Query 025488
Match_columns 252
No_of_seqs 215 out of 384
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 06:21:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025488hhsearch_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 8.7E-49 1.9E-53 332.1 13.8 142 1-158 1-142 (179)
2 PRK04015 DNA/RNA-binding prote 99.8 1.4E-20 2.9E-25 147.2 12.1 88 16-115 2-91 (91)
3 TIGR00285 DNA-binding protein 99.8 6.7E-19 1.4E-23 136.6 11.8 85 18-114 1-87 (87)
4 COG1581 Ssh10b Archaeal DNA-bi 99.7 3E-17 6.5E-22 127.0 11.8 86 17-114 3-90 (91)
5 PF01918 Alba: Alba; InterPro 99.7 6.7E-17 1.5E-21 119.0 9.8 65 19-83 1-69 (70)
6 PF12328 Rpp20: Rpp20 subunit 99.5 3.8E-13 8.3E-18 113.2 9.9 93 18-111 3-144 (144)
7 KOG3973 Uncharacterized conser 98.1 1.7E-05 3.7E-10 75.6 8.7 50 102-155 288-338 (465)
8 KOG0921 Dosage compensation co 97.1 0.0026 5.6E-08 67.3 9.2 16 230-245 1255-1270(1282)
9 KOG3973 Uncharacterized conser 95.5 0.036 7.8E-07 53.5 6.6 16 184-199 369-385 (465)
10 KOG0921 Dosage compensation co 93.9 0.35 7.6E-06 51.9 9.7 7 86-92 1082-1088(1282)
11 PF04232 SpoVS: Stage V sporul 88.5 10 0.00022 29.7 10.4 51 19-71 2-53 (86)
12 KOG3262 H/ACA small nucleolar 77.7 16 0.00035 32.8 8.4 34 106-139 104-138 (215)
13 PF05918 API5: Apoptosis inhib 74.5 1.7 3.6E-05 44.4 1.6 35 59-93 429-465 (556)
14 PF05918 API5: Apoptosis inhib 70.7 1.4 3E-05 45.0 0.0 6 110-115 457-462 (556)
15 PF06792 UPF0261: Uncharacteri 37.2 93 0.002 30.8 6.3 64 17-88 184-250 (403)
16 PF02780 Transketolase_C: Tran 36.6 1E+02 0.0023 24.2 5.6 38 45-84 9-47 (124)
17 PRK02399 hypothetical protein; 34.4 1.1E+02 0.0024 30.3 6.3 65 17-89 185-252 (406)
18 KOG1402 Ornithine aminotransfe 33.5 2.1E+02 0.0046 28.3 7.9 80 32-130 106-186 (427)
19 PRK11634 ATP-dependent RNA hel 30.3 79 0.0017 32.6 4.8 14 57-70 255-268 (629)
20 cd00133 PTS_IIB PTS_IIB: subun 29.8 1.3E+02 0.0029 20.8 4.7 33 53-85 6-38 (84)
21 COG2065 PyrR Pyrimidine operon 26.0 97 0.0021 27.5 3.9 59 44-130 29-87 (179)
22 PRK14463 ribosomal RNA large s 25.6 1.8E+02 0.0039 27.9 6.0 41 29-69 133-173 (349)
23 CHL00199 infC translation init 24.9 4E+02 0.0086 23.6 7.6 56 16-71 94-152 (182)
24 PRK05261 putative phosphoketol 24.4 1.1E+02 0.0024 32.8 4.7 29 46-74 614-643 (785)
25 cd05566 PTS_IIB_galactitol PTS 24.2 1.7E+02 0.0036 21.6 4.5 34 49-84 5-38 (89)
26 PRK14459 ribosomal RNA large s 23.7 2.2E+02 0.0047 27.8 6.2 58 29-86 154-225 (373)
27 cd04823 ALAD_PBGS_aspartate_ri 22.8 4.9E+02 0.011 25.2 8.2 55 29-87 53-123 (320)
28 cd05568 PTS_IIB_bgl_like PTS_I 22.4 1.1E+02 0.0023 22.0 3.1 31 48-80 4-34 (85)
29 PRK13660 hypothetical protein; 21.2 3.4E+02 0.0073 23.9 6.4 63 29-91 27-89 (182)
30 TIGR00106 uncharacterized prot 20.8 1.4E+02 0.003 23.5 3.6 32 26-58 14-45 (97)
31 PRK14460 ribosomal RNA large s 20.8 1.4E+02 0.003 28.6 4.3 58 28-85 134-201 (354)
No 1
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=8.7e-49 Score=332.07 Aligned_cols=142 Identities=48% Similarity=0.761 Sum_probs=136.4
Q ss_pred CCCceeccCCCCCCCCCCCeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHHhcCCCeeEeEE
Q 025488 1 MDRYQKVEKPKPESPINENEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTAI 80 (252)
Q Consensus 1 Md~Y~rv~kp~~~~p~~~NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~I 80 (252)
||.|++|-||.+++|++.|+|||+.+++|+|||.||+.+|+++..++|||+|||.||+|||+||||||+|+++|||+|.|
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 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeeccccccCCCccceeeEEeeEEEEEEecCCCCCCCCCCCCCCCCCCCcchhhhhHHhhhcCCCCCCCCcccc
Q 025488 81 SSVSITDTWEPIEEGLVPVEMTRHVSMISITFSTRELNKNSPGYQSPHNAEQPKLQYRYQQQQQQQNQPPRQGRIPYT 158 (252)
