Query 025950
Match_columns 245
No_of_seqs 172 out of 378
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 11:24:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025950.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025950hhsearch_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 3.4E-46 7.5E-51 314.3 13.4 144 1-144 1-144 (179)
2 PRK04015 DNA/RNA-binding prote 99.8 1.5E-20 3.3E-25 146.1 11.3 90 16-115 2-91 (91)
3 TIGR00285 DNA-binding protein 99.8 2.6E-19 5.6E-24 138.0 11.2 87 18-114 1-87 (87)
4 COG1581 Ssh10b Archaeal DNA-bi 99.8 1.1E-18 2.4E-23 134.0 11.4 89 17-115 3-91 (91)
5 PF01918 Alba: Alba; InterPro 99.7 1.6E-16 3.5E-21 116.4 9.9 64 19-82 1-68 (70)
6 PF12328 Rpp20: Rpp20 subunit 99.4 6.3E-13 1.4E-17 111.3 9.5 93 18-111 3-144 (144)
7 KOG0921 Dosage compensation co 96.9 0.0049 1.1E-07 64.9 9.3 9 218-226 1258-1266(1282)
8 KOG3973 Uncharacterized conser 95.7 0.096 2.1E-06 50.3 10.2 14 101-114 287-300 (465)
9 PF04232 SpoVS: Stage V sporul 90.6 4.3 9.3E-05 31.6 9.7 66 19-86 2-72 (86)
10 PF05918 API5: Apoptosis inhib 82.8 0.39 8.4E-06 48.6 0.0 19 59-77 429-447 (556)
11 KOG3262 H/ACA small nucleolar 78.4 10 0.00023 33.7 7.4 9 106-114 104-112 (215)
12 PF09363 XFP_C: XFP C-terminal 54.7 50 0.0011 29.6 6.8 42 44-89 33-75 (203)
13 PF06792 UPF0261: Uncharacteri 42.6 67 0.0015 31.6 6.2 45 17-61 184-231 (403)
14 PRK05261 putative phosphoketol 42.4 41 0.00089 35.7 5.0 29 46-74 614-643 (785)
15 PRK02399 hypothetical protein; 41.0 77 0.0017 31.2 6.3 45 17-61 185-232 (406)
16 KOG0523 Transketolase [Carbohy 40.8 30 0.00066 35.7 3.7 50 18-70 481-530 (632)
17 COG0290 InfC Translation initi 40.6 1.4E+02 0.003 26.3 7.2 71 18-95 90-163 (176)
18 KOG3428 Small nuclear ribonucl 39.8 16 0.00035 29.6 1.3 10 180-189 95-104 (109)
19 PF02780 Transketolase_C: Tran 38.3 1E+02 0.0022 24.1 5.7 26 45-70 9-34 (124)
20 KOG1402 Ornithine aminotransfe 35.0 2.1E+02 0.0046 28.1 8.1 81 32-131 106-187 (427)
21 cd08982 GH43_3 Glycosyl hydrol 34.7 44 0.00095 30.6 3.5 38 102-139 248-288 (295)
22 PRK14463 ribosomal RNA large s 34.0 1.3E+02 0.0027 28.7 6.5 42 28-69 132-173 (349)
23 TIGR00106 uncharacterized prot 33.5 73 0.0016 24.9 4.1 33 25-58 13-45 (97)
24 COG2065 PyrR Pyrimidine operon 31.5 61 0.0013 28.5 3.6 53 43-122 28-80 (179)
25 PRK10824 glutaredoxin-4; Provi 29.3 58 0.0013 26.3 3.0 16 96-111 62-77 (115)
26 PF02089 Palm_thioest: Palmito 29.1 65 0.0014 30.1 3.6 41 44-88 5-48 (279)
27 COG2359 SpoVS Stage V sporulat 28.7 2.8E+02 0.006 21.5 8.1 65 20-87 3-73 (87)
28 TIGR00232 tktlase_bact transke 27.7 1E+02 0.0022 31.9 5.0 25 46-70 541-565 (653)
29 cd05013 SIS_RpiR RpiR-like pro 27.2 1.6E+02 0.0036 22.2 5.1 36 32-69 2-37 (139)
30 PRK14459 ribosomal RNA large s 27.2 2.3E+02 0.0049 27.5 7.1 59 29-87 154-226 (373)
31 PF01985 CRS1_YhbY: CRS1 / Yhb 26.6 2.8E+02 0.006 20.8 6.9 53 19-73 18-70 (84)
32 cd00133 PTS_IIB PTS_IIB: subun 25.8 2.2E+02 0.0049 19.4 5.3 32 55-86 8-39 (84)
33 COG1416 Uncharacterized conser 24.3 99 0.0022 25.3 3.4 44 19-62 6-49 (112)
34 cd08499 PBP2_Ylib_like The sub 23.9 1.3E+02 0.0029 28.5 4.8 52 32-85 302-356 (474)
35 cd08504 PBP2_OppA The substrat 23.9 1.9E+02 0.004 27.6 5.8 50 33-84 325-381 (498)
36 PF02310 B12-binding: B12 bind 23.3 3.1E+02 0.0067 20.7 6.0 40 35-74 42-82 (121)
37 CHL00199 infC translation init 22.7 5.3E+02 0.011 22.7 8.0 56 17-72 95-153 (182)
38 cd05566 PTS_IIB_galactitol PTS 20.7 2.9E+02 0.0064 20.1 5.2 36 48-85 4-39 (89)
39 CHL00144 odpB pyruvate dehydro 20.6 1.2E+02 0.0026 28.5 3.8 25 46-70 202-226 (327)
40 PF00496 SBP_bac_5: Bacterial 20.5 1.9E+02 0.0041 26.1 4.9 51 33-85 269-332 (374)
41 PRK15062 hydrogenase isoenzyme 20.2 2.5E+02 0.0055 27.3 5.8 51 19-75 110-163 (364)
No 1
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.4e-46 Score=314.34 Aligned_cols=144 Identities=44% Similarity=0.682 Sum_probs=139.4
Q ss_pred CCCceeccCCCCCCCCCCCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEE
Q 025950 1 MDRYQRVEKPKAEAPINENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSI 80 (245)
Q Consensus 1 Md~Y~rV~kp~~~~p~~~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I 80 (245)
||.|++|.||.+++|++.|+|||+.+++++|||.||+.+|+++.++.|||+|||+||+|+|+||||||+|+++|||+|.|
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 025950 81 GSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDTSSTGYQPPLPADQVKPWNEFEDEGE 144 (245)
Q Consensus 81 ~sv~i~d~~ePleEGl~~~~~~R~Vs~I~ItLsk~~lD~~~pGYQ~Pl~~~~vk~~~~~~~~~~ 144 (245)
.+++|+|.|+|++|||++++++||||+|+|+||+++||++++|||+|.|..+.+.+...+|+..
