2-90 (91)
5 PF01918 Alba: Alba; InterPro 99.8 8.4E-18 1.8E-22 110.9 9.8 64 19-82 1-68 (70)
6 PF12328 Rpp20: Rpp20 subunit 99.5 1.9E-13 4.1E-18 102.4 9.6 93 18-111 3-144 (144)
7 PF04232 SpoVS: Stage V sporul 79.6 17 0.00038 25.0 11.6 51 19-71 2-53 (86)
8 PF09363 XFP_C: XFP C-terminal 61.1 25 0.00054 27.9 5.4 42 44-89 33-75 (203)
9 PF06792 UPF0261: Uncharacteri 47.4 65 0.0014 28.2 6.2 46 16-61 183-231 (403)
10 PRK05261 putative phosphoketol 46.5 36 0.00079 32.2 4.8 39 45-87 613-652 (785)
11 PRK02399 hypothetical protein; 42.2 92 0.002 27.3 6.3 65 17-89 185-252 (406)
12 PF02089 Palm_thioest: Palmito 40.9 34 0.00073 28.4 3.3 40 45-88 6-48 (279)
13 cd05013 SIS_RpiR RpiR-like pro 38.8 1E+02 0.0022 20.9 5.2 37 32-70 2-38 (139)
14 PF02780 Transketolase_C: Tran 36.0 56 0.0012 22.8 3.5 27 44-70 8-34 (124)
15 KOG0523 Transketolase [Carbohy 35.0 77 0.0017 29.3 4.9 52 18-74 481-532 (632)
16 COG2065 PyrR Pyrimidine operon 31.1 54 0.0012 25.5 2.9 51 44-121 29-79 (179)
17 PF12404 DUF3663: Peptidase ; 30.2 1.5E+02 0.0033 20.0 4.6 41 19-60 27-67 (77)
18 TIGR00106 uncharacterized prot 27.4 86 0.0019 21.7 3.2 33 25-58 13-45 (97)
19 TIGR03127 RuMP_HxlB 6-phospho 24.9 2.5E+02 0.0055 20.6 5.6 35 31-67 18-52 (179)
20 KOG1402 Ornithine aminotransfe 24.8 4.8E+02 0.01 22.9 8.2 72 44-131 115-187 (427)
21 PF01985 CRS1_YhbY: CRS1 / Yhb 23.0 2.3E+02 0.0051 18.7 7.0 54 18-73 17-70 (84)
22 PRK05416 glmZ(sRNA)-inactivati 22.8 1.4E+02 0.0031 24.6 4.1 40 31-71 229-270 (288)
23 cd04236 AAK_NAGS-Urea AAK_NAGS 22.5 1.1E+02 0.0024 25.1 3.5 31 31-61 54-84 (271)
24 COG5069 SAC6 Ca2+-binding acti 22.1 42 0.00092 30.3 1.0 23 120-143 355-377 (612)
25 PRK11382 frlB fructoselysine-6 21.9 2.8E+02 0.006 23.0 5.8 41 31-71 30-70 (340)
26 PRK04531 acetylglutamate kinas 21.5 1.5E+02 0.0032 25.7 4.1 32 31-62 53-84 (398)
27 PF03727 Hexokinase_2: Hexokin 20.7 90 0.002 24.8 2.5 45 18-62 184-241 (243)
28 cd05006 SIS_GmhA Phosphoheptos 20.5 3.5E+02 0.0075 19.9 5.6 41 31-71 17-59 (177)
29 PF01910 DUF77: Domain of unkn 20.2 1.6E+02 0.0035 20.0 3.4 29 26-55 12-40 (92)
No 1
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.4e-45 Score=276.20 Aligned_cols=142 Identities=44% Similarity=0.697 Sum_probs=139.0
Q ss_pred CCCceecccCCCCCCCCCCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEE
Q 042002 1 MDRYQRVEKPKAETPINENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVGLHQNTAI 80 (143)
Q Consensus 1 m~~y~rv~~~~~~~~~~~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~~gL~q~~~i 80 (143)
||.|.++.+||++.|++.|+|||+.+++++||+.||..+|++++.+.|||+|+|+||.|+|+||||||||++||||.|++
T Consensus 1 ~~~e~~~~kP~~d~pp~a~emrV~~g~kirN~i~~A~~~L~~~~~r~VVfsg~Grai~KTVscaEilKrRipgLhQ~t~l 80 (179)
T KOG2567|consen 1 MSVEQPASKPFPDLPPDANEMRVKSGSKIRNLIEFATELLQKGSHRCVVFSGSGRAIVKTVSCAEILKRRIPGLHQVTRL 80 (179)
T ss_pred CccccccCCCcccCCCCcceEEEccCchHHHHHHHHHHHhhCCCeeEEEEecCCcceeeeeeHHHHHhhhCcchhhhcee
Confidence 89999999999999999999999999999999999999999989999999999999999999999999999999999999
Q ss_pred EEEEeecceeecccCCccceeeeeeeEEEEEEecCCCCCCCCCCCCCCCCCCCCCCCcCCCC
Q 042002 81 GSTDITDMWEPLEEGLLPLETTRHVSVITVTLSKKELDTSSTGYQPPIPADQVKPWVENDYH 142 (143)
Q Consensus 81 ~~v~i~d~~~p~~eg~~~~~~~R~vs~I~I~Lsk~~ld~~~~GyQ~P~~~~~v~~~~~~~~~ 142 (143)
.++.+.|.|+|.++||+.+...|+||.|+|+||+++||++++|||+|.|.........-||.