Q Consensus 81 ~s~~i~D~~EP~eEgld~v~~~R~Vs~I~ItLSk~~LD~~~pGYQ~P~~~~~vk~~~~~~~~~~~~~~~~~~~~~~~~ 158 (252)
.+++|+|+|+|.+|||++|+++||||+|+|+||+++||++++|||+|.+ +|.++.++|.+|+
T Consensus 81 ~~~sv~d~W~p~~eGl~pl~vtRhVp~l~IlLS~deL~~~~~GyQ~P~~----------------~p~p~~~~~~p~~ 142 (179)
T KOG2567|consen 81 RYTSVEDVWEPTEEGLEPLEVTRHVPMLHILLSLDELDPTSPGYQPPNP----------------QPHPRSQPRHPYS 142 (179)
T ss_pred eeeehhhcccccccCccceEEeeccceEEEEEecccCCCCCCCccCCCC----------------CCCCCCcccCCcc
Confidence 9999999999999999999999999999999999999999999999998 2456677787774
No 2
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.85 E-value=1.4e-20 Score=147.24 Aligned_cols=88 Identities=32% Similarity=0.477 Sum_probs=75.8
Q ss_pred CCCCeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHHhcCCCeeEeE--EEEEEeeecccccc
Q 025488 16 INENEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTA--ISSVSITDTWEPIE 93 (252)
Q Consensus 16 ~~~NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~--I~s~~i~D~~EP~e 93 (252)
.++|+|+|+++ +++|||.+++.+|+ ++.++|+|||+|+||+|||+||||||+||...+++.+ |+|..+.+ +
T Consensus 2 ~~en~i~Ig~k-pvmnYV~~~~~~l~-~g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v~v~~I~i~se~i~~-----~ 74 (91)
T PRK04015 2 AEENVVLVGKK-PVMNYVLAVLTQFN-QGAKEVVIKARGRAISKAVDVAEIVRNRFLPDVEIKEIKIGTEEVTS-----E 74 (91)
T ss_pred CCCCEEEEcCC-cHHHHHHHHHHHHh-CCCCeEEEEEeccccchhhhHHHHHHHhccCCeEEEEEEeccEEeec-----C
Confidence 35799999986 89999999999999 5899999999999999999999999999977788877 56665543 2
Q ss_pred CCCccceeeEEeeEEEEEEecC
Q 025488 94 EGLVPVEMTRHVSMISITFSTR 115 (252)
Q Consensus 94 Egld~v~~~R~Vs~I~ItLSk~ 115 (252)
+| .+++||+|+|+|++.
T Consensus 75 ~g-----~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 75 DG-----RESNVSTIEIVLEKK 91 (91)
T ss_pred CC-----cEEEEEEEEEEEecC
Confidence 33 478999999999973
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=6.7e-19 Score=136.59 Aligned_cols=85 Identities=32% Similarity=0.452 Sum_probs=73.2
Q ss_pred CCeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHHhcCCCeeEeEE--EEEEeeeccccccCC
Q 025488 18 ENEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTAI--SSVSITDTWEPIEEG 95 (252)
Q Consensus 18 ~NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~I--~s~~i~D~~EP~eEg 95 (252)
+|.|+|.++ +++|||.+++.+|++ +.++|+|||+|+||+|||+|||+||+||...+++.+| +|.++. .++|
T Consensus 1 e~~i~vG~K-PvmnYVlavlt~fn~-g~~eV~iKarG~aIskAVdvaeiik~r~~~~v~v~~I~i~te~~~-----~~~G 73 (87)
T TIGR00285 1 ENVVYIGNK-PVMNYVLAVLTQLNS-GADEVIIKARGRAISRAVDVAEIVRNRFIPDIKIKKIKIGTEEIK-----SEQG 73 (87)
T ss_pred CCEEEEcCC-cHHHHHHHHHHHHhC-CCCeEEEEEecchhhhHHHHHHHHHHhccCCceEEEEEeccEEee-----cCCC
Confidence 489999986 899999999999985 8999999999999999999999999999777788776 665553 2344
Q ss_pred CccceeeEEeeEEEEEEec
Q 025488 96 LVPVEMTRHVSMISITFST 114 (252)
Q Consensus 96 ld~v~~~R~Vs~I~ItLSk 114 (252)
.+++||+|+|+|++
T Consensus 74 -----~~~~VStIEI~l~~ 87 (87)
T TIGR00285 74 -----REVNVSTIEIVLAK 87 (87)
T ss_pred -----ceeeEEEEEEEEeC
Confidence 37899999999975
No 4
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=99.74 E-value=3e-17 Score=127.01 Aligned_cols=86 Identities=34% Similarity=0.481 Sum_probs=72.1
Q ss_pred CCCeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHHhcCCCeeEeE--EEEEEeeeccccccC
Q 025488 17 NENEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTA--ISSVSITDTWEPIEE 94 (252)
Q Consensus 17 ~~NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~--I~s~~i~D~~EP~eE 94 (252)
++|.|+|.++ +++|||..++.+|++ +.++|+|||.|+||||||++|||+++||..-.|+.+ |+|.+++ .++
T Consensus 3 ~envV~vG~K-PvmNYVlAvlt~fn~-g~~eViiKARGraIskAVDvaeivRnrf~p~v~ik~Iki~se~~~-----~~~ 75 (91)