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 9999999999999999999999999999999999999999999999999888888777777653
No 2
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.84 E-value=1.5e-20 Score=146.12 Aligned_cols=90 Identities=33% Similarity=0.450 Sum_probs=72.8
Q ss_pred CCCCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEecccccccccC
Q 025950 16 INENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEG 95 (245)
Q Consensus 16 ~~~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ePleEG 95 (245)
..+|+|+|++|+ +.+||.+++.+|++ +.++|+|||+|+||+|||+||||||+||...++ +..+++.++-...++|
T Consensus 2 ~~en~i~Ig~kp-vmnYV~~~~~~l~~-g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v~---v~~I~i~se~i~~~~g 76 (91)
T PRK04015 2 AEENVVLVGKKP-VMNYVLAVLTQFNQ-GAKEVVIKARGRAISKAVDVAEIVRNRFLPDVE---IKEIKIGTEEVTSEDG 76 (91)
T ss_pred CCCCEEEEcCCc-HHHHHHHHHHHHhC-CCCeEEEEEeccccchhhhHHHHHHHhccCCeE---EEEEEeccEEeecCCC
Confidence 357999999985 55999999999994 899999999999999999999999999865554 4444444433333455
Q ss_pred CCcceeeeeeeeEEEEEecC
Q 025950 96 LLPLETTRHVSMITITLSKK 115 (245)
Q Consensus 96 l~~~~~~R~Vs~I~ItLsk~ 115 (245)
.+++||+|+|+|+++
T Consensus 77 -----~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 77 -----RESNVSTIEIVLEKK 91 (91)
T ss_pred -----cEEEEEEEEEEEecC
Confidence 679999999999874
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=99.81 E-value=2.6e-19 Score=138.03 Aligned_cols=87 Identities=34% Similarity=0.454 Sum_probs=74.7
Q ss_pred CCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEecccccccccCCC
Q 025950 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLL 97 (245)
Q Consensus 18 ~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ePleEGl~ 97 (245)
+|.|+|++|+-| +||..++.+|++ +.++|+|||+|+||+|||+|||+||+||...+ ++..+++.++-.+.++|
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 589999999666 999999999986 89999999999999999999999999986554 56666666665566677
Q ss_pred cceeeeeeeeEEEEEec
Q 025950 98 PLETTRHVSMITITLSK 114 (245)
Q Consensus 98 ~~~~~R~Vs~I~ItLsk 114 (245)
.+++||+|+|+|++
T Consensus 74 ---~~~~VStIEI~l~~ 87 (87)
T TIGR00285 74 ---REVNVSTIEIVLAK 87 (87)
T ss_pred ---ceeeEEEEEEEEeC
Confidence 67899999999975
No 4
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=99.79 E-value=1.1e-18 Score=134.00 Aligned_cols=89 Identities=37% Similarity=0.523 Sum_probs=76.4
Q ss_pred CCCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEecccccccccCC
Q 025950 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGL 96 (245)
Q Consensus 17 ~~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ePleEGl 96 (245)
++|.|+|.+|+-| |||..++.+|++ +.++|+|||.|+||||||++||||++||-- .++|..++|.++-...++|
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 4699999999666 999999999997 799999999999999999999999999832 3477788887766666666
Q ss_pred CcceeeeeeeeEEEEEecC
Q 025950 97 LPLETTRHVSMITITLSKK 115 (245)
Q Consensus 97 ~~~~~~R~Vs~I~ItLsk~ 115 (245)
.+++||+|+|.|.+.
