Query 028304
Match_columns 210
No_of_seqs 142 out of 348
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 09:26:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028304.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028304hhsearch_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 3.6E-49 7.9E-54 327.0 13.6 144 1-144 1-144 (179)
2 PRK04015 DNA/RNA-binding prote 99.9 3.3E-21 7.2E-26 147.1 11.5 90 16-115 2-91 (91)
3 TIGR00285 DNA-binding protein 99.8 4.4E-20 9.5E-25 139.8 11.5 87 18-114 1-87 (87)
4 COG1581 Ssh10b Archaeal DNA-bi 99.8 1.2E-19 2.6E-24 137.3 11.8 87 17-114 3-90 (91)
5 PF01918 Alba: Alba; InterPro 99.7 1.8E-16 3.9E-21 113.5 10.1 65 19-83 1-69 (70)
6 PF12328 Rpp20: Rpp20 subunit 99.3 6.2E-12 1.3E-16 103.2 9.8 93 18-111 3-144 (144)
7 KOG3973 Uncharacterized conser 91.7 0.13 2.8E-06 48.6 2.7 16 155-170 447-462 (465)
8 PF05918 API5: Apoptosis inhib 91.3 0.059 1.3E-06 53.2 0.0 35 59-93 429-465 (556)
9 PF04232 SpoVS: Stage V sporul 80.1 24 0.00052 26.9 9.1 51 19-71 2-53 (86)
10 KOG3293 Small nuclear ribonucl 78.7 2.1 4.6E-05 34.9 2.9 23 149-171 99-122 (134)
11 PTZ00070 40S ribosomal protein 78.4 1.9 4.1E-05 39.0 2.8 14 154-167 17-30 (257)
12 KOG3973 Uncharacterized conser 67.9 5.2 0.00011 38.1 3.2 19 101-119 287-305 (465)
13 KOG0105 Alternative splicing f 66.0 5.8 0.00013 34.9 2.9 19 154-173 93-111 (241)
14 PTZ00034 40S ribosomal protein 61.8 8.2 0.00018 31.4 2.8 10 89-98 67-76 (124)
15 PF12861 zf-Apc11: Anaphase-pr 59.5 4.1 8.8E-05 31.1 0.7 8 188-195 55-62 (85)
16 PTZ00034 40S ribosomal protein 56.8 13 0.00029 30.2 3.3 12 154-165 112-123 (124)
17 PTZ00146 fibrillarin; Provisio 53.7 12 0.00026 34.4 2.8 6 161-166 46-51 (293)
18 KOG3262 H/ACA small nucleolar 53.3 20 0.00043 31.5 3.9 6 108-113 106-111 (215)
19 KOG0116 RasGAP SH3 binding pro 52.3 13 0.00027 35.9 2.9 7 49-55 241-247 (419)
20 KOG2945 Predicted RNA-binding 49.8 13 0.00027 35.4 2.4 8 151-158 331-338 (365)
21 PF09363 XFP_C: XFP C-terminal 47.2 48 0.0011 29.1 5.4 42 44-89 33-75 (203)
22 PRK10590 ATP-dependent RNA hel 44.3 29 0.00063 32.7 3.9 10 60-69 258-267 (456)
23 PRK05261 putative phosphoketol 43.2 39 0.00084 35.1 4.9 30 45-74 613-643 (785)
24 PF11705 RNA_pol_3_Rpc31: DNA- 39.5 19 0.00041 31.3 1.8 6 161-166 18-23 (233)
25 KOG3172 Small nuclear ribonucl 35.8 37 0.00081 27.2 2.7 8 160-167 103-110 (119)
26 PRK10590 ATP-dependent RNA hel 34.0 68 0.0015 30.2 4.7 23 33-55 258-280 (456)
27 KOG3457 Sec61 protein transloc 32.9 64 0.0014 24.9 3.5 16 191-206 65-80 (88)
28 PF02780 Transketolase_C: Tran 32.4 1.3E+02 0.0029 22.8 5.4 28 45-74 9-36 (124)
29 KOG0523 Transketolase [Carbohy 31.0 81 0.0017 32.1 4.8 64 18-93 481-546 (632)
30 PF07794 DUF1633: Protein of u 29.2 95 0.0021 31.3 4.9 25 167-191 485-518 (790)
31 PRK02399 hypothetical protein; 28.3 1.7E+02 0.0037 28.3 6.3 64 18-89 186-252 (406)