T COG1581 3 EENVVLVGKK-PVMNYVLAVLTQFNE-GADEVIIKARGRAISKAVDVAEIVRNRFIPDVQIKDIKIGTEELE-----GED 75 (91)
T ss_pred CccEEEEcCc-chHHHHHHHHHHHHc-CCCEEEEEecchhhHhhHhHHHHHHHhcCCCceEEEEEecceeee-----cCC
Confidence 4699999986 899999999999997 699999999999999999999999999966566654 5555542 133
Q ss_pred CCccceeeEEeeEEEEEEec
Q 025488 95 GLVPVEMTRHVSMISITFST 114 (252)
Q Consensus 95 gld~v~~~R~Vs~I~ItLSk 114 (252)
| .+++||+|+|.|.+
T Consensus 76 g-----r~~~VS~IeI~L~k 90 (91)
T COG1581 76 G-----RTRNVSTIEIVLAK 90 (91)
T ss_pred C-----ceeeEEEEEEEEec
Confidence 3 37899999999986
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=99.71 E-value=6.7e-17 Score=118.97 Aligned_cols=65 Identities=38% Similarity=0.612 Sum_probs=58.1
Q ss_pred CeEEEcCCCchhHHHHHHHHHH---hhcCCCEEEEEEcchhHHHHHHHHHHHHHhcC-CCeeEeEEEEE
Q 025488 19 NEIRITTQGAIRNYITYATTLL---QEKHAKEIVLKAMGQAINKTVAIAEIIKKRIP-QLHQDTAISSV 83 (252)
Q Consensus 19 NeIrVt~~~~i~nyV~~A~~lL---~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi~-gLhQit~I~s~ 83 (252)
|+|+|++++++++||.+|+++| ++.+.++|+|+|+|+||+|||+||||||+++. +|||++.+.++
T Consensus 1 n~I~V~~~~~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv~~~t~t 69 (70)
T PF01918_consen 1 NEIYVSSNSPIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQVNKITST 69 (70)
T ss_dssp SEEEE-STS-HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEEEEEEEE
T ss_pred CEEEECCCCCHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEEEEEecc
Confidence 7999999999999999999999 44578999999999999999999999999995 89999988653
No 6
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=99.45 E-value=3.8e-13 Score=113.23 Aligned_cols=93 Identities=22% Similarity=0.340 Sum_probs=67.2
Q ss_pred CCeEEEcCCCchhHHHHHHHHHHhhc-------------------C------------CCEEEEEEcchhHHHHHHHHHH
Q 025488 18 ENEIRITTQGAIRNYITYATTLLQEK-------------------H------------AKEIVLKAMGQAINKTVAIAEI 66 (252)
Q Consensus 18 ~NeIrVt~~~~i~nyV~~A~~lL~~k-------------------~------------~~~VvIkg~G~AIsKAV~vAEI 66 (252)
++.|+|+++++|+..|..+.+||..- . .++|+|||||+||.||++||.-
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 57999999999999999999999641 1 2799999999999999999999
Q ss_pred HHHhcCCCeeEeEEEEEEeeecccccc------------------CCCccceeeEEeeEEEEE
Q 025488 67 IKKRIPQLHQDTAISSVSITDTWEPIE------------------EGLVPVEMTRHVSMISIT 111 (252)
Q Consensus 67 LKrRi~gLhQit~I~s~~i~D~~EP~e------------------Egld~v~~~R~Vs~I~It 111 (252)
|++.. ++...+.++|+++.|++++.+ +..++...+|.||+|+|.
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 677788999999999999763 445678999999999984
No 7
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=98.06 E-value=1.7e-05 Score=75.63 Aligned_cols=50 Identities=22% Similarity=0.159 Sum_probs=22.6
Q ss_pred eEEeeEEEEEEecCCCCC-CCCCCCCCCCCCCCcchhhhhHHhhhcCCCCCCCCc
Q 025488 102 TRHVSMISITFSTRELNK-NSPGYQSPHNAEQPKLQYRYQQQQQQQNQPPRQGRI 155 (252)
Q Consensus 102 ~R~Vs~I~ItLSk~~LD~-~~pGYQ~P~~~~~vk~~~~~~~~~~~~~~~~~~~~~ 155 (252)
++..|+|+=.+-...-|. .-+==.+|.|+|+ ..+++.+|..+++.-++++
T Consensus 288 e~Taski~k~~igrvPDRGGR~nE~~ppppem----pswqqqq~~~~~~ggrggg 338 (465)
T KOG3973|consen 288 ERTASKIHKLSIGRVPDRGGRTNEMVPPPPEM----PSWQQQQHTFDRQGGRGGG 338 (465)
T ss_pred hhhhhhhcccccccCCCCCCCcccCCCCCCCC----CcHHHhcCCCCCCCCcCCC
Confidence 345566664444333354 2222345555543 3344555544444433333
No 8
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=97.06 E-value=0.0026 Score=67.31 Aligned_cols=16 Identities=56% Similarity=0.854 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCCCCCC
Q 025488 230 GGGRGYARGRGRTGGR 245 (252)
Q Consensus 230 ~~grg~~rg~~~~~~~ 245 (252)
|-+|+++||++.+.+.