T Consensus 77 ----r~~~VS~IeI~L~k~ 91 (91)
T COG1581 77 ----RTRNVSTIEIVLAKK 91 (91)
T ss_pred ----ceeeEEEEEEEEecC
Confidence 578999999999863
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=99.69 E-value=1.6e-16 Score=116.40 Aligned_cols=64 Identities=39% Similarity=0.654 Sum_probs=57.2
Q ss_pred CeEEEcCCcchHHHHHHHHHHH---hhcCCCeEEEEEcChhHHHHHHHHHHHHHHhC-CceeeeEEEE
Q 025950 19 NEIRITTQGRMRNYITYATTLL---QEKGSNEIVLKAMGRAINKTVMIAELIKRRIA-GLHQNTSIGS 82 (245)
Q Consensus 19 NeIrVt~k~~i~~yV~~A~~lL---~~~g~~eVvIka~G~AIsKAV~vAEILKrri~-GLhQ~t~I~s 82 (245)
|+|+|++++++.+||.+|+++| ++.+.++|+|+|+|+||+|||+||||||+++. +|||++.+.+
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 8999988764
No 6
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=99.43 E-value=6.3e-13 Score=111.34 Aligned_cols=93 Identities=25% Similarity=0.369 Sum_probs=67.1
Q ss_pred CCeEEEcCCcchHHHHHHHHHHHhhc-------------------C------------CCeEEEEEcChhHHHHHHHHHH
Q 025950 18 ENEIRITTQGRMRNYITYATTLLQEK-------------------G------------SNEIVLKAMGRAINKTVMIAEL 66 (245)
Q Consensus 18 ~NeIrVt~k~~i~~yV~~A~~lL~~~-------------------g------------~~eVvIka~G~AIsKAV~vAEI 66 (245)
++.|+|+++++|-..|..+.+||..- . .++|+|||||+||.|||+||.-
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 025950 67 IKRRIAGLHQNTSIGSTDITDMWEPLE------------------EGLLPLETTRHVSMITIT 111 (245)
Q Consensus 67 LKrri~GLhQ~t~I~sv~i~d~~ePle------------------EGl~~~~~~R~Vs~I~It 111 (245)
|++.. ++--.+.++||.+.|++++.+ +..++..++|+||+|+|.
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 98875 677779999999999998763 456778999999999984
No 7
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.88 E-value=0.0049 Score=64.94 Aligned_cols=9 Identities=56% Similarity=1.003 Sum_probs=3.5
Q ss_pred CCCCCCCCC
Q 025950 218 RGRGRGRAR 226 (245)
Q Consensus 218 rgrgr~rg~ 226 (245)
|++||+++.
T Consensus 1258 rgggrgagg 1266 (1282)
T KOG0921|consen 1258 RGGGRGAGG 1266 (1282)
T ss_pred CCCCCCCCC
Confidence 333333333
No 8
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=95.70 E-value=0.096 Score=50.30 Aligned_cols=14 Identities=21% Similarity=0.010 Sum_probs=7.9
Q ss_pred eeeeeeeEEEEEec
Q 025950 101 TTRHVSMITITLSK 114 (245)
Q Consensus 101 ~~R~Vs~I~ItLsk 114 (245)
.++..|+|+=.+--
T Consensus 287 Re~Taski~k~~ig 300 (465)
T KOG3973|consen 287 RERTASKIHKLSIG 300 (465)
T ss_pred hhhhhhhhcccccc
Confidence 34566677655543
No 9
>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=90.60 E-value=4.3 Score=31.61 Aligned_cols=66 Identities=18% Similarity=0.314 Sum_probs=40.9
Q ss_pred CeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHHHhC--C--ceeeeEEEEEEec
Q 025950 19 NEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMG-RAINKTVMIAELIKRRIA--G--LHQNTSIGSTDIT 86 (245)
Q Consensus 19 NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G-~AIsKAV~vAEILKrri~--G--LhQ~t~I~sv~i~ 86 (245)
+.++|+++++....-......|.+ ...|.|.|+| .|++.||.-.-|-+.-+. | |+..-.+..+++.
T Consensus 2 e~LKVSs~S~p~~vAgAIa~~lre--~~~v~lqaiGa~AvnqAvKAIAiAR~~l~~~g~dl~~~P~F~~v~i~ 72 (86)
T PF04232_consen 2 EVLKVSSKSNPNAVAGAIAGVLRE--GGKVELQAIGAGAVNQAVKAIAIARGYLAPDGIDLVCVPAFIDVEID 72 (86)
T ss_dssp -EEEE-TT--HHHHHHHHHHHHHH--TSEEEEEE-SHHHHHHHHHHHHHHHHHHGGGTEEEEEEEEEEEEEET
T ss_pred ceEEEcCCCCHHHHHHHHHHHHhc--CCcEEEEEECHHHHHHHHHHHHHHHHhhhhhCceEEEEeeEEEEeeC
Confidence 468999998886665555556765 3599999999 788888887766665542 3 4444444444443
No 10
>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=82.82 E-value=0.39 Score=48.61 Aligned_cols=19 Identities=21% Similarity=0.190 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHhCCceee
Q 025950 59 KTVMIAELIKRRIAGLHQN 77 (245)
Q Consensus 59 KAV~vAEILKrri~GLhQ~ 77 (245)
.|+.+++=|-.-+..||-.
