Query 025558
Match_columns 251
No_of_seqs 168 out of 363
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:03:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025558.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025558hhsearch_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 3.3E-47 7.1E-52 322.6 14.1 144 1-144 1-144 (179)
2 PRK04015 DNA/RNA-binding prote 99.8 2.1E-20 4.5E-25 146.2 11.4 90 16-115 2-91 (91)
3 TIGR00285 DNA-binding protein 99.8 4E-19 8.7E-24 137.9 11.2 87 18-114 1-87 (87)
4 COG1581 Ssh10b Archaeal DNA-bi 99.8 2E-18 4.4E-23 133.6 11.4 89 17-115 3-91 (91)
5 PF01918 Alba: Alba; InterPro 99.7 2.6E-16 5.7E-21 115.7 9.9 64 19-82 1-68 (70)
6 PF12328 Rpp20: Rpp20 subunit 99.4 4.5E-13 9.7E-18 112.8 9.3 93 18-111 3-144 (144)
7 KOG0921 Dosage compensation co 96.9 0.0043 9.4E-08 65.7 9.5 10 196-205 1234-1243(1282)
8 KOG0921 Dosage compensation co 96.7 0.0084 1.8E-07 63.6 9.9 24 195-218 1225-1249(1282)
9 KOG3973 Uncharacterized conser 95.8 0.057 1.2E-06 52.2 8.9 19 101-119 287-305 (465)
10 PF04232 SpoVS: Stage V sporul 92.5 4.2 9.2E-05 31.9 11.7 51 19-71 2-53 (86)
11 PF05918 API5: Apoptosis inhib 86.4 0.42 9E-06 48.6 2.0 33 59-91 429-463 (556)
12 KOG3262 H/ACA small nucleolar 86.4 5.2 0.00011 35.8 8.6 8 107-114 105-112 (215)
13 PF05918 API5: Apoptosis inhib 69.5 1.5 3.3E-05 44.7 0.0 11 61-71 384-394 (556)
14 KOG1402 Ornithine aminotransfe 57.1 56 0.0012 32.2 8.0 88 31-137 105-194 (427)
15 KOG0523 Transketolase [Carbohy 48.1 18 0.00039 37.5 3.4 53 18-75 481-533 (632)
16 PF06792 UPF0261: Uncharacteri 46.4 54 0.0012 32.4 6.2 46 17-62 184-232 (403)
17 PF02089 Palm_thioest: Palmito 46.3 24 0.00051 33.2 3.6 41 44-88 5-48 (279)
18 PRK02399 hypothetical protein; 44.4 62 0.0014 32.1 6.3 46 17-62 185-233 (406)
19 PF09363 XFP_C: XFP C-terminal 42.6 99 0.0021 27.9 6.8 42 44-89 33-75 (203)
20 COG2065 PyrR Pyrimidine operon 42.1 77 0.0017 28.1 5.9 53 43-122 28-80 (179)
21 KOG3428 Small nuclear ribonucl 41.6 15 0.00032 30.1 1.3 11 186-196 95-105 (109)
22 PRK14463 ribosomal RNA large s 37.9 1.1E+02 0.0025 29.2 6.9 42 28-69 132-173 (349)
23 COG2359 SpoVS Stage V sporulat 36.3 2.1E+02 0.0045 22.4 8.1 47 20-69 3-51 (87)
24 KOG2945 Predicted RNA-binding 33.5 44 0.00096 32.6 3.4 10 107-116 288-297 (365)
25 PRK05261 putative phosphoketol 33.2 82 0.0018 33.8 5.5 30 46-75 614-644 (785)
26 cd08982 GH43_3 Glycosyl hydrol 32.6 50 0.0011 30.4 3.5 38 102-139 248-288 (295)
27 PF02780 Transketolase_C: Tran 31.8 1.5E+02 0.0032 23.3 5.7 38 45-84 9-47 (124)
28 cd05013 SIS_RpiR RpiR-like pro 29.8 1.4E+02 0.0031 22.7 5.2 36 32-69 2-37 (139)
29 TIGR00106 uncharacterized prot 29.3 91 0.002 24.5 4.0 33 25-58 13-45 (97)
30 KOG3212 Uncharacterized conser 27.0 1.8E+02 0.0039 26.3 5.8 64 31-95 69-150 (208)
31 PRK14459 ribosomal RNA large s 26.2 2.2E+02 0.0047 27.8 6.8 59 29-87 154-226 (373)
32 PRK11634 ATP-dependent RNA hel 25.7 1.3E+02 0.0028 31.1 5.4 13 57-69 255-267 (629)
33 PF02310 B12-binding: B12 bind 24.6 2.8E+02 0.0061 21.0 6.0 39 36-74 43-82 (121)
34 COG0290 InfC Translation initi 24.5 4E+02 0.0086 23.6 7.4 59 17-75 89-150 (176)
35 cd00133 PTS_IIB PTS_IIB: subun 23.3 2.6E+02 0.0056 19.2 5.3 32 55-86 8-39 (84)
36 KOG3820 Aromatic amino acid hy 22.8 1.5E+02 0.0032 29.7 4.9 103 20-130 39-161 (461)
37 PRK14467 ribosomal RNA large s 22.6 2.4E+02 0.0052 27.1 6.2 56 31-86 134-194 (348)
38 PRK10824 glutaredoxin-4; Provi 22.5 80 0.0017 25.7 2.6 16 96-111 62-77 (115)
39 PF01985 CRS1_YhbY: CRS1 / Yhb 22.1 3.5E+02 0.0076 20.4 7.0 53 19-73 18-70 (84)
40 TIGR00232 tktlase_bact transke 21.8 1.5E+02 0.0034 30.7 5.1 25 46-70 541-565 (653)
41 PRK14455 ribosomal RNA large s 21.2 2.5E+02 0.0054 26.9 6.1 57 31-88 144-208 (356)
42 PRK11634 ATP-dependent RNA hel 20.9 1.4E+02 0.0029 30.9 4.5 8 45-52 270-277 (629)
43 COG0011 Uncharacterized conser 20.8 1.3E+02 0.0029 24.1 3.5 45 25-70 15-60 (100)
44 PRK14460 ribosomal RNA large s 20.7 1.8E+02 0.004 27.9 5.0 57 29-85 135-201 (354)
45 cd05566 PTS_IIB_galactitol PTS 20.5 3E+02 0.0066 20.1 5.3 36 48-85 4-39 (89)
46 PRK13660 hypothetical protein; 20.4 3.6E+02 0.0078 23.7 6.4 59 31-89 29-87 (182)
47 TIGR01648 hnRNP-R-Q heterogene 20.4 4.5E+02 0.0099 27.2 8.0 9 106-114 297-305 (578)
No 1
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.3e-47 Score=322.61 Aligned_cols=144 Identities=44% Similarity=0.682 Sum_probs=140.3
Q ss_pred CCCceeccCCCCCCCCCCCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCceeeeEE
Q 025558 1 MDRYQRVEKPKAEAPINENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSI 80 (251)
Q Consensus 1 Md~Y~rv~kp~~~~p~~~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I 80 (251)
||.|++|.||++++|++.|+|+|+.+++|+|||.||+.+|+++.+.+|||+|||+||+|||+||||||+|+++|||.|.|
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 EEEEecccccccccCCCcceeeeeeeEEEEEEecCCCCCCCCCCCCCCCCCCCCCCCcccccCC
Q 025558 81 GSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDTSSTGYQPPLPADQVKPWNEFEDEGE 144 (251)
Q Consensus 81 ~sv~i~d~~ePleEGld~~~~~R~VS~I~ItLSk~~lD~~~pGYQ~Pl~~~~vk~~~~~~~~~~ 144 (251)
.+++|+|.|+|++|||++++++||||+|+|+||+++||++++|||+|.|..+.+.+...+|+..