T Consensus 1255 GfgrgggrgagggGgf 1270 (1282)
T KOG0921|consen 1255 GFGRGGGRGAGGGGGF 1270 (1282)
T ss_pred CcCCCCCCCCCCCCCC
Confidence 3334444444443333
No 9
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=95.49 E-value=0.036 Score=53.47 Aligned_cols=16 Identities=63% Similarity=1.039 Sum_probs=7.2
Q ss_pred cccCCC-ccCCCCCCcc
Q 025488 184 RGRGRS-YARGGYGNYQ 199 (252)
Q Consensus 184 rgrgrg-~gr~~~g~~~ 199 (252)
||+||| +|+|+.++|.
T Consensus 369 rGgGRGggG~GGGggyq 385 (465)
T KOG3973|consen 369 RGGGRGGGGRGGGGGYQ 385 (465)
T ss_pred CCCCCCCCCCCCCCCCc
Confidence 333443 4455555443
No 10
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=93.93 E-value=0.35 Score=51.91 Aligned_cols=7 Identities=29% Similarity=0.876 Sum_probs=3.3
Q ss_pred eeccccc
Q 025488 86 TDTWEPI 92 (252)
Q Consensus 86 ~D~~EP~ 92 (252)
.|+|.-+
T Consensus 1082 VDdWIkl 1088 (1282)
T KOG0921|consen 1082 VDDWIKL 1088 (1282)
T ss_pred eeceeeE
Confidence 3555433
No 11
>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=88.48 E-value=10 Score=29.70 Aligned_cols=51 Identities=18% Similarity=0.320 Sum_probs=35.4
Q ss_pred CeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcc-hhHHHHHHHHHHHHHhc
Q 025488 19 NEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMG-QAINKTVAIAEIIKKRI 71 (252)
Q Consensus 19 NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G-~AIsKAV~vAEILKrRi 71 (252)
+.++|+++++....-..-...|.+. ..+.|.++| .|++.||.-.-|-+.-+
T Consensus 2 e~LKVSs~S~p~~vAgAIa~~lre~--~~v~lqaiGa~AvnqAvKAIAiAR~~l 53 (86)
T PF04232_consen 2 EVLKVSSKSNPNAVAGAIAGVLREG--GKVELQAIGAGAVNQAVKAIAIARGYL 53 (86)
T ss_dssp -EEEE-TT--HHHHHHHHHHHHHHT--SEEEEEE-SHHHHHHHHHHHHHHHHHH
T ss_pred ceEEEcCCCCHHHHHHHHHHHHhcC--CcEEEEEECHHHHHHHHHHHHHHHHhh
Confidence 4689999998888887777777753 599999999 57888887766666544
No 12
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=77.74 E-value=16 Score=32.79 Aligned_cols=34 Identities=18% Similarity=0.111 Sum_probs=15.0
Q ss_pred eEEEEEEecC-CCCCCCCCCCCCCCCCCCcchhhh
Q 025488 106 SMISITFSTR-ELNKNSPGYQSPHNAEQPKLQYRY 139 (252)
Q Consensus 106 s~I~ItLSk~-~LD~~~pGYQ~P~~~~~vk~~~~~ 139 (252)
..++|+||-. .-....|+=+-=++.+.+-|++.|
T Consensus 104 ~~fsIK~~dgv~assfk~g~k~fi~p~KllPl~RF 138 (215)
T KOG3262|consen 104 VHFSIKPSDGVQASSFKPGDKLFIDPDKLLPLDRF 138 (215)
T ss_pred cEEEEecCCCceeecccCCCeEEecccccCcHhhc
Confidence 4555666531 111123333333445555565555
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=74.45 E-value=1.7 Score=44.36 Aligned_cols=35 Identities=20% Similarity=0.292 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHhcCCCeeEeEE-EE-EEeeecccccc
Q 025488 59 KTVAIAEIIKKRIPQLHQDTAI-SS-VSITDTWEPIE 93 (252)
Q Consensus 59 KAV~vAEILKrRi~gLhQit~I-~s-~~i~D~~EP~e 93 (252)
.|+.+++=|-.-+..||-..-+ .+ ..|+-.|.+..
T Consensus 429 ~aLkt~~NI~~lik~L~~~pPsf~~~~~itlSWk~~~ 465 (556)
T PF05918_consen 429 TALKTTNNILALIKDLFHNPPSFKSTKNITLSWKEAK 465 (556)
T ss_dssp HHHHHHHHHHHHHCC----------------TTS---
T ss_pred HHHHHHhhHHHHHHHHhhCCcccccccccceeeeecc
Confidence 4554444444445556544322 22 23555665443
No 14
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=70.66 E-value=1.4 Score=44.98 Aligned_cols=6 Identities=50% Similarity=0.551 Sum_probs=1.4
Q ss_pred EEEecC
Q 025488 110 ITFSTR 115 (252)
Q Consensus 110 ItLSk~ 115 (252)
|+||-.