T Consensus 429 ~aLkt~~NI~~lik~L~~~ 447 (556)
T PF05918_consen 429 TALKTTNNILALIKDLFHN 447 (556)
T ss_dssp HHHHHHHHHHHHHCC----
T ss_pred HHHHHHhhHHHHHHHHhhC
Confidence 4554444444555555433
No 11
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=78.43 E-value=10 Score=33.72 Aligned_cols=9 Identities=22% Similarity=0.176 Sum_probs=4.8
Q ss_pred eeEEEEEec
Q 025950 106 SMITITLSK 114 (245)
Q Consensus 106 s~I~ItLsk 114 (245)
..++|+|+-
T Consensus 104 ~~fsIK~~d 112 (215)
T KOG3262|consen 104 VHFSIKPSD 112 (215)
T ss_pred cEEEEecCC
Confidence 455666553
No 12
>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=54.75 E-value=50 Score=29.58 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=31.3
Q ss_pred CCCeEEEEEcC-hhHHHHHHHHHHHHHHhCCceeeeEEEEEEecccc
Q 025950 44 GSNEIVLKAMG-RAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMW 89 (245)
Q Consensus 44 g~~eVvIka~G-~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ 89 (245)
....|||-+.| -..--++..|.+|++.+++| +|..|.|.|-.
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 46789999999 56778999999999999999 78888887754
No 13
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=42.60 E-value=67 Score=31.58 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=38.8
Q ss_pred CCCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcC---hhHHHHH
Q 025950 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMG---RAINKTV 61 (245)
Q Consensus 17 ~~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G---~AIsKAV 61 (245)
+.-.|=||.=+.-...|..+...|++++++.+++||.| +|+.+-|
T Consensus 184 ~kp~I~iTmfGvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li 231 (403)
T PF06792_consen 184 DKPLIGITMFGVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLI 231 (403)
T ss_pred CCcEEEEECCCCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHH
Confidence 45688899888888999999999999899999999998 6777654
No 14
>PRK05261 putative phosphoketolase; Provisional
Probab=42.38 E-value=41 Score=35.75 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=27.6
Q ss_pred CeEEEEEcChhHHH-HHHHHHHHHHHhCCc
Q 025950 46 NEIVLKAMGRAINK-TVMIAELIKRRIAGL 74 (245)
Q Consensus 46 ~eVvIka~G~AIsK-AV~vAEILKrri~GL 74 (245)
..|+|-|.|.-+.. |+.+|++|++.+++|
T Consensus 614 pDvvL~atGsev~leAlaAa~~L~~~~pgi 643 (785)
T PRK05261 614 PDVVLACAGDVPTLETLAAADLLREHFPDL 643 (785)
T ss_pred CCEEEEEeCcHhhHHHHHHHHHHHhhCCCC
Confidence 58999999999999 999999999999988
No 15
>PRK02399 hypothetical protein; Provisional
Probab=40.99 E-value=77 Score=31.24 Aligned_cols=45 Identities=27% Similarity=0.388 Sum_probs=37.0
Q ss_pred CCCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcC---hhHHHHH
Q 025950 17 NENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMG---RAINKTV 61 (245)
Q Consensus 17 ~~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G---~AIsKAV 61 (245)
+.-.|=||.=+.-..+|..+...|++++++.+++||.| +|+.+-|
T Consensus 185 ~kp~Ig~TmfGvTtp~v~~~~~~Le~~GyEvlVFHATG~GGraME~Li 232 (406)
T PRK02399 185 DKPLIGLTMFGVTTPCVQAAREELEARGYEVLVFHATGTGGRAMEKLI 232 (406)
T ss_pred CCceEEEecCCCcHHHHHHHHHHHHhCCCeEEEEcCCCCchHHHHHHH
Confidence 34567788766777999999999998899999999998 6777654
No 16
>KOG0523 consensus Transketolase [Carbohydrate transport and metabolism]
Probab=40.76 E-value=30 Score=35.68 Aligned_cols=50 Identities=20% Similarity=0.230 Sum_probs=36.6
Q ss_pred CCeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHH
Q 025950 18 ENEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRR 70 (245)
Q Consensus 18 ~NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrr 70 (245)
.|-|.++.... .-|..+.-.|++ ..+.|+|-|.|.++..|+..||.|..+
T Consensus 481 ~~~~~~~~~~~--~~igkg~~vl~~-~~~dV~LiG~Gs~v~~cl~AA~~L~~~ 530 (632)
T KOG0523|consen 481 QNLPIYNNTEI--EEIGKGKYVLQE-VEPDVILIGTGSEVQECLEAAELLSED 530 (632)
T ss_pred ccccccCCCch--hhhccccEEEec-CCCCEEEEeccHHHHHHHHHHHHHHhc
Confidence 45555554433 345555556665 458999999999999999999999965
No 17
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=40.58 E-value=1.4e+02 Score=26.31 Aligned_cols=71 Identities=18% Similarity=0.338 Sum_probs=48.3
Q ss_pred CCeEEEcCC---cchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEeccccccccc
Q 025950 18 ENEIRITTQ---GRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEE 94 (245)
Q Consensus 18 ~NeIrVt~k---~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ePleE 94 (245)
-.||++..+ .++.--+..|..+|++...-.|+|+-.|+.+...=.-..+|.+-...|.. +.+|+ .+|.-|