T Consensus 81 ~~~sv~d~W~p~~eGl~pl~vtRhVp~l~IlLS~deL~~~~~GyQ~P~~~p~p~~~~~~p~~~~ 144 (179)
T KOG2567|consen 81 RYTSVEDVWEPTEEGLEPLEVTRHVPMLHILLSLDELDPTSPGYQPPNPQPHPRSQPRHPYSPR 144 (179)
T ss_pred eeeehhhcccccccCccceEEeeccceEEEEEecccCCCCCCCccCCCCCCCCCCcccCCcccc
Confidence 9999999999999999999999999999999999999999999999999999998888887654
No 2
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.84 E-value=2.1e-20 Score=146.23 Aligned_cols=90 Identities=34% Similarity=0.458 Sum_probs=73.6
Q ss_pred CCCCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccccccccC
Q 025558 16 INENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEG 95 (251)
Q Consensus 16 ~~~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ePleEG 95 (251)
..+|+|+|++|+.| +||.+++.+|+ ++.++|+|||+|+||+|||+|||+||+||...++ +..+++.++-...++|
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-NYVLAVLTQFN-QGAKEVVIKARGRAISKAVDVAEIVRNRFLPDVE---IKEIKIGTEEVTSEDG 76 (91)
T ss_pred CCCCEEEEcCCcHH-HHHHHHHHHHh-CCCCeEEEEEeccccchhhhHHHHHHHhccCCeE---EEEEEeccEEeecCCC
Confidence 36799999998555 99999999999 4899999999999999999999999999865454 4455554443333455
Q ss_pred CCcceeeeeeeEEEEEEecC
Q 025558 96 LLPLETTRHVSMITITLSKK 115 (251)
Q Consensus 96 ld~~~~~R~VS~I~ItLSk~ 115 (251)
.+|+||+|+|+|+|+
T Consensus 77 -----~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 77 -----RESNVSTIEIVLEKK 91 (91)
T ss_pred -----cEEEEEEEEEEEecC
Confidence 789999999999974
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=99.80 E-value=4e-19 Score=137.86 Aligned_cols=87 Identities=34% Similarity=0.454 Sum_probs=75.6
Q ss_pred CCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccccccccCCC
Q 025558 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLL 97 (251)
Q Consensus 18 ~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ePleEGld 97 (251)
+|.|+|++|+-| +||..++.+|++ +.++|+|||+|+||+|||+|||+||+||...+ ++..+++.++-.+.++|
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 489999999777 999999999986 89999999999999999999999999986543 56777777666666677
Q ss_pred cceeeeeeeEEEEEEec
Q 025558 98 PLETTRHVSMITITLSK 114 (251)
Q Consensus 98 ~~~~~R~VS~I~ItLSk 114 (251)
.+++||+|+|+|++
T Consensus 74 ---~~~~VStIEI~l~~ 87 (87)
T TIGR00285 74 ---REVNVSTIEIVLAK 87 (87)
T ss_pred ---ceeeEEEEEEEEeC
Confidence 77899999999975
No 4
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=99.78 E-value=2e-18 Score=133.57 Aligned_cols=89 Identities=37% Similarity=0.523 Sum_probs=77.7
Q ss_pred CCCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccccccccCC
Q 025558 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGL 96 (251)
Q Consensus 17 ~~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ePleEGl 96 (251)
++|.|+|.+|+.| |||..++.+|++ +.++|+|||.|+||||||++||+|+.||-- .++|..|+|.++-...+++
T Consensus 3 ~envV~vG~KPvm-NYVlAvlt~fn~-g~~eViiKARGraIskAVDvaeivRnrf~p---~v~ik~Iki~se~~~~~~g- 76 (91)
T COG1581 3 EENVVLVGKKPVM-NYVLAVLTQFNE-GADEVIIKARGRAISKAVDVAEIVRNRFIP---DVQIKDIKIGTEELEGEDG- 76 (91)
T ss_pred CccEEEEcCcchH-HHHHHHHHHHHc-CCCEEEEEecchhhHhhHhHHHHHHHhcCC---CceEEEEEecceeeecCCC-
Confidence 4699999999777 999999999997 799999999999999999999999999832 4568888887776666666
Q ss_pred CcceeeeeeeEEEEEEecC
Q 025558 97 LPLETTRHVSMITITLSKK 115 (251)
Q Consensus 97 d~~~~~R~VS~I~ItLSk~ 115 (251)
.+++||+|+|.|.+.
T Consensus 77 ----r~~~VS~IeI~L~k~ 91 (91)
T COG1581 77 ----RTRNVSTIEIVLAKK 91 (91)
T ss_pred ----ceeeEEEEEEEEecC
Confidence 678999999999873
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=99.68 E-value=2.6e-16 Score=115.75 Aligned_cols=64 Identities=39% Similarity=0.654 Sum_probs=57.0
Q ss_pred CeEEEcCCCchHHHHHHHHHHH---hhcCCCeEEEEEcChhHHHHHHHHHHHHHHhc-CceeeeEEEE
Q 025558 19 NEIRITTQGRMRNYITYATTLL---QEKGSNEIVLKAMGRAINKTVMIAELIKRRIA-GLHQNTSIGS 82 (251)
Q Consensus 19 NeIrVt~k~~i~~yV~~Al~LL---~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~-GLhQ~t~I~s 82 (251)
|+|+|++++++.+||.+|+++| ++.++++|+|+|+|+||+|||+|||+||+++. +|||++.+.+
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 44479999999999999999999999999995 8999887764
No 6
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=99.44 E-value=4.5e-13 Score=112.81 Aligned_cols=93 Identities=25% Similarity=0.369 Sum_probs=67.4
Q ss_pred CCeEEEcCCCchHHHHHHHHHHHhhc-------------------C------------CCeEEEEEcChhHHHHHHHHHH
Q 025558 18 ENEIRITTQGRMRNYITYATTLLQEK-------------------G------------SNEIVLKAMGRAINKTVMIAEL 66 (251)
Q Consensus 18 ~NeIrVt~k~~i~~yV~~Al~LL~~~-------------------g------------~~eVvIkg~G~AIsKAV~VAEI 66 (251)
++.|||+++++|-+.|..+.+||..- . .++|+|||||+||+|||+||..