T Consensus 457 itlSWk 462 (556)
T PF05918_consen 457 ITLSWK 462 (556)
T ss_dssp ---TTS
T ss_pred cceeee
Confidence 555543
No 15
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=37.19 E-value=93 Score=30.82 Aligned_cols=64 Identities=19% Similarity=0.293 Sum_probs=46.5
Q ss_pred CCCeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcc---hhHHHHHHHHHHHHHhcCCCeeEeEEEEEEeeec
Q 025488 17 NENEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMG---QAINKTVAIAEIIKKRIPQLHQDTAISSVSITDT 88 (252)
Q Consensus 17 ~~NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G---~AIsKAV~vAEILKrRi~gLhQit~I~s~~i~D~ 88 (252)
+.-.|=||.=+-...+|..|.+.|++.+++.+++||.| +|+.+-|. . .-++-+..|.++++.|+
T Consensus 184 ~kp~I~iTmfGvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li~------~--G~~~~VlDlTttEl~d~ 250 (403)
T PF06792_consen 184 DKPLIGITMFGVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLIR------E--GQFDGVLDLTTTELADE 250 (403)
T ss_pred CCcEEEEECCCCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHHH------c--CCcEEEEECcHHHHHHH
Confidence 45578888877778899999999999999999999998 56666542 1 11344455555555554
No 16
>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=36.63 E-value=1e+02 Score=24.16 Aligned_cols=38 Identities=13% Similarity=0.309 Sum_probs=28.6
Q ss_pred CCEEEEEEcchhHHHHHHHHHHHHHhcCCC-eeEeEEEEEE
Q 025488 45 AKEIVLKAMGQAINKTVAIAEIIKKRIPQL-HQDTAISSVS 84 (252)
Q Consensus 45 ~~~VvIkg~G~AIsKAV~vAEILKrRi~gL-hQit~I~s~~ 84 (252)
-+.|+|-++|..+..|+..|++|+.. |+ ..+..+.+..
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 46889999999999999999999986 43 2444554443
No 17
>PRK02399 hypothetical protein; Provisional
Probab=34.42 E-value=1.1e+02 Score=30.32 Aligned_cols=65 Identities=17% Similarity=0.251 Sum_probs=46.6
Q ss_pred CCCeEEEcCCCchhHHHHHHHHHHhhcCCCEEEEEEcc---hhHHHHHHHHHHHHHhcCCCeeEeEEEEEEeeecc
Q 025488 17 NENEIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMG---QAINKTVAIAEIIKKRIPQLHQDTAISSVSITDTW 89 (252)
Q Consensus 17 ~~NeIrVt~~~~i~nyV~~A~~lL~~k~~~~VvIkg~G---~AIsKAV~vAEILKrRi~gLhQit~I~s~~i~D~~ 89 (252)
+.-.|=||.=+-...+|..|.+.|++++++.+|+||.| +|+.+-|. . .-++-+..|.++++.|++
T Consensus 185 ~kp~Ig~TmfGvTtp~v~~~~~~Le~~GyEvlVFHATG~GGraME~Li~------~--G~~~gVlDlTttEv~d~l 252 (406)
T PRK02399 185 DKPLIGLTMFGVTTPCVQAAREELEARGYEVLVFHATGTGGRAMEKLID------S--GLIAGVLDLTTTEVCDEL 252 (406)
T ss_pred CCceEEEecCCCcHHHHHHHHHHHHhCCCeEEEEcCCCCchHHHHHHHH------c--CCceEEEEcchHHHHHHH
Confidence 34567777766666899999999999899999999998 57666442 1 114555566666666653
No 18
>KOG1402 consensus Ornithine aminotransferase [Amino acid transport and metabolism]
Probab=33.53 E-value=2.1e+02 Score=28.29 Aligned_cols=80 Identities=16% Similarity=0.222 Sum_probs=48.2
Q ss_pred HHHHHHHHHhhcCCCEEEEEEcc-hhHHHHHHHHHHHHHhcCCCeeEeEEEEEEeeeccccccCCCccceeeEEeeEEEE
Q 025488 32 YITYATTLLQEKHAKEIVLKAMG-QAINKTVAIAEIIKKRIPQLHQDTAISSVSITDTWEPIEEGLVPVEMTRHVSMISI 110 (252)
Q Consensus 32 yV~~A~~lL~~k~~~~VvIkg~G-~AIsKAV~vAEILKrRi~gLhQit~I~s~~i~D~~EP~eEgld~v~~~R~Vs~I~I 110 (252)