T Consensus 90 vKEik~rp~Id~hD~~~K~k~~~rFLe~GdkVKvtirfrGRe~~h~elG~~~l~r~~~~~~~---~~~ve----~~pk~e 162 (176)
T COG0290 90 VKEIKLRPKIDEHDYETKLKNARRFLEKGDKVKVTIRFRGREMAHQELGVKVLERVAEDLED---IAKVE----SEPKME 162 (176)
T ss_pred EEEEEeecCcCcchHHHHHHHHHHHHHCCCeEEEEEEEechhhhhHHHHHHHHHHHHHHhhh---hheee----cccccC
Confidence 467777765 44545566788888875577899999999999887777777776554532 33333 256666
Q ss_pred C
Q 025950 95 G 95 (245)
Q Consensus 95 G 95 (245)
|
T Consensus 163 g 163 (176)
T COG0290 163 G 163 (176)
T ss_pred C
Confidence 6
No 18
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=39.83 E-value=16 Score=29.64 Aligned_cols=10 Identities=100% Similarity=1.880 Sum_probs=4.7
Q ss_pred CCCcccccCC
Q 025950 180 GRGRGRGRGR 189 (245)
Q Consensus 180 g~grgrgrg~ 189 (245)
+|+++||+|+
T Consensus 95 ~rgrgrg~Gr 104 (109)
T KOG3428|consen 95 GRGRGRGRGR 104 (109)
T ss_pred cccccccccc
Confidence 3444444444
No 19
>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=38.26 E-value=1e+02 Score=24.12 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=24.4
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHHHH
Q 025950 45 SNEIVLKAMGRAINKTVMIAELIKRR 70 (245)
Q Consensus 45 ~~eVvIka~G~AIsKAV~vAEILKrr 70 (245)
-+.|+|-++|..+..|+..|++|+.+
T Consensus 9 g~di~iia~G~~~~~al~A~~~L~~~ 34 (124)
T PF02780_consen 9 GADITIIAYGSMVEEALEAAEELEEE 34 (124)
T ss_dssp SSSEEEEEETTHHHHHHHHHHHHHHT
T ss_pred CCCEEEEeehHHHHHHHHHHHHHHHc
Confidence 46899999999999999999999998
No 20
>KOG1402 consensus Ornithine aminotransferase [Amino acid transport and metabolism]
Probab=34.98 E-value=2.1e+02 Score=28.10 Aligned_cols=81 Identities=22% Similarity=0.346 Sum_probs=50.0
Q ss_pred HHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHHHhCCceeeeEEEEEEecccccccccCCCcceeeeeeeeEEE
Q 025950 32 YITYATTLLQEKGSNEIVLKAMG-RAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITI 110 (245)
Q Consensus 32 yV~~A~~lL~~~g~~eVvIka~G-~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ePleEGl~~~~~~R~Vs~I~I 110 (245)
|-.|..+|| +.+.|.=+.+| .|...|+.+|-..-.+.+++-+.-.+--......| -|..++ |
T Consensus 106 f~~~vt~lf---~~~kvlpmnTGaEa~Eta~KLaR~wgy~~K~ip~nka~il~~~~nFh------------GrT~~a--i 168 (427)
T KOG1402|consen 106 FAEYVTKLF---GYDKVLPMNTGAEAVETACKLARKWGYRKKNIPKNKAKILSAENNFH------------GRTLGA--I 168 (427)
T ss_pred HHHHHHHhc---CcceeeecccchhHHHHHHHHHHHHHHhhccCCccceeEEEeccccc------------Cceeee--E
Confidence 334444444 46788888899 68888888888777777666443332212222222 255555 4
Q ss_pred EEecCCCCCCCCCCCCCCCcC
Q 025950 111 TLSKKDLDTSSTGYQPPLPAD 131 (245)
Q Consensus 111 tLsk~~lD~~~pGYQ~Pl~~~ 131 (245)
.||.++ .+-.+||+++|-.
T Consensus 169 s~s~d~--ds~~~fgp~~P~~ 187 (427)
T KOG1402|consen 169 SLSTDP--DSWDGFGPFLPGV 187 (427)
T ss_pred EecCCc--chhhccCCCCCCc
Confidence 567766 4556999999983
No 21
>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=34.68 E-value=44 Score=30.64 Aligned_cols=38 Identities=16% Similarity=0.345 Sum_probs=28.0
Q ss_pred eeeeeeEEEEEecC---CCCCCCCCCCCCCCcCCCCCCCcc
Q 025950 102 TRHVSMITITLSKK---DLDTSSTGYQPPLPADQVKPWNEF 139 (245)
Q Consensus 102 ~R~Vs~I~ItLsk~---~lD~~~pGYQ~Pl~~~~vk~~~~~ 139 (245)
.|.+....|+...+ .+++.-..||.|||.+++||+++.
T Consensus 248 ~R~~~i~pv~~~~dG~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 (295)
T cd08982 248 ERRIGLFPAFFDEDGVLYCNTAFGDYPMILPDKKIDPPEDL 288 (295)
T ss_pred CceeEEEEEEECCCCcEEEcccCCcCcccCCCCCCcccccc
Confidence 46665556666543 357777899999999999998653
No 22
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=33.97 E-value=1.3e+02 Score=28.73 Aligned_cols=42 Identities=10% Similarity=0.170 Sum_probs=27.3
Q ss_pred chHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHH
Q 025950 28 RMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKR 69 (245)
Q Consensus 28 ~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKr 69 (245)
.....+.....++...+.+.|+|.|||.-..+--.|.+.|+.
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 334455555555544468999999999877665566655554
No 23
>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=33.46 E-value=73 Score=24.93 Aligned_cols=33 Identities=27% Similarity=0.466 Sum_probs=26.9
Q ss_pred CCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHH
Q 025950 25 TQGRMRNYITYATTLLQEKGSNEIVLKAMGRAIN 58 (245)
Q Consensus 25 ~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIs 58 (245)
....+..||..|+++|++.+. ...+++||-.|.