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 HHHHhcCceeeeEEEEEEecccccccc------------------cCCCcceeeeeeeEEEEE
Q 025558 67 IKRRIAGLHQNTSIGSTDITDMWEPLE------------------EGLLPLETTRHVSMITIT 111 (251)
Q Consensus 67 LKrRi~GLhQ~t~I~sv~i~d~~ePle------------------EGld~~~~~R~VS~I~It 111 (251)
|++.. ++.-.+.++||.+.|++++.+ +..++..++|.||+|+|.
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 98876 677789999999999998653 456778999999999984
No 7
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.93 E-value=0.0043 Score=65.71 Aligned_cols=10 Identities=40% Similarity=0.507 Sum_probs=4.7
Q ss_pred CcCcCCCCCC
Q 025558 196 SFRGRGWGYG 205 (251)
Q Consensus 196 ~~~g~grgy~ 205 (251)
||++-|+||+
T Consensus 1234 GfrnnggGdy 1243 (1282)
T KOG0921|consen 1234 GFRNNGGGDY 1243 (1282)
T ss_pred ccccCCCCCC
Confidence 4455445533
No 8
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.74 E-value=0.0084 Score=63.61 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=11.7
Q ss_pred CCcCcCCC-CCCCCCCCCCCCCCCC
Q 025558 195 RSFRGRGW-GYGSQSGGYYDYGELE 218 (251)
Q Consensus 195 ~~~~g~gr-gy~~~~~g~~~~~~~~ 218 (251)
.||+|-.| ||-+-.+|+|..+...
T Consensus 1225 ~GyrGvsrgGfrnnggGdyrnpggg 1249 (1282)
T KOG0921|consen 1225 NGYRGVSRGGFRNNGGGDYRNPGGG 1249 (1282)
T ss_pred CCCccccCCccccCCCCCCCCCCCC
Confidence 34555444 3444455565554433
No 9
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=95.75 E-value=0.057 Score=52.17 Aligned_cols=19 Identities=21% Similarity=0.043 Sum_probs=10.4
Q ss_pred eeeeeeEEEEEEecCCCCC
Q 025558 101 TTRHVSMITITLSKKDLDT 119 (251)
Q Consensus 101 ~~R~VS~I~ItLSk~~lD~ 119 (251)
.++..|.|+=++.-..-|.
T Consensus 287 Re~Taski~k~~igrvPDR 305 (465)
T KOG3973|consen 287 RERTASKIHKLSIGRVPDR 305 (465)
T ss_pred hhhhhhhhcccccccCCCC
Confidence 4566677776554433244
No 10
>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=92.51 E-value=4.2 Score=31.87 Aligned_cols=51 Identities=16% Similarity=0.331 Sum_probs=34.9
Q ss_pred CeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHHHh
Q 025558 19 NEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMG-RAINKTVMIAELIKRRI 71 (251)
Q Consensus 19 NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G-~AIsKAV~VAEILKrRi 71 (251)
+.++|+++++....-..-...|.+ ...|.|.++| .|+++||.-.-|-+.-+
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 468999999996666555557766 3699999999 78998888776666554
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=86.39 E-value=0.42 Score=48.64 Aligned_cols=33 Identities=21% Similarity=0.244 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHhcCceeeeEEEEE--Eecccccc
Q 025558 59 KTVMIAELIKRRIAGLHQNTSIGST--DITDMWEP 91 (251)
Q Consensus 59 KAV~VAEILKrRi~GLhQ~t~I~sv--~i~d~~eP 91 (251)
.|+.+++=|-.-+..||-..-+... .|+-.|.+
T Consensus 429 ~aLkt~~NI~~lik~L~~~pPsf~~~~~itlSWk~ 463 (556)
T PF05918_consen 429 TALKTTNNILALIKDLFHNPPSFKSTKNITLSWKE 463 (556)
T ss_dssp HHHHHHHHHHHHHCC----------------TTS-
T ss_pred HHHHHHhhHHHHHHHHhhCCcccccccccceeeee
Confidence 5666666666667777654332222 25556654
No 12
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=86.37 E-value=5.2 Score=35.85 Aligned_cols=8 Identities=25% Similarity=0.239 Sum_probs=4.1
Q ss_pred EEEEEEec
Q 025558 107 MITITLSK 114 (251)
Q Consensus 107 ~I~ItLSk 114 (251)
.++|+|+-
T Consensus 105 ~fsIK~~d 112 (215)
T KOG3262|consen 105 HFSIKPSD 112 (215)
T ss_pred EEEEecCC
Confidence 45555543
No 13
>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=69.54 E-value=1.5 Score=44.70 Aligned_cols=11 Identities=18% Similarity=0.063 Sum_probs=4.4
Q ss_pred HHHHHHHHHHh
Q 025558 61 VMIAELIKRRI 71 (251)
Q Consensus 61 V~VAEILKrRi 71 (251)
..+++.++.-+
T Consensus 384 ~yl~~~~q~yi 394 (556)
T PF05918_consen 384 QYLARGTQAYI 394 (556)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 33444444333
No 14
>KOG1402 consensus Ornithine aminotransferase [Amino acid transport and metabolism]
Probab=57.11 E-value=56 Score=32.17 Aligned_cols=88 Identities=22% Similarity=0.365 Sum_probs=54.6
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccccccccCCCcceeeeeeeEEE
Q 025558 31 NYITYATTLLQEKGSNEIVLKAMG-RAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMIT 109 (251)
Q Consensus 31 ~yV~~Al~LL~~~g~~eVvIkg~G-~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ePleEGld~~~~~R~VS~I~ 109 (251)
.|-.+..+|| +++.|.=+.+| .|+..|+.+|-..-.+.+++-+.-.+- +.....| --|..++|.
T Consensus 105 ~f~~~vt~lf---~~~kvlpmnTGaEa~Eta~KLaR~wgy~~K~ip~nka~i-l~~~~nF-----------hGrT~~ais 169 (427)
T KOG1402|consen 105 EFAEYVTKLF---GYDKVLPMNTGAEAVETACKLARKWGYRKKNIPKNKAKI-LSAENNF-----------HGRTLGAIS 169 (427)
T ss_pred HHHHHHHHhc---CcceeeecccchhHHHHHHHHHHHHHHhhccCCccceeE-EEecccc-----------cCceeeeEE
Confidence 3444444444 47888889999 688888888887777777665433222 2222222 125666654
Q ss_pred EEEecCCCCCCCCCCCCCCCC-CCCCCCC
Q 025558 110 ITLSKKDLDTSSTGYQPPLPA-DQVKPWN 137 (251)
Q Consensus 110 ItLSk~~lD~~~pGYQ~Pl~~-~~vk~~~ 137 (251)
||.++ .+-.+||+|+|- .+.-|..