T Consensus 81 ~~~sv~d~W~p~~eGl~pl~vtRhVp~l~IlLS~deL~~~~~GyQ~P~~~p~p~~~~~~p~~ 142 (179)
T KOG2567|consen 81 RYTSVEDVWEPTEEGLEPLEVTRHVPMLHILLSLDELDPTSPGYQPPNPQPHPRSQPRHPYS 142 (179)
T ss_pred eeeehhhcccccccCccceEEeeccceEEEEEecccCCCCCCCccCCCCCCCCCCcccCCcc
Confidence 99999999999999999999999999999999999999999999999999998888888886
No 2
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.89 E-value=2.8e-22 Score=139.12 Aligned_cols=90 Identities=32% Similarity=0.446 Sum_probs=73.8
Q ss_pred CCCCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEEEEEEeecceeecccC
Q 042002 16 INENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVGLHQNTAIGSTDITDMWEPLEEG 95 (143)
Q Consensus 16 ~~~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~~gL~q~~~i~~v~i~d~~~p~~eg 95 (143)
..+|+|+|++++.+ +|+.+++.+|++ |.++|+|+|+|+||+|||+|||+||+||.+.+ ++..+.+..+-...++|
T Consensus 2 ~~en~i~Ig~kpvm-nYV~~~~~~l~~-g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v---~v~~I~i~se~i~~~~g 76 (91)
T PRK04015 2 AEENVVLVGKKPVM-NYVLAVLTQFNQ-GAKEVVIKARGRAISKAVDVAEIVRNRFLPDV---EIKEIKIGTEEVTSEDG 76 (91)
T ss_pred CCCCEEEEcCCcHH-HHHHHHHHHHhC-CCCeEEEEEeccccchhhhHHHHHHHhccCCe---EEEEEEeccEEeecCCC
Confidence 46799999999755 999999999994 89999999999999999999999999984334 44444554444334566
Q ss_pred CccceeeeeeeEEEEEEecC
Q 042002 96 LLPLETTRHVSVITVTLSKK 115 (143)
Q Consensus 96 ~~~~~~~R~vs~I~I~Lsk~ 115 (143)
..|+||+|+|.|++.
T Consensus 77 -----~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 77 -----RESNVSTIEIVLEKK 91 (91)
T ss_pred -----cEEEEEEEEEEEecC
Confidence 689999999999873
No 3
>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=99.87 E-value=2.4e-21 Score=133.22 Aligned_cols=87 Identities=33% Similarity=0.447 Sum_probs=75.2
Q ss_pred CCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEEEEEEeecceeecccCCc
Q 042002 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVGLHQNTAIGSTDITDMWEPLEEGLL 97 (143)
Q Consensus 18 ~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~~gL~q~~~i~~v~i~d~~~p~~eg~~ 97 (143)
+|.|+|++|+-| +||.+++.+|++ |.++|+|+|+|+||+|||++||+||+||...+ ++..+++..+-.+.++|
T Consensus 1 e~~i~vG~KPvm-nYVlavlt~fn~-g~~eV~iKarG~aIskAVdvaeiik~r~~~~v---~v~~I~i~te~~~~~~G-- 73 (87)
T TIGR00285 1 ENVVYIGNKPVM-NYVLAVLTQLNS-GADEVIIKARGRAISRAVDVAEIVRNRFIPDI---KIKKIKIGTEEIKSEQG-- 73 (87)
T ss_pred CCEEEEcCCcHH-HHHHHHHHHHhC-CCCeEEEEEecchhhhHHHHHHHHHHhccCCc---eEEEEEeccEEeecCCC--
Confidence 489999999977 999999999996 89999999999999999999999999985433 66666666666666777
Q ss_pred cceeeeeeeEEEEEEec
Q 042002 98 PLETTRHVSVITVTLSK 114 (143)
Q Consensus 98 ~~~~~R~vs~I~I~Lsk 114 (143)
+.|+||+|+|.|.+
T Consensus 74 ---~~~~VStIEI~l~~ 87 (87)
T TIGR00285 74 ---REVNVSTIEIVLAK 87 (87)
T ss_pred ---ceeeEEEEEEEEeC
Confidence 68899999999975
No 4
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=99.87 E-value=3e-21 Score=132.00 Aligned_cols=88 Identities=35% Similarity=0.494 Sum_probs=78.0
Q ss_pred CCCCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhc-CCceeEEEEEEEEeecceeeccc
Q 042002 16 INENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRI-VGLHQNTAIGSTDITDMWEPLEE 94 (143)
Q Consensus 16 ~~~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~-~gL~q~~~i~~v~i~d~~~p~~e 94 (143)
..+|.|+|++|+-+ |||..++.+|++ |.++|+|+|+|+||||||++||+++.|| |++ ++..+++..+-...++
T Consensus 2 ~~envV~vG~KPvm-NYVlAvlt~fn~-g~~eViiKARGraIskAVDvaeivRnrf~p~v----~ik~Iki~se~~~~~~ 75 (91)
T COG1581 2 AEENVVLVGKKPVM-NYVLAVLTQFNE-GADEVIIKARGRAISKAVDVAEIVRNRFIPDV----QIKDIKIGTEELEGED 75 (91)
T ss_pred CCccEEEEcCcchH-HHHHHHHHHHHc-CCCEEEEEecchhhHhhHhHHHHHHHhcCCCc----eEEEEEecceeeecCC
Confidence 35699999999988 999999999997 8999999999999999999999999998 655 7777777776666667
Q ss_pred CCccceeeeeeeEEEEEEec
Q 042002 95 GLLPLETTRHVSVITVTLSK 114 (143)
Q Consensus 95 g~~~~~~~R~vs~I~I~Lsk 114 (143)
| +.++||+|+|.|.+
T Consensus 76 g-----r~~~VS~IeI~L~k 90 (91)
T COG1581 76 G-----RTRNVSTIEIVLAK 90 (91)
T ss_pred C-----ceeeEEEEEEEEec
Confidence 7 68899999999986
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=99.76 E-value=8.4e-18 Score=110.92 Aligned_cols=64 Identities=38% Similarity=0.609 Sum_probs=57.5
Q ss_pred CeEEEcCCCchhHHHHHHHHHH---hhcCCCeEEEEEcChhHHHHHHHHHHHHHhcC-CceeEEEEEE
Q 042002 19 NEIRITTQGRMRNYITYATTLL---QEKGSNEISLKAMGRAINKTVMIAELIKRRIV-GLHQNTAIGS 82 (143)
Q Consensus 19 n~I~V~~~~~i~~yv~~a~~lL---~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~~-gL~q~~~i~~ 82 (143)
|+|+|++++++.+||.+|+.+| +..+.++|+|+|+|+||+|||+|||+||+++. ++||++.+..