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 345888999999999987566 788999987664
No 24
>COG2065 PyrR Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=31.52 E-value=61 Score=28.48 Aligned_cols=53 Identities=32% Similarity=0.462 Sum_probs=34.8
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEecccccccccCCCcceeeeeeeeEEEEEecCCCCCCCC
Q 025950 43 KGSNEIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLDTSST 122 (245)
Q Consensus 43 ~g~~eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~d~~ePleEGl~~~~~~R~Vs~I~ItLsk~~lD~~~p 122 (245)
++.+.++|-|.= ++-|.+||.|++++..| . | ..-.+-.|.|||+++.|..+.+
T Consensus 28 k~~~~~vlvGIk---trGv~lA~rl~~~i~~~------E-------------g-----~~vp~g~lDIt~yRDDl~~~~~ 80 (179)
T COG2065 28 KGLDNLVLVGIK---TRGVPLAERLAERIEEL------E-------------G-----IEVPVGELDITLYRDDLTQKGP 80 (179)
T ss_pred CCCCceEEEeEe---cCCHHHHHHHHHHHHHH------h-------------C-----CCCCeeeEEeEEeechhhhcCc
Confidence 367777777653 45677888888886533 1 1 1123457899999998877554
No 25
>PRK10824 glutaredoxin-4; Provisional
Probab=29.35 E-value=58 Score=26.30 Aligned_cols=16 Identities=6% Similarity=-0.022 Sum_probs=8.6
Q ss_pred CCcceeeeeeeeEEEE
Q 025950 96 LLPLETTRHVSMITIT 111 (245)
Q Consensus 96 l~~~~~~R~Vs~I~It 111 (245)
|...+-.+.||.|.|-
T Consensus 62 l~~~sg~~TVPQIFI~ 77 (115)
T PRK10824 62 LPKYANWPTFPQLWVD 77 (115)
T ss_pred HHHHhCCCCCCeEEEC
Confidence 3333445666666663
No 26
>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=29.06 E-value=65 Score=30.09 Aligned_cols=41 Identities=22% Similarity=0.256 Sum_probs=23.2
Q ss_pred CCCeEEEEEcChhHH---HHHHHHHHHHHHhCCceeeeEEEEEEeccc
Q 025950 44 GSNEIVLKAMGRAIN---KTVMIAELIKRRIAGLHQNTSIGSTDITDM 88 (245)
Q Consensus 44 g~~eVvIka~G~AIs---KAV~vAEILKrri~GLhQ~t~I~sv~i~d~ 88 (245)
..+.|+|||||-... -.-.+.++|++.++|.+ +.+|++.+.
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 357899999997653 35678899999999874 777777554
No 27
>COG2359 SpoVS Stage V sporulation protein SpoVS [Function unknown]
Probab=28.72 E-value=2.8e+02 Score=21.49 Aligned_cols=65 Identities=18% Similarity=0.329 Sum_probs=38.9
Q ss_pred eEEEcCCcchHHHHHHHHH-HHhhcCCCeEEEEEcC-hhHHHHHHHHHHHHHHh--CC--ceeeeEEEEEEecc
Q 025950 20 EIRITTQGRMRNYITYATT-LLQEKGSNEIVLKAMG-RAINKTVMIAELIKRRI--AG--LHQNTSIGSTDITD 87 (245)
Q Consensus 20 eIrVt~k~~i~~yV~~A~~-lL~~~g~~eVvIka~G-~AIsKAV~vAEILKrri--~G--LhQ~t~I~sv~i~d 87 (245)
.+.|++++.- |-|.=|+. +|.+ ...+.|.|+| .|++.||...-|-+.=+ .| |..+-.+..++|.+
T Consensus 3 vLKVsa~S~P-nsVAGAlAgvlr~--~g~aEiQAiGagAvNQaVKAiAiaRgflapsGidL~~vPaF~~i~i~~ 73 (87)
T COG2359 3 VLKVSAKSNP-NSVAGALAGVLRE--RGKAEIQAIGAGAVNQAVKAIAIARGFLAPSGIDLVCVPAFTEIEIEG 73 (87)
T ss_pred eEEeccCCCc-chHHHHHHHHHHh--cCceeeeeechHHHHHHHHHHHHHhhccCccCCcEEEeeeeEEEEecC
Confidence 4567777766 55666665 6665 5678888998 57888877544443333 23 44444444445543
No 28
>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=27.71 E-value=1e+02 Score=31.85 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=23.3
Q ss_pred CeEEEEEcChhHHHHHHHHHHHHHH
Q 025950 46 NEIVLKAMGRAINKTVMIAELIKRR 70 (245)
Q Consensus 46 ~eVvIka~G~AIsKAV~vAEILKrr 70 (245)
+.|+|-|.|.-+..|+.+|++|+.+
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 29
>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=27.23 E-value=1.6e+02 Score=22.21 Aligned_cols=36 Identities=19% Similarity=0.175 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHH
Q 025950 32 YITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKR 69 (245)
Q Consensus 32 yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKr 69 (245)
.|..+.++|.+ .+.|.|.|.|....-|...+..|+.
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 46677788875 5899999999877777777776665
No 30
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=27.22 E-value=2.3e+02 Score=27.50 Aligned_cols=59 Identities=15% Similarity=0.316 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHhhc-------CCCeEEEEEcChhHH---HHHHHHHHHHHHh---CCc-eeeeEEEEEEecc
Q 025950 29 MRNYITYATTLLQEK-------GSNEIVLKAMGRAIN---KTVMIAELIKRRI---AGL-HQNTSIGSTDITD 87 (245)
Q Consensus 29 i~~yV~~A~~lL~~~-------g~~eVvIka~G~AIs---KAV~vAEILKrri---~GL-hQ~t~I~sv~i~d 87 (245)
|-.+|..+...|.+. ....|+|.|||.-.. ..+.+.++|+... -++ +-.+.|+|+-+..