T Consensus 170 --~s~d~--ds~~~fgp~~P~~~~~v~Y~ 194 (427)
T KOG1402|consen 170 --LSTDP--DSWDGFGPFLPGVVDKVPYG 194 (427)
T ss_pred --ecCCc--chhhccCCCCCCcceeeccC
Confidence 78777 455699999998 4444433
No 15
>KOG0523 consensus Transketolase [Carbohydrate transport and metabolism]
Probab=48.12 E-value=18 Score=37.47 Aligned_cols=53 Identities=21% Similarity=0.261 Sum_probs=38.4
Q ss_pred CCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCce
Q 025558 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLH 75 (251)
Q Consensus 18 ~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLh 75 (251)
.|-|.++....+ -|..+-..|++ ..+.|+|-|.|.++..|+..||.|..+ +|+
T Consensus 481 ~~~~~~~~~~~~--~igkg~~vl~~-~~~dV~LiG~Gs~v~~cl~AA~~L~~~--gi~ 533 (632)
T KOG0523|consen 481 QNLPIYNNTEIE--EIGKGKYVLQE-VEPDVILIGTGSEVQECLEAAELLSED--GIK 533 (632)
T ss_pred ccccccCCCchh--hhccccEEEec-CCCCEEEEeccHHHHHHHHHHHHHHhc--Cce
Confidence 455555544433 55555556665 458999999999999999999999955 454
No 16
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=46.37 E-value=54 Score=32.45 Aligned_cols=46 Identities=26% Similarity=0.369 Sum_probs=39.6
Q ss_pred CCCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcC---hhHHHHHH
Q 025558 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMG---RAINKTVM 62 (251)
Q Consensus 17 ~~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G---~AIsKAV~ 62 (251)
+.-.|=||.=+.-...|..+...|++.+++.+++||.| +|+.+-|.
T Consensus 184 ~kp~I~iTmfGvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li~ 232 (403)
T PF06792_consen 184 DKPLIGITMFGVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLIR 232 (403)
T ss_pred CCcEEEEECCCCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHHH
Confidence 45688899888888999999999999899999999998 78877664
No 17
>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=46.33 E-value=24 Score=33.18 Aligned_cols=41 Identities=22% Similarity=0.256 Sum_probs=23.7
Q ss_pred CCCeEEEEEcChhHH---HHHHHHHHHHHHhcCceeeeEEEEEEeccc
Q 025558 44 GSNEIVLKAMGRAIN---KTVMIAELIKRRIAGLHQNTSIGSTDITDM 88 (251)
Q Consensus 44 g~~eVvIkg~G~AIs---KAV~VAEILKrRi~GLhQ~t~I~sv~i~d~ 88 (251)
..+.|+|||||-... -.-.+.++|++.+||.+ +.+|++.+.
T Consensus 5 ~~PvViwHGmGD~~~~~~~m~~i~~~i~~~~PG~y----V~si~ig~~ 48 (279)
T PF02089_consen 5 PLPVVIWHGMGDSCCNPSSMGSIKELIEEQHPGTY----VHSIEIGND 48 (279)
T ss_dssp S--EEEE--TT--S--TTTHHHHHHHHHHHSTT------EEE--SSSS
T ss_pred CCcEEEEEcCccccCChhHHHHHHHHHHHhCCCce----EEEEEECCC
Confidence 357899999997654 35678899999999966 777777654
No 18
>PRK02399 hypothetical protein; Provisional
Probab=44.36 E-value=62 Score=32.05 Aligned_cols=46 Identities=26% Similarity=0.358 Sum_probs=37.4
Q ss_pred CCCeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcC---hhHHHHHH
Q 025558 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMG---RAINKTVM 62 (251)
Q Consensus 17 ~~NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G---~AIsKAV~ 62 (251)
+.-.|=||.=+.-..+|..+...|++++++.+|+||.| +|+.+-|.
T Consensus 185 ~kp~Ig~TmfGvTtp~v~~~~~~Le~~GyEvlVFHATG~GGraME~Li~ 233 (406)
T PRK02399 185 DKPLIGLTMFGVTTPCVQAAREELEARGYEVLVFHATGTGGRAMEKLID 233 (406)
T ss_pred CCceEEEecCCCcHHHHHHHHHHHHhCCCeEEEEcCCCCchHHHHHHHH
Confidence 34567777766667899999999999889999999998 68777653
No 19
>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=42.56 E-value=99 Score=27.92 Aligned_cols=42 Identities=19% Similarity=0.366 Sum_probs=30.2
Q ss_pred CCCeEEEEEcC-hhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccc
Q 025558 44 GSNEIVLKAMG-RAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMW 89 (251)
Q Consensus 44 g~~eVvIkg~G-~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ 89 (251)
....|||-+.| -..--+|..|.+|++.+|+|. |..|.|.|-.
T Consensus 33 ~ePDVVlA~aGd~pT~E~lAA~~lLr~~~P~lk----iRvVNVvDLm 75 (203)
T PF09363_consen 33 EEPDVVLACAGDVPTLEVLAAASLLREHFPELK----IRVVNVVDLM 75 (203)
T ss_dssp TT-SEEEEEESHHHHHHHHHHHHHHHHT--T------EEEEEESBGG
T ss_pred CCCCEEEEecCchhhHHHHHHHHHHHHhccCce----EEEEEEeEcc
Confidence 46889999999 466678999999999999876 7777777654
No 20
>COG2065 PyrR Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=42.08 E-value=77 Score=28.08 Aligned_cols=53 Identities=30% Similarity=0.422 Sum_probs=35.7
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccccccccCCCcceeeeeeeEEEEEEecCCCCCCCC
Q 025558 43 KGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDTSST 122 (251)
Q Consensus 43 ~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ePleEGld~~~~~R~VS~I~ItLSk~~lD~~~p 122 (251)
++.+.++|-|+= ++-|.+||.|++++..|.+ .+-.+-.|.|||+++.|..+.+
T Consensus 28 k~~~~~vlvGIk---trGv~lA~rl~~~i~~~Eg------------------------~~vp~g~lDIt~yRDDl~~~~~ 80 (179)
T COG2065 28 KGLDNLVLVGIK---TRGVPLAERLAERIEELEG------------------------IEVPVGELDITLYRDDLTQKGP 80 (179)
T ss_pred CCCCceEEEeEe---cCCHHHHHHHHHHHHHHhC------------------------CCCCeeeEEeEEeechhhhcCc
Confidence 367788887763 4567888888888653321 1123457899999998877654
No 21
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=41.63 E-value=15 Score=30.13 Aligned_cols=11 Identities=91% Similarity=1.721 Sum_probs=5.4
Q ss_pred CCCcccccCCC
Q 025558 186 GRGRGRGRGRS 196 (251)
Q Consensus 186 g~grgrgrg~~ 196 (251)
+|+++||+|+|
T Consensus 95 ~rgrgrg~Grg 105 (109)
T KOG3428|consen 95 GRGRGRGRGRG 105 (109)
T ss_pred ccccccccccC
Confidence 45555554443
No 22
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=37.91 E-value=1.1e+02 Score=29.20 Aligned_cols=42 Identities=10% Similarity=0.170 Sum_probs=27.7
Q ss_pred chHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHH
Q 025558 28 RMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKR 69 (251)
Q Consensus 28 ~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKr 69 (251)
.....+.....++.....+.|+|.|||.-..+--.|.+.|+.