T Consensus 1 n~I~V~~~~~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv~~~t~ 68 (70)
T PF01918_consen 1 NEIYVSSNSPIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQVNKITS 68 (70)
T ss_dssp SEEEE-STS-HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEEEEEEE
T ss_pred CEEEECCCCCHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEEEEEec
Confidence 7999999999999999999999 44589999999999999999999999999995 8999988865
No 6
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=99.49 E-value=1.9e-13 Score=102.42 Aligned_cols=93 Identities=25% Similarity=0.364 Sum_probs=67.5
Q ss_pred CCeEEEcCCCchhHHHHHHHHHHhhc-------------------C------------CCeEEEEEcChhHHHHHHHHHH
Q 042002 18 ENEIRITTQGRMRNYITYATTLLQEK-------------------G------------SNEISLKAMGRAINKTVMIAEL 66 (143)
Q Consensus 18 ~n~I~V~~~~~i~~yv~~a~~lL~~~-------------------~------------~~~Vvi~g~G~AI~kAV~vAEi 66 (143)
++.|||+.+++|-+.|.++.++|..- + ..+|+|+|||+||.||+++|.-
T Consensus 3 ~~~iyVss~TPfmSavKRv~K~L~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~v~gtGkAIeKal~la~~ 82 (144)
T PF12328_consen 3 PKVIYVSSKTPFMSAVKRVRKLLDKAEKRATSSVNLAKKKKSQKKKIAQLAEGSEALKSEEVTVKGTGKAIEKALSLALW 82 (144)
T ss_dssp TTEEE--SS--HHHHHHHHHHHHHHHHHH----------------T-------------SEEEEEEEGGGHHHHHHHHHH
T ss_pred CcEEEEecCCchHHHHHHHHHHHHhhhccccccccccccccccccccccccccccccCccEEEEEeccHHHHHHHHHHHH
Confidence 58999999999999999999999631 1 2799999999999999999999
Q ss_pred HHHhcCCceeEEEEEEEEeecceeecc------------------cCCccceeeeeeeEEEEE
Q 042002 67 IKRRIVGLHQNTAIGSTDITDMWEPLE------------------EGLLPLETTRHVSVITVT 111 (143)
Q Consensus 67 lKrr~~gL~q~~~i~~v~i~d~~~p~~------------------eg~~~~~~~R~vs~I~I~ 111 (143)
+++.. ++--.++++++.+.|++++.+ ++.+...+.|.||+|+|.
T Consensus 83 Fq~~~-~~~V~V~TgTV~vvDdi~~~e~~~~~~~~~~~~~~~~~~~~~~~esR~R~vS~VEv~ 144 (144)
T PF12328_consen 83 FQRKK-GYKVEVRTGTVEVVDDIVEDEDEDEDEEESEEREDDDDDEDEEPESRTRWVSMVEVA 144 (144)
T ss_dssp HHHTT----EEEEEEEEEEEEE-----------------------------EEEEEEEEEEEE
T ss_pred HhhcC-CeEEEEEeceEEEEEEEeeccccccccccccccccCccccccCccceEEeeEEEEEC
Confidence 98886 677889999999999999653 445668899999999984
No 7
>PF04232 SpoVS: Stage V sporulation protein S (SpoVS); InterPro: IPR007347 In Bacillus subtilis this protein interferes with sporulation at an early stage and this inhibitory effect is overcome by SpoIIB and SpoVG. SpoVS seems to play a positive role in allowing progression beyond stage V of sporulation. Null mutations in the spoVS gene block sporulation at stage V, impairing the development of heat resistance and coat assembly [].; PDB: 2EH1_B 2EK0_B.