|-.|..+|| +++.|.=...| .|+..|+.+|-..-.+.+++-+...+-.......| -|..++ |
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 46788888888 57888888888776666654433322111111111 233343 5
Q ss_pred EEecCCCCCCCCCCCCCCCC
Q 025488 111 TFSTRELNKNSPGYQSPHNA 130 (252)
Q Consensus 111 tLSk~~LD~~~pGYQ~P~~~ 130 (252)
.||.++ .+-.+||+++|-
T Consensus 169 s~s~d~--ds~~~fgp~~P~ 186 (427)
T KOG1402|consen 169 SLSTDP--DSWDGFGPFLPG 186 (427)
T ss_pred EecCCc--chhhccCCCCCC
Confidence 677777 566799999997
No 19
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=30.32 E-value=79 Score=32.63 Aligned_cols=14 Identities=29% Similarity=0.498 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHh
Q 025488 57 INKTVAIAEIIKKR 70 (252)
Q Consensus 57 IsKAV~vAEILKrR 70 (252)
...|..+++.|+.+
T Consensus 255 k~~a~~l~~~L~~~ 268 (629)
T PRK11634 255 KNATLEVAEALERN 268 (629)
T ss_pred HHHHHHHHHHHHhC
Confidence 45556666666653
No 20
>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=29.84 E-value=1.3e+02 Score=20.77 Aligned_cols=33 Identities=18% Similarity=0.339 Sum_probs=21.6
Q ss_pred cchhHHHHHHHHHHHHHhcCCCeeEeEEEEEEe
Q 025488 53 MGQAINKTVAIAEIIKKRIPQLHQDTAISSVSI 85 (252)
Q Consensus 53 ~G~AIsKAV~vAEILKrRi~gLhQit~I~s~~i 85 (252)
.+..+..+..+++.||+.++.+.....++..++
T Consensus 6 c~~G~~~s~~l~~~l~~~~~~~~~~~~~~~~~~ 38 (84)
T cd00133 6 CGSGIGSSSMLAEKLEKAAKELGIEVKVEAQGL 38 (84)
T ss_pred CCCcHhHHHHHHHHHHHHHHHCCCeEEEEEccc
Confidence 444555666788888888876666556655444
No 21
>COG2065 PyrR Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=25.98 E-value=97 Score=27.45 Aligned_cols=59 Identities=25% Similarity=0.451 Sum_probs=33.4
Q ss_pred CCCEEEEEEcchhHHHHHHHHHHHHHhcCCCeeEeEEEEEEeeeccccccCCCccceeeEEeeEEEEEEecCCCCCCCCC
Q 025488 44 HAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTAISSVSITDTWEPIEEGLVPVEMTRHVSMISITFSTRELNKNSPG 123 (252)
Q Consensus 44 ~~~~VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~I~s~~i~D~~EP~eEgld~v~~~R~Vs~I~ItLSk~~LD~~~pG 123 (252)
+.+.++|-|+= ++-|.+||.|+.++..| ||+ ..-+-.|.|||.++.|..+.+
T Consensus 29 ~~~~~vlvGIk---trGv~lA~rl~~~i~~~-------------------Eg~-----~vp~g~lDIt~yRDDl~~~~~- 80 (179)
T COG2065 29 GLDNLVLVGIK---TRGVPLAERLAERIEEL-------------------EGI-----EVPVGELDITLYRDDLTQKGP- 80 (179)
T ss_pred CCCceEEEeEe---cCCHHHHHHHHHHHHHH-------------------hCC-----CCCeeeEEeEEeechhhhcCc-
Confidence 45666665542 34566777777765311 111 112346789999988888665
Q ss_pred CCCCCCC
Q 025488 124 YQSPHNA 130 (252)
Q Consensus 124 YQ~P~~~ 130 (252)
.+++...
T Consensus 81 ~~p~~~~ 87 (179)
T COG2065 81 LRPQAKT 87 (179)
T ss_pred cCCcccC
Confidence 4444433
No 22
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=25.64 E-value=1.8e+02 Score=27.87 Aligned_cols=41 Identities=10% Similarity=0.240 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHH
Q 025488 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKK 69 (252)
Q Consensus 29 i~nyV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKr 69 (252)
....+..+..++.....+.|++.|||....+.-.|.+.|+.