T Consensus 132 t~~EI~~qv~~~~~~~~i~~IvfmG~GEPl~n~~~vi~~l~~ 173 (349)
T PRK14463 132 TTAEIVNQVCAVKRDVPVRNIVFMGMGEPLANLDNVIPALQI 173 (349)
T ss_pred CHHHHHHHHHHHHhcCCccEEEEecCCcchhcHHHHHHHHHH
Confidence 344455555555444468999999999877666566666664
No 23
>COG2359 SpoVS Stage V sporulation protein SpoVS [Function unknown]
Probab=36.35 E-value=2.1e+02 Score=22.37 Aligned_cols=47 Identities=19% Similarity=0.369 Sum_probs=32.5
Q ss_pred eEEEcCCCchHHHHHHHHH-HHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHH
Q 025558 20 EIRITTQGRMRNYITYATT-LLQEKGSNEIVLKAMG-RAINKTVMIAELIKR 69 (251)
Q Consensus 20 eIrVt~k~~i~~yV~~Al~-LL~~~g~~eVvIkg~G-~AIsKAV~VAEILKr 69 (251)
.+.|++++.- |-|.=|+. +|.+ ...+.|.++| .|++.||...-|-+.
T Consensus 3 vLKVsa~S~P-nsVAGAlAgvlr~--~g~aEiQAiGagAvNQaVKAiAiaRg 51 (87)
T COG2359 3 VLKVSAKSNP-NSVAGALAGVLRE--RGKAEIQAIGAGAVNQAVKAIAIARG 51 (87)
T ss_pred eEEeccCCCc-chHHHHHHHHHHh--cCceeeeeechHHHHHHHHHHHHHhh
Confidence 4678888777 55555555 6665 5688889999 588888875544433
No 24
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=33.54 E-value=44 Score=32.64 Aligned_cols=10 Identities=20% Similarity=0.285 Sum_probs=4.3
Q ss_pred EEEEEEecCC
Q 025558 107 MITITLSKKD 116 (251)
Q Consensus 107 ~I~ItLSk~~ 116 (251)
+|.|+.+++.
T Consensus 288 ~~v~~~~k~~ 297 (365)
T KOG2945|consen 288 TVVLHSSKDR 297 (365)
T ss_pred ceeeeccccc
Confidence 4444444443
No 25
>PRK05261 putative phosphoketolase; Provisional
Probab=33.20 E-value=82 Score=33.77 Aligned_cols=30 Identities=23% Similarity=0.427 Sum_probs=28.2
Q ss_pred CeEEEEEcChhHHH-HHHHHHHHHHHhcCce
Q 025558 46 NEIVLKAMGRAINK-TVMIAELIKRRIAGLH 75 (251)
Q Consensus 46 ~eVvIkg~G~AIsK-AV~VAEILKrRi~GLh 75 (251)
..|+|-|.|.-+.. ||..|++|+..+|+|.
T Consensus 614 pDvvL~atGsev~leAlaAa~~L~~~~pgik 644 (785)
T PRK05261 614 PDVVLACAGDVPTLETLAAADLLREHFPDLK 644 (785)
T ss_pred CCEEEEEeCcHhhHHHHHHHHHHHhhCCCCC
Confidence 58999999999999 9999999999999876
No 26
>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=32.63 E-value=50 Score=30.42 Aligned_cols=38 Identities=16% Similarity=0.345 Sum_probs=27.6
Q ss_pred eeeeeEEEEEEecC---CCCCCCCCCCCCCCCCCCCCCCcc
Q 025558 102 TRHVSMITITLSKK---DLDTSSTGYQPPLPADQVKPWNEF 139 (251)
Q Consensus 102 ~R~VS~I~ItLSk~---~lD~~~pGYQ~Pl~~~~vk~~~~~ 139 (251)
.|++....|+...+ .+++.-..||.|||++++||+++.
T Consensus 248 ~R~~~i~pv~~~~dG~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 (295)
T cd08982 248 ERRIGLFPAFFDEDGVLYCNTAFGDYPMILPDKKIDPPEDL 288 (295)
T ss_pred CceeEEEEEEECCCCcEEEcccCCcCcccCCCCCCcccccc
Confidence 46665556665443 367777899999999999998543
No 27
>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=31.84 E-value=1.5e+02 Score=23.30 Aligned_cols=38 Identities=16% Similarity=0.336 Sum_probs=29.0
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHHHHhcCce-eeeEEEEEE
Q 025558 45 SNEIVLKAMGRAINKTVMIAELIKRRIAGLH-QNTSIGSTD 84 (251)
Q Consensus 45 ~~eVvIkg~G~AIsKAV~VAEILKrRi~GLh-Q~t~I~sv~ 84 (251)
-+.|+|-++|..+..|+..|++|+.+ |+. ..+.+.++.
T Consensus 9 g~di~iia~G~~~~~al~A~~~L~~~--Gi~~~vi~~~~i~ 47 (124)
T PF02780_consen 9 GADITIIAYGSMVEEALEAAEELEEE--GIKAGVIDLRTIK 47 (124)
T ss_dssp SSSEEEEEETTHHHHHHHHHHHHHHT--TCEEEEEEEEEEE
T ss_pred CCCEEEEeehHHHHHHHHHHHHHHHc--CCceeEEeeEEEe
Confidence 46899999999999999999999998 543 133444443
No 28
>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=29.75 E-value=1.4e+02 Score=22.69 Aligned_cols=36 Identities=19% Similarity=0.175 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHH
Q 025558 32 YITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKR 69 (251)
Q Consensus 32 yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKr 69 (251)
.|..+.++|.+ .+.|.|.|.|....-|..++..|+.