Probab=79.59 E-value=17 Score=24.97 Aligned_cols=51 Identities=16% Similarity=0.345 Sum_probs=34.0
Q ss_pred CeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHHhc
Q 042002 19 NEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMG-RAINKTVMIAELIKRRI 71 (143)
Q Consensus 19 n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G-~AI~kAV~vAEilKrr~ 71 (143)
+.++|+.+++-...-..-...+.+ ...+.|.|+| .|++.||.-.-+-+.-+
T Consensus 2 e~LKVSs~S~p~~vAgAIa~~lre--~~~v~lqaiGa~AvnqAvKAIAiAR~~l 53 (86)
T PF04232_consen 2 EVLKVSSKSNPNAVAGAIAGVLRE--GGKVELQAIGAGAVNQAVKAIAIARGYL 53 (86)
T ss_dssp -EEEE-TT--HHHHHHHHHHHHHH--TSEEEEEE-SHHHHHHHHHHHHHHHHHH
T ss_pred ceEEEcCCCCHHHHHHHHHHHHhc--CCcEEEEEECHHHHHHHHHHHHHHHHhh
Confidence 468899999987766666667775 3589999999 68888877666655444
No 8
>PF09363 XFP_C: XFP C-terminal domain; InterPro: IPR018969 Phosphoketolases (PK) are key enzymes of the pentose phosphate pathway of heterofermentative and facultative homofermentative lactic acid bacteria and of the D-fructose 6-phosphate shunt of bifidobacteria. PK activity has been sporadically reported in other microorganisms including eukaryotic yeasts. Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase is a thiamine diphosphate (ThdP)-dependent enzyme found in bacteria such as Bifidobacterium sp [, ]. This enzyme has dual-specificity with the following catalytic activities: 4.1.2.9 from EC: xylose 5-P + Pi = acetyl-P + glyeraldehyde-3-P 4.1.2.22 from EC: fructose-6-P + Pi = acetyl-P + erythrose-4-P Phosphoketolases are distantly related to transketolases, e.g. IPR005475 from INTERPRO.; GO: 0016832 aldehyde-lyase activity, 0005975 carbohydrate metabolic process; PDB: 3AI7_B 3AHC_A 3AHJ_A 3AHG_A 3AHE_A 3AHI_A 3AHD_A 3AHF_A 3AHH_A.
Probab=61.10 E-value=25 Score=27.95 Aligned_cols=42 Identities=17% Similarity=0.306 Sum_probs=31.7
Q ss_pred CCCeEEEEEcC-hhHHHHHHHHHHHHHhcCCceeEEEEEEEEeecce
Q 042002 44 GSNEISLKAMG-RAINKTVMIAELIKRRIVGLHQNTAIGSTDITDMW 89 (143)
Q Consensus 44 ~~~~Vvi~g~G-~AI~kAV~vAEilKrr~~gL~q~~~i~~v~i~d~~ 89 (143)
+..-||+-|.| -..--++..|.+|++.+|+| +|..|.+.|-.
T Consensus 33 ~ePDVVlA~aGd~pT~E~lAA~~lLr~~~P~l----kiRvVNVvDLm 75 (203)
T PF09363_consen 33 EEPDVVLACAGDVPTLEVLAAASLLREHFPEL----KIRVVNVVDLM 75 (203)
T ss_dssp TT-SEEEEEESHHHHHHHHHHHHHHHHT--T------EEEEEESBGG
T ss_pred CCCCEEEEecCchhhHHHHHHHHHHHHhccCc----eEEEEEEeEcc
Confidence 47889999999 56667899999999999999 89999888754
No 9
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=47.37 E-value=65 Score=28.17 Aligned_cols=46 Identities=24% Similarity=0.330 Sum_probs=38.0
Q ss_pred CCCCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcC---hhHHHHH
Q 042002 16 INENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMG---RAINKTV 61 (143)
Q Consensus 16 ~~~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G---~AI~kAV 61 (143)
.+.-.|=+|.=+.-..+|..+...|++.|+..+++||.| +|+.+-|
T Consensus 183 ~~kp~I~iTmfGvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li 231 (403)
T PF06792_consen 183 EDKPLIGITMFGVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLI 231 (403)
T ss_pred CCCcEEEEECCCCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHH
Confidence 345688888877777899999999999899999999998 6776654
No 10
>PRK05261 putative phosphoketolase; Provisional
Probab=46.47 E-value=36 Score=32.21 Aligned_cols=39 Identities=21% Similarity=0.369 Sum_probs=32.5
Q ss_pred CCeEEEEEcChhHHH-HHHHHHHHHHhcCCceeEEEEEEEEeec
Q 042002 45 SNEISLKAMGRAINK-TVMIAELIKRRIVGLHQNTAIGSTDITD 87 (143)
Q Consensus 45 ~~~Vvi~g~G~AI~k-AV~vAEilKrr~~gL~q~~~i~~v~i~d 87 (143)
...|+|-|.|.-+.. |+..|++|++.+||+ ++.-|.+.|
T Consensus 613 ~pDvvL~atGsev~leAlaAa~~L~~~~pgi----kvRVVSv~d 652 (785)
T PRK05261 613 EPDVVLACAGDVPTLETLAAADLLREHFPDL----KIRVVNVVD 652 (785)
T ss_pred CCCEEEEEeCcHhhHHHHHHHHHHHhhCCCC----CEEEEEech
Confidence 358999999999999 999999999999998 555555443
No 11
>PRK02399 hypothetical protein; Provisional
Probab=42.22 E-value=92 Score=27.32 Aligned_cols=65 Identities=20% Similarity=0.243 Sum_probs=43.9
Q ss_pred CCCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcC---hhHHHHHHHHHHHHHhcCCceeEEEEEEEEeecce
Q 042002 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMG---RAINKTVMIAELIKRRIVGLHQNTAIGSTDITDMW 89 (143)
Q Consensus 17 ~~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G---~AI~kAV~vAEilKrr~~gL~q~~~i~~v~i~d~~ 89 (143)
+.-.|=+|.=+.-..+|..+...|++.|++.+++||.| +|+.+-|. . +-++-...+.+.++.|++
T Consensus 185 ~kp~Ig~TmfGvTtp~v~~~~~~Le~~GyEvlVFHATG~GGraME~Li~-------~-G~~~gVlDlTttEv~d~l 252 (406)
T PRK02399 185 DKPLIGLTMFGVTTPCVQAAREELEARGYEVLVFHATGTGGRAMEKLID-------S-GLIAGVLDLTTTEVCDEL 252 (406)
T ss_pred CCceEEEecCCCcHHHHHHHHHHHHhCCCeEEEEcCCCCchHHHHHHHH-------c-CCceEEEEcchHHHHHHH
Confidence 34456777655555899999999999899999999998 57766442 1 113444455555555543
No 12
>PF02089 Palm_thioest: Palmitoyl protein thioesterase; InterPro: IPR002472 Neuronal ceroid lipofuscinoses (NCL) represent a group of encephalopathies that occur in 1 in 12,500 children. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis []. The most common mutation results in intracellular accumulation of the polypeptide and undetectable enzyme activity in the brain. Direct sequencing of cDNAs derived from brain RNA of INCL patients has shown a mis-sense transversion of A to T at nucleotide position 364, which results in substitution of Trp for Arg at position 122 in the protein - Arg 122 is immediately adjacent to a lipase consensus sequence that contains the putative active site Ser of PPT. The occurrence of this and two other independent mutations in the PPT gene strongly suggests that defects in this gene cause INCL.; GO: 0008474 palmitoyl-(protein) hydrolase activity, 0006464 protein modification process; PDB: 3GRO_B 1PJA_A 1EXW_A 1EH5_A 1EI9_A.