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 345555555555431 246799999997664 4556666666631 133 1235666664443
No 31
>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=26.57 E-value=2.8e+02 Score=20.78 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=42.3
Q ss_pred CeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhCC
Q 025950 19 NEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIAG 73 (245)
Q Consensus 19 NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~G 73 (245)
..|.|.+.+-..+.|......|+. +.-|.|+-.+.+-...-.+|+.|..+...
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 459999999888999999999986 68999999998888899999999999764
No 32
>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=25.82 E-value=2.2e+02 Score=19.45 Aligned_cols=32 Identities=16% Similarity=0.313 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHHHHHHhCCceeeeEEEEEEec
Q 025950 55 RAINKTVMIAELIKRRIAGLHQNTSIGSTDIT 86 (245)
Q Consensus 55 ~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i~ 86 (245)
..+..+..+++.||+.++.+.....++..++.
T Consensus 8 ~G~~~s~~l~~~l~~~~~~~~~~~~~~~~~~~ 39 (84)
T cd00133 8 SGIGSSSMLAEKLEKAAKELGIEVKVEAQGLS 39 (84)
T ss_pred CcHhHHHHHHHHHHHHHHHCCCeEEEEEcccc
Confidence 34455667788888888766655555554444
No 33
>COG1416 Uncharacterized conserved protein [Function unknown]
Probab=24.34 E-value=99 Score=25.26 Aligned_cols=44 Identities=23% Similarity=0.204 Sum_probs=33.4
Q ss_pred CeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHH
Q 025950 19 NEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVM 62 (245)
Q Consensus 19 NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~ 62 (245)
-.++|+.-+++.--|.-+.+||++....+|.+.+-|.||.--..
T Consensus 6 VV~hv~~~~k~~~~l~Nl~Nll~~~p~~~IeVV~~g~ai~~l~~ 49 (112)
T COG1416 6 VVYHVDEESKVNMVLGNLTNLLEDDPSVEIEVVAHGPAIAFLSE 49 (112)
T ss_pred EEEEeccHHHHHHHHHHHHHHhcCCCCceEEEEEeCchhHHhhh
Confidence 35678877788888888999999777788888888877754333
No 34
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=23.90 E-value=1.3e+02 Score=28.52 Aligned_cols=52 Identities=25% Similarity=0.278 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhcCCC---eEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEe
Q 025950 32 YITYATTLLQEKGSN---EIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDI 85 (245)
Q Consensus 32 yV~~A~~lL~~~g~~---eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i 85 (245)
=+..|.+||++.+.+ +|.|...... ....+|++|+..++.+--.++|..++-
T Consensus 302 d~~~A~~lL~eaG~~~~~~l~l~~~~~~--~~~~~a~~i~~~l~~~GI~v~i~~~~~ 356 (474)
T cd08499 302 DPEKAKELLAEAGYPDGFETTLWTNDNR--ERIKIAEFIQQQLAQIGIDVEIEVMEW 356 (474)
T ss_pred CHHHHHHHHHHcCCCCCceEEEEecCCC--chhHHHHHHHHHHHHcCceEEEEeccH
Confidence 368899999876653 5666554433 345677777777654433355554443
No 35
>cd08504 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which
Probab=23.89 E-value=1.9e+02 Score=27.63 Aligned_cols=50 Identities=22% Similarity=0.218 Sum_probs=33.4
Q ss_pred HHHHHHHHhhcCCC------eEEEEEcChhHHHHHHHHHHHHHHhCC-ceeeeEEEEEE
Q 025950 33 ITYATTLLQEKGSN------EIVLKAMGRAINKTVMIAELIKRRIAG-LHQNTSIGSTD 84 (245)
Q Consensus 33 V~~A~~lL~~~g~~------eVvIka~G~AIsKAV~vAEILKrri~G-LhQ~t~I~sv~ 84 (245)
+..|..||++.+.+ +|.|.-... .....+|++|+..+.. +--.+++..++
T Consensus 325 ~~kA~~lL~~aG~~~~~~~~~l~i~~~~~--~~~~~~a~~i~~~l~~~iGI~v~i~~~~ 381 (498)
T cd08504 325 PEKAKKLLAEAGYELGKNPLKLTLLYNTS--ENHKKIAEAIQQMWKKNLGVKVTLKNVE 381 (498)
T ss_pred HHHHHHHHHHcCcccCCCCceEEEEecCc--hhHHHHHHHHHHHHHHcCCCeEEEEecc
Confidence 68899999875542 566655543 5667888888888765 54445555444
No 36
>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=23.31 E-value=3.1e+02 Score=20.71 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=30.8
Q ss_pred HHHHHHhhcCCCeEEEEE-cChhHHHHHHHHHHHHHHhCCc
Q 025950 35 YATTLLQEKGSNEIVLKA-MGRAINKTVMIAELIKRRIAGL 74 (245)
Q Consensus 35 ~A~~lL~~~g~~eVvIka-~G~AIsKAV~vAEILKrri~GL 74 (245)
..+..+.+...+-|.|+. +...+..+..+++.+|+..++.