T Consensus 2 ~i~~~~~~i~~--~~~i~i~g~g~s~~~a~~~~~~l~~ 37 (139)
T cd05013 2 ALEKAVDLLAK--ARRIYIFGVGSSGLVAEYLAYKLLR 37 (139)
T ss_pred HHHHHHHHHHh--CCEEEEEEcCchHHHHHHHHHHHHH
Confidence 46677888875 6899999999977777777777665
No 29
>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=29.29 E-value=91 Score=24.54 Aligned_cols=33 Identities=27% Similarity=0.466 Sum_probs=27.2
Q ss_pred CCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHH
Q 025558 25 TQGRMRNYITYATTLLQEKGSNEIVLKAMGRAIN 58 (251)
Q Consensus 25 ~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIs 58 (251)
....+..||..|+++|++.+. ...+++||-.|.
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 345788999999999997666 788999997765
No 30
>KOG3212 consensus Uncharacterized conserved protein related to IojAP [Function unknown]
Probab=27.05 E-value=1.8e+02 Score=26.32 Aligned_cols=64 Identities=17% Similarity=0.250 Sum_probs=44.1
Q ss_pred HHHHHHHHHHhhcCCCeEEE--------------EEcChhHHHHHHHHHHHHHHhcCcee----eeEEEEEEeccccccc
Q 025558 31 NYITYATTLLQEKGSNEIVL--------------KAMGRAINKTVMIAELIKRRIAGLHQ----NTSIGSTDITDMWEPL 92 (251)
Q Consensus 31 ~yV~~Al~LL~~~g~~eVvI--------------kg~G~AIsKAV~VAEILKrRi~GLhQ----~t~I~sv~i~d~~ePl 92 (251)
.+|...++||.+...+.|.+ -+.|..--.+.++||-|.++++-+.| .+.|.+++ .++|...
T Consensus 69 ~~ve~vv~lLrdenadDVfVi~vpeem~y~dh~VIcSgrs~rhl~aiAe~lv~m~Kik~~kgd~hvriegk~-s~dW~v~ 147 (208)
T KOG3212|consen 69 LTVEEVVKLLRDENADDVFVIPVPEEMFYADHTVICSGRSDRHLRAIAEALVYMAKIKSQKGDKHVRIEGKQ-SSDWIVI 147 (208)
T ss_pred hhHHHHHHHHHhcccCceEEEeccccceeeeeEEEEecCchHHHHHHHHHHHHHHHHhhcCCCccccccccc-CCCeEEE
Confidence 56999999998766665543 57787777788888888777643321 25666666 6778766
Q ss_pred ccC
Q 025558 93 EEG 95 (251)
Q Consensus 93 eEG 95 (251)
+-|
T Consensus 148 D~g 150 (208)
T KOG3212|consen 148 DYG 150 (208)
T ss_pred Eec
Confidence 544
No 31
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=26.20 E-value=2.2e+02 Score=27.77 Aligned_cols=59 Identities=15% Similarity=0.316 Sum_probs=33.5
Q ss_pred hHHHHHHHHHHHhhc-------CCCeEEEEEcChhHH---HHHHHHHHHHHHh---cCc-eeeeEEEEEEecc
Q 025558 29 MRNYITYATTLLQEK-------GSNEIVLKAMGRAIN---KTVMIAELIKRRI---AGL-HQNTSIGSTDITD 87 (251)
Q Consensus 29 i~~yV~~Al~LL~~~-------g~~eVvIkg~G~AIs---KAV~VAEILKrRi---~GL-hQ~t~I~sv~i~d 87 (251)
|-.+|..+...|... ....|+|.|||...- ..+.+.++|+... -++ +-.++|+|+-+..
T Consensus 154 Iv~Qv~~~~~~~~~~~~~~~~~~i~nVvfmGmGEPLlN~d~V~~~i~~l~~~~~~g~gis~r~ITvST~Gl~~ 226 (373)
T PRK14459 154 IVEQVRAAARALRDGEVPGGPGRLSNVVFMGMGEPLANYKRVVAAVRRITAPAPEGLGISARNVTVSTVGLVP 226 (373)
T ss_pred HHHHHHHHHHHhhhcccccCCCceeEEEEecCCcchhhHHHHHHHHHHHhCcccccCCccCCEEEEECcCchh
Confidence 335555555555431 256799999997664 4555666666631 233 1146666664443
No 32
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=25.72 E-value=1.3e+02 Score=31.05 Aligned_cols=13 Identities=38% Similarity=0.519 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHH
Q 025558 57 INKTVMIAELIKR 69 (251)
Q Consensus 57 IsKAV~VAEILKr 69 (251)
...|..|++.|+.
T Consensus 255 k~~a~~l~~~L~~ 267 (629)
T PRK11634 255 KNATLEVAEALER 267 (629)
T ss_pred HHHHHHHHHHHHh
Confidence 4445555555554
No 33
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=24.61 E-value=2.8e+02 Score=21.05 Aligned_cols=39 Identities=15% Similarity=0.227 Sum_probs=30.6
Q ss_pred HHHHHhhcCCCeEEEEE-cChhHHHHHHHHHHHHHHhcCc
Q 025558 36 ATTLLQEKGSNEIVLKA-MGRAINKTVMIAELIKRRIAGL 74 (251)
Q Consensus 36 Al~LL~~~g~~eVvIkg-~G~AIsKAV~VAEILKrRi~GL 74 (251)
.+..+.+...+-|.|+. +...+..+..+++.+|+..++.
T Consensus 43 l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~ 82 (121)
T PF02310_consen 43 LVEALRAERPDVVGISVSMTPNLPEAKRLARAIKERNPNI 82 (121)
T ss_dssp HHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTS
T ss_pred HHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCC
Confidence 33344444678999999 9999999999999999987763
No 34
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=24.45 E-value=4e+02 Score=23.65 Aligned_cols=59 Identities=14% Similarity=0.285 Sum_probs=42.2
Q ss_pred CCCeEEEcCC---CchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCce
Q 025558 17 NENEIRITTQ---GRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLH 75 (251)
Q Consensus 17 ~~NeIrVt~k---~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLh 75 (251)
.-.||+++-+ ..+..=+..|..+|++...-.|+|+-.|+.+...=.-..+|.+-...|.
T Consensus 89 ~vKEik~rp~Id~hD~~~K~k~~~rFLe~GdkVKvtirfrGRe~~h~elG~~~l~r~~~~~~ 150 (176)
T COG0290 89 QVKEIKLRPKIDEHDYETKLKNARRFLEKGDKVKVTIRFRGREMAHQELGVKVLERVAEDLE 150 (176)
T ss_pred EEEEEEeecCcCcchHHHHHHHHHHHHHCCCeEEEEEEEechhhhhHHHHHHHHHHHHHHhh
Confidence 3467777755 3455556778888887556789999999999988777777766654443
No 35
>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=23.30 E-value=2.6e+02 Score=19.24 Aligned_cols=32 Identities=16% Similarity=0.313 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHHHHHHhcCceeeeEEEEEEec
Q 025558 55 RAINKTVMIAELIKRRIAGLHQNTSIGSTDIT 86 (251)
Q Consensus 55 ~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~ 86 (251)
..+..+..+++.||+.++.+.....++..++.