Probab=40.89 E-value=34 Score=28.42 Aligned_cols=40 Identities=23% Similarity=0.218 Sum_probs=22.5
Q ss_pred CCeEEEEEcChhHH---HHHHHHHHHHHhcCCceeEEEEEEEEeecc
Q 042002 45 SNEISLKAMGRAIN---KTVMIAELIKRRIVGLHQNTAIGSTDITDM 88 (143)
Q Consensus 45 ~~~Vvi~g~G~AI~---kAV~vAEilKrr~~gL~q~~~i~~v~i~d~ 88 (143)
.+.|+|||||-... -.-.+.+.+++.+||. .+.++++.+.
T Consensus 6 ~PvViwHGmGD~~~~~~~m~~i~~~i~~~~PG~----yV~si~ig~~ 48 (279)
T PF02089_consen 6 LPVVIWHGMGDSCCNPSSMGSIKELIEEQHPGT----YVHSIEIGND 48 (279)
T ss_dssp --EEEE--TT--S--TTTHHHHHHHHHHHSTT------EEE--SSSS
T ss_pred CcEEEEEcCccccCChhHHHHHHHHHHHhCCCc----eEEEEEECCC
Confidence 46789999997654 3567889999999996 5566666544
No 13
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=38.80 E-value=1e+02 Score=20.87 Aligned_cols=37 Identities=19% Similarity=0.143 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHh
Q 042002 32 YITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRR 70 (143)
Q Consensus 32 yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr 70 (143)
.+..+..++.+ .+.|.+.|.|....-|...+..+++-
T Consensus 2 ~i~~~~~~i~~--~~~i~i~g~g~s~~~a~~~~~~l~~~ 38 (139)
T cd05013 2 ALEKAVDLLAK--ARRIYIFGVGSSGLVAEYLAYKLLRL 38 (139)
T ss_pred HHHHHHHHHHh--CCEEEEEEcCchHHHHHHHHHHHHHc
Confidence 35667777764 68999999999887777777777653
No 14
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=35.95 E-value=56 Score=22.77 Aligned_cols=27 Identities=19% Similarity=0.358 Sum_probs=24.9
Q ss_pred CCCeEEEEEcChhHHHHHHHHHHHHHh
Q 042002 44 GSNEISLKAMGRAINKTVMIAELIKRR 70 (143)
Q Consensus 44 ~~~~Vvi~g~G~AI~kAV~vAEilKrr 70 (143)
.-..|.|-++|..+..|+..|+.|+.+
T Consensus 8 ~g~di~iia~G~~~~~al~A~~~L~~~ 34 (124)
T PF02780_consen 8 EGADITIIAYGSMVEEALEAAEELEEE 34 (124)
T ss_dssp SSSSEEEEEETTHHHHHHHHHHHHHHT
T ss_pred CCCCEEEEeehHHHHHHHHHHHHHHHc
Confidence 346899999999999999999999998
No 15
>KOG0523 consensus Transketolase [Carbohydrate transport and metabolism]
Probab=35.03 E-value=77 Score=29.29 Aligned_cols=52 Identities=21% Similarity=0.250 Sum_probs=36.0
Q ss_pred CCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhcCCc
Q 042002 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVGL 74 (143)
Q Consensus 18 ~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~~gL 74 (143)
.|-+.+..... --+..+...|.+ +.+.|+|-|.|.++..|+..||.|..+ ||
T Consensus 481 ~~~~~~~~~~~--~~igkg~~vl~~-~~~dV~LiG~Gs~v~~cl~AA~~L~~~--gi 532 (632)
T KOG0523|consen 481 QNLPIYNNTEI--EEIGKGKYVLQE-VEPDVILIGTGSEVQECLEAAELLSED--GI 532 (632)
T ss_pred ccccccCCCch--hhhccccEEEec-CCCCEEEEeccHHHHHHHHHHHHHHhc--Cc
Confidence 34444444332 234444445555 558999999999999999999999966 55
No 16
>COG2065 PyrR Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=31.09 E-value=54 Score=25.50 Aligned_cols=51 Identities=27% Similarity=0.428 Sum_probs=33.0
Q ss_pred CCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEEEEEEeecceeecccCCccceeeeeeeEEEEEEecCCCCCCC
Q 042002 44 GSNEISLKAMGRAINKTVMIAELIKRRIVGLHQNTAIGSTDITDMWEPLEEGLLPLETTRHVSVITVTLSKKELDTSS 121 (143)
Q Consensus 44 ~~~~Vvi~g~G~AI~kAV~vAEilKrr~~gL~q~~~i~~v~i~d~~~p~~eg~~~~~~~R~vs~I~I~Lsk~~ld~~~ 121 (143)
+.+.++|-|.- ++.+.+|+.|++++..+ || ..-.+-.+.|+++++-+..+.