32 PF02089 Palm_thioest: Palmito 27.0 77 0.0017 29.0 3.6 41 44-88 5-48 (279)
33 PF06792 UPF0261: Uncharacteri 27.0 1.8E+02 0.0039 28.1 6.2 65 17-89 184-251 (403)
34 KOG0921 Dosage compensation co 25.9 52 0.0011 35.4 2.5 14 157-170 1258-1271(1282)
35 KOG4298 CAP-binding protein co 25.1 45 0.00097 29.5 1.7 20 190-209 188-207 (245)
36 COG5194 APC11 Component of SCF 24.9 33 0.00071 26.3 0.7 11 185-195 54-64 (88)
37 PLN03134 glycine-rich RNA-bind 21.5 1.2E+02 0.0025 24.5 3.4 6 20-25 36-41 (144)
38 KOG2930 SCF ubiquitin ligase, 21.0 43 0.00093 26.8 0.7 10 187-196 83-92 (114)
39 PF06692 MNSV_P7B: Melon necro 21.0 1.1E+02 0.0023 21.9 2.6 31 172-203 2-32 (61)
No 1
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.6e-49 Score=326.96 Aligned_cols=144 Identities=45% Similarity=0.690 Sum_probs=139.8
Q ss_pred CCCceeccCCCCCCCCCCCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEE
Q 028304 1 MDRYQRVEKPKAETPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVGLHQNTVI 80 (210)
Q Consensus 1 Md~Y~rV~kp~~~~p~~~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G~AIsKAV~VAEILKrRi~GLhQ~t~I 80 (210)
||.|++|-||+++.|++.|+|||+.+++++|||.||+.+|++++.+.|||+|||+||+|+|+||||||||++||||+|+|
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 EEEEeeccceecccCCCcceeeeeeeEEEEEEecccCCCCCCCcCCCCCcCCCcccccccCCCC
Q 028304 81 GSTDITDTWEPLEEGLLPLETTRHVSMITITLSKKELNRSSVGYQPPLPAEQVKPLIEFDYDGE 144 (210)
Q Consensus 81 ~tv~i~d~~eP~eEGl~~l~~~R~VS~I~ItLSk~~LD~~~~GYQ~Plp~~~v~~~~~~~~~~~ 144 (210)
.+++++|.|+|.+|||++++++|+||+|+|+||+++||++++|||+|.|....+.+..-+|++.
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 9999999999999999999999999999999999999999999999999888888777777654
No 2
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.86 E-value=3.3e-21 Score=147.11 Aligned_cols=90 Identities=32% Similarity=0.471 Sum_probs=73.8
Q ss_pred CCCCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEEEEEEeeccceecccC
Q 028304 16 IDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVGLHQNTVIGSTDITDTWEPLEEG 95 (210)
Q Consensus 16 ~~~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G~AIsKAV~VAEILKrRi~GLhQ~t~I~tv~i~d~~eP~eEG 95 (210)
..+|+|+|++++.| |||.+++.+|++ +.++|+|||+|+||+|||+|||+||+|+-..+ ++..+++..+-...++|
T Consensus 2 ~~en~i~Ig~kpvm-nYV~~~~~~l~~-g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v---~v~~I~i~se~i~~~~g 76 (91)
T PRK04015 2 AEENVVLVGKKPVM-NYVLAVLTQFNQ-GAKEVVIKARGRAISKAVDVAEIVRNRFLPDV---EIKEIKIGTEEVTSEDG 76 (91)
T ss_pred CCCCEEEEcCCcHH-HHHHHHHHHHhC-CCCeEEEEEeccccchhhhHHHHHHHhccCCe---EEEEEEeccEEeecCCC
Confidence 35899999999755 999999999994 89999999999999999999999999984334 44555555443334556
Q ss_pred CCcceeeeeeeEEEEEEecc
Q 028304 96 LLPLETTRHVSMITITLSKK 115 (210)
Q Consensus 96 l~~l~~~R~VS~I~ItLSk~ 115 (210)
.+|+||+|+|+|++.