T Consensus 42 ~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~ 82 (121)
T PF02310_consen 42 ELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKERNPNI 82 (121)
T ss_dssp HHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTS
T ss_pred HHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCC
Confidence 333444444678999999 9999999999999999886654
No 37
>CHL00199 infC translation initiation factor 3; Provisional
Probab=22.74 E-value=5.3e+02 Score=22.69 Aligned_cols=56 Identities=20% Similarity=0.236 Sum_probs=39.4
Q ss_pred CCCeEEEcCCcc---hHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHHHHhC
Q 025950 17 NENEIRITTQGR---MRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIKRRIA 72 (245)
Q Consensus 17 ~~NeIrVt~k~~---i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILKrri~ 72 (245)
.-.||+++.+-. +.-=+..|.++|++...=.|+|.-.|+-+..+=..-++|.+-+.
T Consensus 95 ~~KEirl~~~I~~hDl~~K~k~~~kFL~~G~kVkv~i~frGRE~~~~e~g~~ll~r~~~ 153 (182)
T CHL00199 95 SIKEVKMRYKIEEHDYKVRINQAFKFLQAGDKVKATLTFRGREIQHLNLAINLLNKMAA 153 (182)
T ss_pred cceEEEecCCCCccHHHHHHHHHHHHHHCCCEEEEEEEEchhHHhhHHHHHHHHHHHHH
Confidence 457899987644 44446778888987556688999999988776555555555443
No 38
>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=20.73 E-value=2.9e+02 Score=20.06 Aligned_cols=36 Identities=17% Similarity=0.222 Sum_probs=19.9
Q ss_pred EEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEe
Q 025950 48 IVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDI 85 (245)
Q Consensus 48 VvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i 85 (245)
+++-+.|.+. +..+++-|++.++.+.....+..+.+
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 45567777777765554445544443
No 39
>CHL00144 odpB pyruvate dehydrogenase E1 component beta subunit; Validated
Probab=20.60 E-value=1.2e+02 Score=28.46 Aligned_cols=25 Identities=12% Similarity=0.304 Sum_probs=23.2
Q ss_pred CeEEEEEcChhHHHHHHHHHHHHHH
Q 025950 46 NEIVLKAMGRAINKTVMIAELIKRR 70 (245)
Q Consensus 46 ~eVvIka~G~AIsKAV~vAEILKrr 70 (245)
+.|+|-+.|..+..|+..|++|+..
T Consensus 202 ~ditiia~G~~v~~al~Aa~~L~~~ 226 (327)
T CHL00144 202 NDITILTYSRMRHHVLQAVKVLVEK 226 (327)
T ss_pred CCEEEEEccHHHHHHHHHHHHHHhc
Confidence 6899999999999999999999764
No 40
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=20.46 E-value=1.9e+02 Score=26.07 Aligned_cols=51 Identities=25% Similarity=0.312 Sum_probs=34.7
Q ss_pred HHHHHHHHhhcCCC-------------eEEEEEcChhHHHHHHHHHHHHHHhCCceeeeEEEEEEe
Q 025950 33 ITYATTLLQEKGSN-------------EIVLKAMGRAINKTVMIAELIKRRIAGLHQNTSIGSTDI 85 (245)
Q Consensus 33 V~~A~~lL~~~g~~-------------eVvIka~G~AIsKAV~vAEILKrri~GLhQ~t~I~sv~i 85 (245)
+..|..||++.+.. .+++......+.+ .+|++|+..+..+.-.++|..++-
T Consensus 269 ~~~A~~lL~~ag~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~a~~l~~~l~~~Gi~v~i~~~~~ 332 (374)
T PF00496_consen 269 PEKARELLEKAGYKKSDGGGWRKDPLPLIILYTSDDPIWK--AIAEALQEQLKKIGIKVEIKPVDF 332 (374)
T ss_dssp HHHHHHHHHHTTHEESTTSEEEETEEEEEEEEETTSHHHH--HHHHHHHHHHHHTTEEEEEEEESH
T ss_pred HHHHHHhHHhhhhhcccccccccccccccccccccccchH--HHHHHHHHHHhhcceeEEEEEeCh
Confidence 78899999875322 4555666666666 788889988765555566666654
No 41
>PRK15062 hydrogenase isoenzymes formation protein HypD; Provisional
Probab=20.18 E-value=2.5e+02 Score=27.33 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=31.9
Q ss_pred CeEEEcCCcchHHHHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHH---HHhCCce
Q 025950 19 NEIRITTQGRMRNYITYATTLLQEKGSNEIVLKAMGRAINKTVMIAELIK---RRIAGLH 75 (245)
Q Consensus 19 NeIrVt~k~~i~~yV~~A~~lL~~~g~~eVvIka~G~AIsKAV~vAEILK---rri~GLh 75 (245)
.+|+|-.+ ...|+++-+++..++||+.|+|--.....+.+.|++ ..+.++.
T Consensus 110 adVriVYS------pldAl~iA~~nP~k~vVF~avGFETTaP~~A~~i~~A~~~~~~Nfs 163 (364)
T PRK15062 110 ADVRIVYS------PLDALKIARENPDKEVVFFAIGFETTAPATAATLLQAKAEGLKNFS 163 (364)
T ss_pred CCEEEEeC------HHHHHHHHHHCCCCeEEEEecCchhccHHHHHHHHHHHHcCCCCEE
Confidence 34666544 235777777767899999999965444444444444 4455554
Done!