T Consensus 29 ~~~~~vlvGIk---trGv~lA~rl~~~i~~~-------------------Eg-----~~vp~g~lDIt~yRDDl~~~~ 79 (179)
T COG2065 29 GLDNLVLVGIK---TRGVPLAERLAERIEEL-------------------EG-----IEVPVGELDITLYRDDLTQKG 79 (179)
T ss_pred CCCceEEEeEe---cCCHHHHHHHHHHHHHH-------------------hC-----CCCCeeeEEeEEeechhhhcC
Confidence 66777776653 35577888888886443 22 223456788899998775543
No 17
>PF12404 DUF3663: Peptidase ; InterPro: IPR008330 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family represents the peptidase B group of leucyl aminopeptidases, which are restricted to the gammaproteobacteria. They contain a C-terminal aminopeptidase catalytic domain and an N-terminal domain of unknown function. They are zinc-dependent exopeptidases (3.4.11.1 from EC) and belong to MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF). They selectively release N-terminal amino acid residues from polypeptides and proteins and are involved in the processing, catabolism and degradation of intracellular proteins [, , ]. Leucyl aminopeptidase forms a homohexamer containing two trimers stacked on top of one another []. Each monomer binds two zinc ions. The zinc-binding and catalytic sites are located within the C-terminal catalytic domain []. The same catalytic aminopeptidase domain is found in the other M17 peptidases IPR011356 from INTERPRO. These two groups of aminopeptidases differ by their N-terminal domains. The N-terminal domain in members of IPR011356 from INTERPRO has been implicated in DNA binding [, ] and it is not associated with members of this family which have a different N-terminal domain and therefore are not expected to bind DNA or be involved in transcriptional regulation. In addition, there are related proteins with the same catalytic domain and unique N-terminal sequences unrelated to any of the two N-terminal domains discussed above. For additional information please see [, , , ]. ; GO: 0004177 aminopeptidase activity, 0008235 metalloexopeptidase activity, 0030145 manganese ion binding, 0005737 cytoplasm
Probab=30.25 E-value=1.5e+02 Score=19.97 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=31.4
Q ss_pred CeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHH
Q 042002 19 NEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKT 60 (143)
Q Consensus 19 n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kA 60 (143)
-.|+++.+..+ ..|..|-..|...|.+.|.+.|-|=-..+.
T Consensus 27 a~IHl~~~~~l-~~IQrAaRkLd~qGI~~V~L~G~~W~lE~~ 67 (77)
T PF12404_consen 27 ATIHLSEGDDL-RAIQRAARKLDGQGIKNVALAGEGWDLESQ 67 (77)
T ss_pred EEEEECCCcch-HHHHHHHHHHhhCCCceEEEecCCcCHHHh
Confidence 37888777776 777888888887899999999987544443
No 18
>TIGR00106 uncharacterized protein, MTH1187 family. This protein has been crystallized in both Methanobacterium thermoautotrophicum and yeast, but its function remains unknown. Both crystal structures showed sulfate ions bound at the interface of two dimers to form a tetramer.
Probab=27.44 E-value=86 Score=21.67 Aligned_cols=33 Identities=27% Similarity=0.487 Sum_probs=26.3
Q ss_pred CCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHH
Q 042002 25 TQGRMRNYITYATTLLQEKGSNEISLKAMGRAIN 58 (143)
Q Consensus 25 ~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~ 58 (143)
....+..||..|++.|++.|. ...+++||-.|.
T Consensus 13 ~~~s~s~yVa~~i~~l~~sGl-~y~~~pm~T~IE 45 (97)
T TIGR00106 13 VGASVSSYVAAAIEVLKESGL-KYELHPMGTLIE 45 (97)
T ss_pred CCCcHHHHHHHHHHHHHHcCC-CeEecCCccEEe
Confidence 345788999999999987566 778888887654
No 19
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=24.94 E-value=2.5e+02 Score=20.57 Aligned_cols=35 Identities=11% Similarity=0.047 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHH
Q 042002 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELI 67 (143)
Q Consensus 31 ~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEil 67 (143)
..+..+..+|.+ .+.|.+.|.|..-.-|-.++..|
T Consensus 18 ~~~~~~~~~l~~--a~~I~i~G~G~S~~~A~~~~~~l 52 (179)
T TIGR03127 18 EELDKLADKIIK--AKRIFVAGAGRSGLVGKAFAMRL 52 (179)
T ss_pred HHHHHHHHHHHh--CCEEEEEecCHHHHHHHHHHHHH
Confidence 457778888864 67999999998754444444333
No 20
>KOG1402 consensus Ornithine aminotransferase [Amino acid transport and metabolism]
Probab=24.75 E-value=4.8e+02 Score=22.86 Aligned_cols=72 Identities=21% Similarity=0.282 Sum_probs=45.0
Q ss_pred CCCeEEEEEcC-hhHHHHHHHHHHHHHhcCCceeEEEEEEEEeecceeecccCCccceeeeeeeEEEEEEecCCCCCCCC
Q 042002 44 GSNEISLKAMG-RAINKTVMIAELIKRRIVGLHQNTAIGSTDITDMWEPLEEGLLPLETTRHVSVITVTLSKKELDTSST 122 (143)
Q Consensus 44 ~~~~Vvi~g~G-~AI~kAV~vAEilKrr~~gL~q~~~i~~v~i~d~~~p~~eg~~~~~~~R~vs~I~I~Lsk~~ld~~~~ 122 (143)
+.+.|.=...| .|...|+.+|-..-.+.+++-+.-.+- +.....| -.|..++| .+|.+| .+--
T Consensus 115 ~~~kvlpmnTGaEa~Eta~KLaR~wgy~~K~ip~nka~i-l~~~~nF-----------hGrT~~ai--s~s~d~--ds~~ 178 (427)
T KOG1402|consen 115 GYDKVLPMNTGAEAVETACKLARKWGYRKKNIPKNKAKI-LSAENNF-----------HGRTLGAI--SLSTDP--DSWD 178 (427)
T ss_pred CcceeeecccchhHHHHHHHHHHHHHHhhccCCccceeE-EEecccc-----------cCceeeeE--EecCCc--chhh
Confidence 57888888999 688888888876666666653221111 1122222 25666654 466666 4667
Q ss_pred CCCCCCCCC
Q 042002 123 GYQPPIPAD 131 (143)
Q Consensus 123 GyQ~P~~~~ 131 (143)
|||.|+|..