T Consensus 133 ~~EI~~qv~~~~~~~~i~~IvfmG~GEPl~n~~~vi~~l~~ 173 (349)
T PRK14463 133 TAEIVNQVCAVKRDVPVRNIVFMGMGEPLANLDNVIPALQI 173 (349)
T ss_pred HHHHHHHHHHHHhcCCccEEEEecCCcchhcHHHHHHHHHH
Confidence 33444444444444468999999999987766666666654
No 23
>CHL00199 infC translation initiation factor 3; Provisional
Probab=24.91 E-value=4e+02 Score=23.62 Aligned_cols=56 Identities=16% Similarity=0.162 Sum_probs=40.4
Q ss_pred CCCCeEEEcCCCchhH---HHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHHhc
Q 025488 16 INENEIRITTQGAIRN---YITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRI 71 (252)
Q Consensus 16 ~~~NeIrVt~~~~i~n---yV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi 71 (252)
..-.||+++.+-..+. =+..|.++|++...=.|+|+-.|+-+..+=..-++|.+-+
T Consensus 94 ~~~KEirl~~~I~~hDl~~K~k~~~kFL~~G~kVkv~i~frGRE~~~~e~g~~ll~r~~ 152 (182)
T CHL00199 94 SSIKEVKMRYKIEEHDYKVRINQAFKFLQAGDKVKATLTFRGREIQHLNLAINLLNKMA 152 (182)
T ss_pred ccceEEEecCCCCccHHHHHHHHHHHHHHCCCEEEEEEEEchhHHhhHHHHHHHHHHHH
Confidence 3457899887654444 4668999998766678889999998887766666665543
No 24
>PRK05261 putative phosphoketolase; Provisional
Probab=24.36 E-value=1.1e+02 Score=32.82 Aligned_cols=29 Identities=28% Similarity=0.575 Sum_probs=27.1
Q ss_pred CEEEEEEcchhHHH-HHHHHHHHHHhcCCC
Q 025488 46 KEIVLKAMGQAINK-TVAIAEIIKKRIPQL 74 (252)
Q Consensus 46 ~~VvIkg~G~AIsK-AV~vAEILKrRi~gL 74 (252)
..|||-+.|.-+.. |+.+|++|+..+++|
T Consensus 614 pDvvL~atGsev~leAlaAa~~L~~~~pgi 643 (785)
T PRK05261 614 PDVVLACAGDVPTLETLAAADLLREHFPDL 643 (785)
T ss_pred CCEEEEEeCcHhhHHHHHHHHHHHhhCCCC
Confidence 58999999999999 999999999998885
No 25
>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=24.20 E-value=1.7e+02 Score=21.57 Aligned_cols=34 Identities=18% Similarity=0.226 Sum_probs=17.9
Q ss_pred EEEEcchhHHHHHHHHHHHHHhcCCCeeEeEEEEEE
Q 025488 49 VLKAMGQAINKTVAIAEIIKKRIPQLHQDTAISSVS 84 (252)
Q Consensus 49 vIkg~G~AIsKAV~vAEILKrRi~gLhQit~I~s~~ 84 (252)
++=+.|.+ .+-.+++-||+.|+.+.....+....
T Consensus 5 ivC~~G~~--tS~~l~~~i~~~~~~~~i~~~v~~~~ 38 (89)
T cd05566 5 VACGTGVA--TSTVVASKVKELLKENGIDVKVEQCK 38 (89)
T ss_pred EECCCCcc--HHHHHHHHHHHHHHHCCCceEEEEec
Confidence 33344443 45566777777776544444444333
No 26
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=23.68 E-value=2.2e+02 Score=27.80 Aligned_cols=58 Identities=19% Similarity=0.325 Sum_probs=34.3
Q ss_pred hhHHHHHHHHHHhhc-------CCCEEEEEEcchhHHH---HHHHHHHHHHhc---CCC-eeEeEEEEEEee
Q 025488 29 IRNYITYATTLLQEK-------HAKEIVLKAMGQAINK---TVAIAEIIKKRI---PQL-HQDTAISSVSIT 86 (252)
Q Consensus 29 i~nyV~~A~~lL~~k-------~~~~VvIkg~G~AIsK---AV~vAEILKrRi---~gL-hQit~I~s~~i~ 86 (252)
|..+|..+...+.+. ..+.|++.|||....+ .+.+.++|+... .++ +--+.|+|+-+.
T Consensus 154 Iv~Qv~~~~~~~~~~~~~~~~~~i~nVvfmGmGEPLlN~d~V~~~i~~l~~~~~~g~gis~r~ITvST~Gl~ 225 (373)
T PRK14459 154 IVEQVRAAARALRDGEVPGGPGRLSNVVFMGMGEPLANYKRVVAAVRRITAPAPEGLGISARNVTVSTVGLV 225 (373)
T ss_pred HHHHHHHHHHHhhhcccccCCCceeEEEEecCCcchhhHHHHHHHHHHHhCcccccCCccCCEEEEECcCch
Confidence 455666666666432 2567999999987654 555666666632 233 224566665443
No 27
>cd04823 ALAD_PBGS_aspartate_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. All of PBGS_aspartate_rich contain an aspartate rich metal binding site with the general sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric magnesiu
Probab=22.77 E-value=4.9e+02 Score=25.17 Aligned_cols=55 Identities=18% Similarity=0.247 Sum_probs=39.3
Q ss_pred hhHHHHHHHHHHhhcCCCEEEEEEc---------ch-------hHHHHHHHHHHHHHhcCCCeeEeEEEEEEeee
Q 025488 29 IRNYITYATTLLQEKHAKEIVLKAM---------GQ-------AINKTVAIAEIIKKRIPQLHQDTAISSVSITD 87 (252)
Q Consensus 29 i~nyV~~A~~lL~~k~~~~VvIkg~---------G~-------AIsKAV~vAEILKrRi~gLhQit~I~s~~i~D 87 (252)
+...+..+..+++ .+.+.|.|.+. |. -|.+||. .||..|+.|..++.++.-+-++