T Consensus 8 ~G~~~s~~l~~~l~~~~~~~~~~~~~~~~~~~ 39 (84)
T cd00133 8 SGIGSSSMLAEKLEKAAKELGIEVKVEAQGLS 39 (84)
T ss_pred CcHhHHHHHHHHHHHHHHHCCCeEEEEEcccc
Confidence 34455567788888888766655555554443
No 36
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=22.79 E-value=1.5e+02 Score=29.71 Aligned_cols=103 Identities=16% Similarity=0.162 Sum_probs=52.4
Q ss_pred eEEEcCCCchHHHHHHHHHHHhhcCCCeEEE---------------EEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEE
Q 025558 20 EIRITTQGRMRNYITYATTLLQEKGSNEIVL---------------KAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTD 84 (251)
Q Consensus 20 eIrVt~k~~i~~yV~~Al~LL~~~g~~eVvI---------------kg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~ 84 (251)
.|.+.+. ++ +-+..++++|++...+-..| ...-..=.+-+.++++|+....-|+- +.+-+.+
T Consensus 39 ~if~~r~-~~-~~l~~~Lk~f~~~~vnl~HiEsR~s~~~~~~~evlv~~~~~~~~l~~~i~~lrq~~~~~~~-~s~~~~~ 115 (461)
T KOG3820|consen 39 LIFSLRN-KV-GALARALKAFEEFHVNLLHIESRPSERRSSGYEVLVELDATRGQLIQAIELLRQNHVALSY-FSSFNRD 115 (461)
T ss_pred EEEEecc-cc-hHHHHHHHHhhhcCceEEEeecccccccCCCceEEEeeccchhhHHHHHHHHHHhccccee-cccchhh
Confidence 4555544 34 77888899987642222112 12222223556677888887543331 1111111
Q ss_pred ecccccccccCCCcceeeeeeeEE-----EEEEecCCCCCCCCCCCCCCCC
Q 025558 85 ITDMWEPLEEGLLPLETTRHVSMI-----TITLSKKDLDTSSTGYQPPLPA 130 (251)
Q Consensus 85 i~d~~ePleEGld~~~~~R~VS~I-----~ItLSk~~lD~~~pGYQ~Pl~~ 130 (251)
+.+. ......=..|+||-+ .|+.+-.+||..|||+--|...
T Consensus 116 ~~~~-----~~~~vpWFPr~IsdLD~can~vl~Yg~eLDadHPGFkD~vYR 161 (461)
T KOG3820|consen 116 LKDN-----KNTSVPWFPRKISDLDQCANRVLKYGPELDADHPGFKDPVYR 161 (461)
T ss_pred hhhc-----cCCCCCccccchhHHHHHHHHHhhcCCCCCCCCCCCCCHHHH
Confidence 1110 000111133555544 2666777999999999877543
No 37
>PRK14467 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.55 E-value=2.4e+02 Score=27.09 Aligned_cols=56 Identities=16% Similarity=0.273 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHh--cCc---eeeeEEEEEEec
Q 025558 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRI--AGL---HQNTSIGSTDIT 86 (251)
Q Consensus 31 ~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi--~GL---hQ~t~I~sv~i~ 86 (251)
.+|..+...|.......||+.|||....+.=.|.+.|+.-. .|| +-.+.|+|+-+.
T Consensus 134 ~Qv~~~~~~~~~~~v~~VvfmGmGEPL~N~d~v~~~l~~l~~~~gl~~~~r~itvsT~G~~ 194 (348)
T PRK14467 134 DQYIQVQKFLGENRIRNVVFMGMGEPLANYENVRKAVQIMTSPWGLDLSKRRITISTSGII 194 (348)
T ss_pred HHHHHHHHHhccCCCCeEEEEccChhhcCHHHHHHHHHHHcChhccCcCCCcEEEECCCCh
Confidence 34444444443334689999999987775555544444432 244 113566665544
No 38
>PRK10824 glutaredoxin-4; Provisional
Probab=22.52 E-value=80 Score=25.67 Aligned_cols=16 Identities=6% Similarity=-0.022 Sum_probs=9.2
Q ss_pred CCcceeeeeeeEEEEE
Q 025558 96 LLPLETTRHVSMITIT 111 (251)
Q Consensus 96 ld~~~~~R~VS~I~It 111 (251)
|..++-.+.||.|.|-
T Consensus 62 l~~~sg~~TVPQIFI~ 77 (115)
T PRK10824 62 LPKYANWPTFPQLWVD 77 (115)
T ss_pred HHHHhCCCCCCeEEEC
Confidence 3334455677777764
No 39
>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=22.05 E-value=3.5e+02 Score=20.36 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=42.4
Q ss_pred CeEEEcCCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcC
Q 025558 19 NEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAG 73 (251)
Q Consensus 19 NeIrVt~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~G 73 (251)
..|.|.+++-..+.|...-..|+. +.-|.|+-.+.+-...-.+|+.|..+...
T Consensus 18 p~v~IGk~Glt~~vi~~i~~~l~~--~eLvKVk~~~~~~~~~~~~~~~l~~~t~~ 70 (84)
T PF01985_consen 18 PVVQIGKNGLTDGVIEEIDDALEK--HELVKVKVLGNCREDRKEIAEQLAEKTGA 70 (84)
T ss_dssp -SEEE-TTSS-HHHHHHHHHHHHH--HSEEEEEETT--HHHHHHHHHHHHHHHTE
T ss_pred CeEEECCCCCCHHHHHHHHHHHHh--CCeeEEEEccCCHHHHHHHHHHHHHHhCC
Confidence 459999999988999999999986 68899999998888889999999999764
No 40
>TIGR00232 tktlase_bact transketolase, bacterial and yeast. This model is designed to capture orthologs of bacterial transketolases. The group includes two from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous.
Probab=21.80 E-value=1.5e+02 Score=30.66 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=23.2
Q ss_pred CeEEEEEcChhHHHHHHHHHHHHHH
Q 025558 46 NEIVLKAMGRAINKTVMIAELIKRR 70 (251)
Q Consensus 46 ~eVvIkg~G~AIsKAV~VAEILKrR 70 (251)
+.|+|-++|.-+..|+.+|++|+.+
T Consensus 541 ~dv~iia~G~~v~~al~Aa~~L~~~ 565 (653)
T TIGR00232 541 PDIILIATGSEVSLAVEAAKKLAAE 565 (653)
T ss_pred CCEEEEEeChHHHHHHHHHHHHHhc
Confidence 6899999999999999999999865
No 41
>PRK14455 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.23 E-value=2.5e+02 Score=26.94 Aligned_cols=57 Identities=16% Similarity=0.341 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhh--cCCCeEEEEEcChhHHH---HHHHHHHHHHHhcCce---eeeEEEEEEeccc
Q 025558 31 NYITYATTLLQE--KGSNEIVLKAMGRAINK---TVMIAELIKRRIAGLH---QNTSIGSTDITDM 88 (251)
Q Consensus 31 ~yV~~Al~LL~~--~g~~eVvIkg~G~AIsK---AV~VAEILKrRi~GLh---Q~t~I~sv~i~d~ 88 (251)
.+|..+...|.. .+.+.|++.|||....+ .+.+.++|+... |+. -.+.|+|.-+...