T Consensus 179 ~fgp~~P~~ 187 (427)
T KOG1402|consen 179 GFGPFLPGV 187 (427)
T ss_pred ccCCCCCCc
Confidence 999999973
No 21
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=23.01 E-value=2.3e+02 Score=18.69 Aligned_cols=54 Identities=17% Similarity=0.234 Sum_probs=42.3
Q ss_pred CCeEEEcCCCchhHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhcCC
Q 042002 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRIVG 73 (143)
Q Consensus 18 ~n~I~V~~~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~~g 73 (143)
+..|.|++.+--.+.+...-..|+. +.-|.|+=.+.+-...=.+|+.|..+.++
T Consensus 17 ~p~v~IGk~Glt~~vi~~i~~~l~~--~eLvKVk~~~~~~~~~~~~~~~l~~~t~~ 70 (84)
T PF01985_consen 17 KPVVQIGKNGLTDGVIEEIDDALEK--HELVKVKVLGNCREDRKEIAEQLAEKTGA 70 (84)
T ss_dssp --SEEE-TTSS-HHHHHHHHHHHHH--HSEEEEEETT--HHHHHHHHHHHHHHHTE
T ss_pred CCeEEECCCCCCHHHHHHHHHHHHh--CCeeEEEEccCCHHHHHHHHHHHHHHhCC
Confidence 3459999999888999999999986 67888999998888899999999999866
No 22
>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional
Probab=22.78 E-value=1.4e+02 Score=24.59 Aligned_cols=40 Identities=20% Similarity=0.429 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcC--hhHHHHHHHHHHHHHhc
Q 042002 31 NYITYATTLLQEKGSNEISLKAMG--RAINKTVMIAELIKRRI 71 (143)
Q Consensus 31 ~yv~~a~~lL~~~~~~~Vvi~g~G--~AI~kAV~vAEilKrr~ 71 (143)
+++.+++-.+...|...++| |.| ..=-|.|.+||.|-+++
T Consensus 229 ~~~~~~~~~~~~~g~~~~~i-~igCtGG~HRSV~~~e~l~~~l 270 (288)
T PRK05416 229 DLLEFWLPGYEREGKSYLTI-AIGCTGGQHRSVAIAERLAERL 270 (288)
T ss_pred HHHHHHHHHHHHcCCCEEEE-EEecCCCcccHHHHHHHHHHHH
Confidence 44445555555557778777 555 34455666666666665
No 23
>cd04236 AAK_NAGS-Urea AAK_NAGS-Urea: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the urea cycle found in animals. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate; NAG is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Ureogenic NAGS activity is dependent on the concentration of glutamate (substrate) and arginine (activator). Domain architecture of ureogenic NAGS consists of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal DUF619 domain. Members of this CD belong to the protein superfamily, the Amino Acid Kinase Family (AAKF).
Probab=22.49 E-value=1.1e+02 Score=25.05 Aligned_cols=31 Identities=6% Similarity=0.183 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcChhHHHHH
Q 042002 31 NYITYATTLLQEKGSNEISLKAMGRAINKTV 61 (143)
Q Consensus 31 ~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV 61 (143)
.-+...+.+|..-|..-|++||-|..|+...
T Consensus 54 ~~l~~dla~L~~lGl~~VlVHGggp~i~~~l 84 (271)
T cd04236 54 QSLSFGLAFLQRMDMKLLVVMGLSAPDGTNM 84 (271)
T ss_pred HHHHHHHHHHHHCCCeEEEEeCCChHHhhhh
Confidence 4677888899888999999999999998554
No 24
>COG5069 SAC6 Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
Probab=22.14 E-value=42 Score=30.34 Aligned_cols=23 Identities=26% Similarity=0.407 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCCCCCCCCcCCCCC
Q 042002 120 SSTGYQPPIPADQVKPWVENDYHG 143 (143)
Q Consensus 120 ~~~GyQ~P~~~~~v~~~~~~~~~~ 143 (143)
.+|| |+|+-.++..++.+||..|
T Consensus 355 t~~~-qe~l~~~~~~eI~e~d~e~ 377 (612)
T COG5069 355 THPG-QEPLEEEEKPEIEEFDAEG 377 (612)
T ss_pred CCcc-cchhhhhcccccCCcchhh
Confidence 6899 9999999999999998754
No 25
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=21.95 E-value=2.8e+02 Score=23.04 Aligned_cols=41 Identities=15% Similarity=0.165 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHhc
Q 042002 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVMIAELIKRRI 71 (143)
Q Consensus 31 ~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~vAEilKrr~ 71 (143)
..+..+...|.+++.+.|.|-|.|..-.-|......+.+..