T Consensus 53 ~d~l~~~v~~~~~-~Gi~~v~lFgv~~~~~KD~~gs~A~~~~g~v~~air---~iK~~~p~l~vi~DVclc~YT~ 123 (320)
T cd04823 53 IDELLKEAEEAVD-LGIPAVALFPVTPPELKSEDGSEAYNPDNLVCRAIR---AIKEAFPELGIITDVALDPYTS 123 (320)
T ss_pred HHHHHHHHHHHHH-cCCCEEEEecCCCcccCCcccccccCCCChHHHHHH---HHHHhCCCcEEEEeeeccCCCC
Confidence 5556666666665 58999999998 11 2566654 5899999999998886654444
No 28
>cd05568 PTS_IIB_bgl_like PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved in sugar utilization. The domain architecture of the IIB-containing protein includes a region N-terminal to the IIB domain which is homologous to the BglG transcription antiterminator with an RNA-binding domain followed by two homologous domains, PRD1 and PRD2 (PTS Regulation Domains). C-terminal to the IIB domain is a domain similar to the PTS IIA domain. In this system, the BglG-like region and the IIB and IIA-like domains are all expressed together as a single multidomain protein. 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 this sensory system with similarity to the bacterial
Probab=22.40 E-value=1.1e+02 Score=21.98 Aligned_cols=31 Identities=19% Similarity=0.293 Sum_probs=20.0
Q ss_pred EEEEEcchhHHHHHHHHHHHHHhcCCCeeEeEE
Q 025488 48 IVLKAMGQAINKTVAIAEIIKKRIPQLHQDTAI 80 (252)
Q Consensus 48 VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~I 80 (252)
+++-+.|.+ .+-.++..|++.|+.+..+..+
T Consensus 4 livC~~G~~--~s~~l~~~l~~~~~~~~~v~~~ 34 (85)
T cd05568 4 LVVCPSGIG--TSRLLKSKLKKLFPEIEIIDVI 34 (85)
T ss_pred EEECCCCHH--HHHHHHHHHHHHCCCceEEEEE
Confidence 444445544 4567789999999876665433
No 29
>PRK13660 hypothetical protein; Provisional
Probab=21.18 E-value=3.4e+02 Score=23.88 Aligned_cols=63 Identities=13% Similarity=0.136 Sum_probs=37.7
Q ss_pred hhHHHHHHHHHHhhcCCCEEEEEEcchhHHHHHHHHHHHHHhcCCCeeEeEEEEEEeeecccc
Q 025488 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTAISSVSITDTWEP 91 (252)
Q Consensus 29 i~nyV~~A~~lL~~k~~~~VvIkg~G~AIsKAV~vAEILKrRi~gLhQit~I~s~~i~D~~EP 91 (252)
|+.-|...+..|-+++..-+++-|.=-.=.=|..||.-||..++.|.-++-+-...-.+.|.+
T Consensus 27 IK~aL~~~l~~~~e~G~~wfi~ggalG~d~wAaEvvl~LK~~yp~lkL~~~~PF~~q~~~W~e 89 (182)
T PRK13660 27 IKKAIKRKLIALLEEGLEWVIISGQLGVELWAAEVVLELKEEYPDLKLAVITPFEEHGENWNE 89 (182)
T ss_pred HHHHHHHHHHHHHHCCCCEEEECCcchHHHHHHHHHHHHHhhCCCeEEEEEeCccchhhcCCH
Confidence 445555555445445766555543222223567788889999988776666655555566643
No 30
>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=20.84 E-value=1.4e+02 Score=23.49 Aligned_cols=32 Identities=25% Similarity=0.437 Sum_probs=25.6
Q ss_pred CCchhHHHHHHHHHHhhcCCCEEEEEEcchhHH
Q 025488 26 QGAIRNYITYATTLLQEKHAKEIVLKAMGQAIN 58 (252)
Q Consensus 26 ~~~i~nyV~~A~~lL~~k~~~~VvIkg~G~AIs 58 (252)
...+..||..|+++|++.+. ...+.+||-.|.
T Consensus 14 ~~s~s~yVa~~i~~l~~sGl-~y~~~pm~T~IE 45 (97)
T TIGR00106 14 GASVSSYVAAAIEVLKESGL-KYELHPMGTLIE 45 (97)
T ss_pred CCcHHHHHHHHHHHHHHcCC-CeEecCCccEEe
Confidence 34789999999999987665 677888887654
No 31
>PRK14460 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.76 E-value=1.4e+02 Score=28.65 Aligned_cols=58 Identities=16% Similarity=0.251 Sum_probs=34.5
Q ss_pred chhHHHHHHHHHHhhc----C-CCEEEEEEcchhHHHHHHHHHHHHHhc--CCCe---eEeEEEEEEe
Q 025488 28 AIRNYITYATTLLQEK----H-AKEIVLKAMGQAINKTVAIAEIIKKRI--PQLH---QDTAISSVSI 85 (252)
Q Consensus 28 ~i~nyV~~A~~lL~~k----~-~~~VvIkg~G~AIsKAV~vAEILKrRi--~gLh---Qit~I~s~~i 85 (252)
-|...|..+...+.+. . .+.|++.|||...-+.-.|.+.||.-. .+|+ -.+.|+|.-+
T Consensus 134 EI~~qv~~~~~~~~~~g~g~~~i~nIvfmGmGEPLln~~~v~~~l~~l~~~~Gl~~~~r~itvsT~G~ 201 (354)
T PRK14460 134 EILGQVLVAREHLGDNGPDHPILRNLVFMGMGEPLLNLDEVMRSLRTLNNEKGLNFSPRRITVSTCGI 201 (354)
T ss_pred HHHHHHHHHHHHHhhccCCCcceeEEEEecCCcccCCHHHHHHHHHHHhhhhccCCCCCeEEEECCCC
Confidence 4555565556666432 1 689999999987766555666665422 2453 2355555544
Done!