T Consensus 144 ~qv~~~~~~~~~~g~~v~~Vv~~GmGEPLln~~~v~~~l~~l~~~~-g~~~s~r~itvsT~G~~~~ 208 (356)
T PRK14455 144 AQVMLVQKYLDETEERVSHIVVMGIGEPFDNYDNVMDFLRIINDDK-GLAIGARHITVSTSGIAPK 208 (356)
T ss_pred HHHHHHHHHHhhcCCCcceEEEeccccccCCHHHHHHHHHHHhccc-CcccCCCceEEEecCchHh
Confidence 444444445543 24789999999987654 555555665431 441 1345555544433
No 42
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=20.91 E-value=1.4e+02 Score=30.93 Aligned_cols=8 Identities=25% Similarity=0.281 Sum_probs=3.1
Q ss_pred CCeEEEEE
Q 025558 45 SNEIVLKA 52 (251)
Q Consensus 45 ~~eVvIkg 52 (251)
+..+.||+
T Consensus 270 ~~~~~lhg 277 (629)
T PRK11634 270 YNSAALNG 277 (629)
T ss_pred CCEEEeeC
Confidence 33333333
No 43
>COG0011 Uncharacterized conserved protein [Function unknown]
Probab=20.77 E-value=1.3e+02 Score=24.14 Aligned_cols=45 Identities=24% Similarity=0.389 Sum_probs=30.4
Q ss_pred CCCchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHH-HHHHHHHHH
Q 025558 25 TQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTV-MIAELIKRR 70 (251)
Q Consensus 25 ~k~~i~~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV-~VAEILKrR 70 (251)
....+..||..|++.|.+.+. .-.++.||--|.=-+ .|.++||.-
T Consensus 15 ~~~svs~yVa~~i~~lk~~gl-ky~~~pm~T~iEg~~del~~~ik~~ 60 (100)
T COG0011 15 GGPSVSKYVAEAIEILKESGL-KYQLGPMGTVIEGELDELMEAVKEA 60 (100)
T ss_pred CCCCHHHHHHHHHHHHHHcCC-ceeecCcceEEEecHHHHHHHHHHH
Confidence 345589999999999997555 567788886555422 244455544
No 44
>PRK14460 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.67 E-value=1.8e+02 Score=27.86 Aligned_cols=57 Identities=14% Similarity=0.251 Sum_probs=33.5
Q ss_pred hHHHHHHHHHHHhhc--C---CCeEEEEEcChhHHHHHHHHHHHHHHh--cCce---eeeEEEEEEe
Q 025558 29 MRNYITYATTLLQEK--G---SNEIVLKAMGRAINKTVMIAELIKRRI--AGLH---QNTSIGSTDI 85 (251)
Q Consensus 29 i~~yV~~Al~LL~~~--g---~~eVvIkg~G~AIsKAV~VAEILKrRi--~GLh---Q~t~I~sv~i 85 (251)
|-.+|..+...+.+. + .+.|++.|||...-+.-.|.+.|+.-. .||+ ..+.|+|.-+
T Consensus 135 I~~qv~~~~~~~~~~g~g~~~i~nIvfmGmGEPLln~~~v~~~l~~l~~~~Gl~~~~r~itvsT~G~ 201 (354)
T PRK14460 135 ILGQVLVAREHLGDNGPDHPILRNLVFMGMGEPLLNLDEVMRSLRTLNNEKGLNFSPRRITVSTCGI 201 (354)
T ss_pred HHHHHHHHHHHHhhccCCCcceeEEEEecCCcccCCHHHHHHHHHHHhhhhccCCCCCeEEEECCCC
Confidence 334554445555421 1 689999999987766555666666432 2554 2355665544
No 45
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. 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 galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=20.49 E-value=3e+02 Score=20.11 Aligned_cols=36 Identities=17% Similarity=0.222 Sum_probs=20.7
Q ss_pred EEEEEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEEe
Q 025558 48 IVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDI 85 (251)
Q Consensus 48 VvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i 85 (251)
+++-+.|.+. +..+++.||+.++.+.....+..+.+
T Consensus 4 livC~~G~~t--S~~l~~~i~~~~~~~~i~~~v~~~~~ 39 (89)
T cd05566 4 LVACGTGVAT--STVVASKVKELLKENGIDVKVEQCKI 39 (89)
T ss_pred EEECCCCccH--HHHHHHHHHHHHHHCCCceEEEEecH
Confidence 3444455444 45667778888866555555544444
No 46
>PRK13660 hypothetical protein; Provisional
Probab=20.36 E-value=3.6e+02 Score=23.72 Aligned_cols=59 Identities=12% Similarity=0.073 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhcCceeeeEEEEEEecccc
Q 025558 31 NYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMW 89 (251)
Q Consensus 31 ~yV~~Al~LL~~~g~~eVvIkg~G~AIsKAV~VAEILKrRi~GLhQ~t~I~sv~i~d~~ 89 (251)
.-|...+..|-+++..-+++.|-=-.=.-|..||.-||..++.|.-.+-+=...-.+.|
T Consensus 29 ~aL~~~l~~~~e~G~~wfi~ggalG~d~wAaEvvl~LK~~yp~lkL~~~~PF~~q~~~W 87 (182)
T PRK13660 29 KAIKRKLIALLEEGLEWVIISGQLGVELWAAEVVLELKEEYPDLKLAVITPFEEHGENW 87 (182)
T ss_pred HHHHHHHHHHHHCCCCEEEECCcchHHHHHHHHHHHHHhhCCCeEEEEEeCccchhhcC
Confidence 33444444333446655544332122235778889999999987754444444444555
No 47
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=20.35 E-value=4.5e+02 Score=27.20 Aligned_cols=9 Identities=56% Similarity=0.667 Sum_probs=5.1
Q ss_pred eEEEEEEec
Q 025558 106 SMITITLSK 114 (251)
Q Consensus 106 S~I~ItLSk 114 (251)
..|+|.+++
T Consensus 297 r~I~V~~Ak 305 (578)
T TIGR01648 297 SEIEVTLAK 305 (578)
T ss_pred EEEEEEEcc
Confidence 456666654
Done!