T Consensus 30 ~~l~~~~~~l~~~~~~~I~~~g~GsS~~aa~~~~~~~~k~~ 70 (340)
T PRK11382 30 PLVHAIVEEMVKRDIDRIYFVACGSPLNAAQTAKHLADRFS 70 (340)
T ss_pred HHHHHHHHHHHhCCCCEEEEEEechHHHHHHHHHHHHHHHc
Confidence 34566777777667899999999999998888877776543
No 26
>PRK04531 acetylglutamate kinase; Provisional
Probab=21.45 E-value=1.5e+02 Score=25.70 Aligned_cols=32 Identities=19% Similarity=0.320 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcChhHHHHHH
Q 042002 31 NYITYATTLLQEKGSNEISLKAMGRAINKTVM 62 (143)
Q Consensus 31 ~yv~~a~~lL~~~~~~~Vvi~g~G~AI~kAV~ 62 (143)
.-+...+.+|..-|..-|++||-|..|...+.
T Consensus 53 ~~l~~dla~L~~~G~~~VlVHGggpqI~~~l~ 84 (398)
T PRK04531 53 EALASSLSFLQEVGLTPIVVHGAGPQLDAELD 84 (398)
T ss_pred HHHHHHHHHHHHCCCcEEEEECCCHHHHHHHH
Confidence 44666777888778999999999998885543
No 27
>PF03727 Hexokinase_2: Hexokinase; InterPro: IPR022673 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways []. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains []. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. Hexokinase (2.7.1.1 from EC), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and PF00349 from PFAM. Some members of the family have two copies of each of these domains. This entry represents the more C-terminal domain.; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 4DHY_A 3ID8_A 4DCH_A 3FGU_A 3QIC_A 3A0I_X 3VEY_A 3IDH_A 3VEV_A 3VF6_A ....
Probab=20.65 E-value=90 Score=24.77 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=28.9
Q ss_pred CCeEEEcC-------CCchhHHHHHHHHHHhhcCCCeEEEE------EcChhHHHHHH
Q 042002 18 ENEIRITT-------QGRMRNYITYATTLLQEKGSNEISLK------AMGRAINKTVM 62 (143)
Q Consensus 18 ~n~I~V~~-------~~~i~~yv~~a~~lL~~~~~~~Vvi~------g~G~AI~kAV~ 62 (143)
.+.+.|+- .+.++.++..++..|-..+...|.+. |.|+||.-|+.
T Consensus 184 ~~~v~VavDGSv~~~~p~f~~~l~~~l~~L~~~~~~~v~~~~~~dgsg~GAAi~AA~a 241 (243)
T PF03727_consen 184 RREVTVAVDGSVYEKYPNFRERLQEALDELLPEEGCKVEFVLSEDGSGVGAAIAAAVA 241 (243)
T ss_dssp SEEEEEEEESHHHHHSTTHHHHHHHHHHHHSTT-CEEEEEEE-SSTHHHHHHHHHHHH
T ss_pred CCceEEEEeCcceeeCHHHHHHHHHHHHHhcccccceEEEEEecCchHHHHHHHHHHh
Confidence 34566654 36678888888887765334567774 66777766653
No 28
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=20.50 E-value=3.5e+02 Score=19.85 Aligned_cols=41 Identities=22% Similarity=0.244 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhh--cCCCeEEEEEcChhHHHHHHHHHHHHHhc
Q 042002 31 NYITYATTLLQE--KGSNEISLKAMGRAINKTVMIAELIKRRI 71 (143)
Q Consensus 31 ~yv~~a~~lL~~--~~~~~Vvi~g~G~AI~kAV~vAEilKrr~ 71 (143)
..+..|..++.+ .+.+.|.+-|.|..-.-|-..+..|..++
T Consensus 17 ~~i~~a~~~i~~~i~~~~~I~i~G~G~S~~~A~~~~~~l~~~~ 59 (177)
T cd05006 17 EAIEQAAQLLAEALLNGGKILICGNGGSAADAQHFAAELVKRF 59 (177)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEeCcHHHHHHHHHHHHHhchh
Confidence 456666666643 14678999999988888888888776654
No 29
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=20.18 E-value=1.6e+02 Score=20.02 Aligned_cols=29 Identities=21% Similarity=0.418 Sum_probs=23.5
Q ss_pred CCchhHHHHHHHHHHhhcCCCeEEEEEcCh
Q 042002 26 QGRMRNYITYATTLLQEKGSNEISLKAMGR 55 (143)
Q Consensus 26 ~~~i~~yv~~a~~lL~~~~~~~Vvi~g~G~ 55 (143)
++.+..||..|+..|.+.|. ...+.+||-
T Consensus 12 ~~s~~~~V~~~i~~i~~sgl-~y~v~pm~T 40 (92)
T PF01910_consen 12 GESVSAYVAEAIEVIKESGL-KYEVGPMGT 40 (92)
T ss_dssp SSHHHHHHHHHHHHHHTSSS-EEEEETTEE
T ss_pred CCCHHHHHHHHHHHHHHcCC-ceEEcCCcc
Confidence 66799999999999987665 577788774
Done!