T Consensus 77 -----~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 77 -----RESNVSTIEIVLEKK 91 (91)
T ss_pred -----cEEEEEEEEEEEecC
Confidence 689999999999874
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=99.83 E-value=4.4e-20 Score=139.84 Aligned_cols=87 Identities=32% Similarity=0.471 Sum_probs=76.0
Q ss_pred CCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEEEEEEeeccceecccCCC
Q 028304 18 ENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVGLHQNTVIGSTDITDTWEPLEEGLL 97 (210)
Q Consensus 18 ~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G~AIsKAV~VAEILKrRi~GLhQ~t~I~tv~i~d~~eP~eEGl~ 97 (210)
+|.|+|++||-| |||.+++.+|++ |.++|+|||+|+||+|||+|||+||+|+...+ ++..+++.++-.+.++|
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 589999999988 999999999996 89999999999999999999999999984333 66667777666666777
Q ss_pred cceeeeeeeEEEEEEec
Q 028304 98 PLETTRHVSMITITLSK 114 (210)
Q Consensus 98 ~l~~~R~VS~I~ItLSk 114 (210)
.+|+||+|+|.|.+
T Consensus 74 ---~~~~VStIEI~l~~ 87 (87)
T TIGR00285 74 ---REVNVSTIEIVLAK 87 (87)
T ss_pred ---ceeeEEEEEEEEeC
Confidence 78899999999975
No 4
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=99.82 E-value=1.2e-19 Score=137.27 Aligned_cols=87 Identities=34% Similarity=0.532 Sum_probs=78.2
Q ss_pred CCCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcChhHHHHHHHHHHHHHhc-CCceeEEEEEEEEeeccceecccC
Q 028304 17 DENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRI-VGLHQNTVIGSTDITDTWEPLEEG 95 (210)
Q Consensus 17 ~~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G~AIsKAV~VAEILKrRi-~GLhQ~t~I~tv~i~d~~eP~eEG 95 (210)
++|.|+|++|+.| |||..++.+|++ |.++|+|||+|+||||||++||+++.|| |++ ++..+++.++-...++|
T Consensus 3 ~envV~vG~KPvm-NYVlAvlt~fn~-g~~eViiKARGraIskAVDvaeivRnrf~p~v----~ik~Iki~se~~~~~~g 76 (91)
T COG1581 3 EENVVLVGKKPVM-NYVLAVLTQFNE-GADEVIIKARGRAISKAVDVAEIVRNRFIPDV----QIKDIKIGTEELEGEDG 76 (91)
T ss_pred CccEEEEcCcchH-HHHHHHHHHHHc-CCCEEEEEecchhhHhhHhHHHHHHHhcCCCc----eEEEEEecceeeecCCC
Confidence 4699999999988 999999999998 7999999999999999999999999998 665 78888887766666667
Q ss_pred CCcceeeeeeeEEEEEEec
Q 028304 96 LLPLETTRHVSMITITLSK 114 (210)
Q Consensus 96 l~~l~~~R~VS~I~ItLSk 114 (210)
.+++||+|+|.|.+
T Consensus 77 -----r~~~VS~IeI~L~k 90 (91)
T COG1581 77 -----RTRNVSTIEIVLAK 90 (91)
T ss_pred -----ceeeEEEEEEEEec
Confidence 68899999999986
No 5
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function. The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
Probab=99.69 E-value=1.8e-16 Score=113.53 Aligned_cols=65 Identities=40% Similarity=0.653 Sum_probs=58.0
Q ss_pred CEEEEcCCCchHHHHHHHHHHH---hhCCCCeEEEEEcChhHHHHHHHHHHHHHhcC-CceeEEEEEEE
Q 028304 19 NEIRITSQGRMRSYITYAMTLL---QERGSNEIVFKAMGRAINKTVTIVELIKRRIV-GLHQNTVIGST 83 (210)
Q Consensus 19 NeIrVt~k~~irnYV~~A~~lL---~~~g~~eVvIkA~G~AIsKAV~VAEILKrRi~-GLhQ~t~I~tv 83 (210)
|+|+|++++++.+||.+|+.+| ++.+.++|+|+|+|+||+|||+|||+||+++. +|||++.+.+.
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 44479999999999999999999999999994 89999988753
No 6
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=99.34 E-value=6.2e-12 Score=103.17 Aligned_cols=93 Identities=26% Similarity=0.370 Sum_probs=67.1
Q ss_pred CCEEEEcCCCchHHHHHHHHHHHhhC-------------------C------------CCeEEEEEcChhHHHHHHHHHH
Q 028304 18 ENEIRITSQGRMRSYITYAMTLLQER-------------------G------------SNEIVFKAMGRAINKTVTIVEL 66 (210)
Q Consensus 18 ~NeIrVt~k~~irnYV~~A~~lL~~~-------------------g------------~~eVvIkA~G~AIsKAV~VAEI 66 (210)
++.|+|++++++-..|.++.++|..- + ..+|+|+|||+||+||++||.-
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 58999999999999999999999521 1 2799999999999999999999
Q ss_pred HHHhcCCceeEEEEEEEEeeccceecc------------------cCCCcceeeeeeeEEEEE
Q 028304 67 IKRRIVGLHQNTVIGSTDITDTWEPLE------------------EGLLPLETTRHVSMITIT 111 (210)
Q Consensus 67 LKrRi~GLhQ~t~I~tv~i~d~~eP~e------------------EGl~~l~~~R~VS~I~It 111 (210)
+++.- ++--.++++||.+.|++++.+ ++.++..++|.||+|+|.
T Consensus 83 Fq~~~-~~~V~V~TgTV~vvDdi~~~e~~~~~~~~~~~~~~~~~~~~~~~esR~R~vS~VEv~ 144 (144)
T PF12328_consen 83 FQRKK-GYKVEVRTGTVEVVDDIVEDEDEDEDEEESEEREDDDDDEDEEPESRTRWVSMVEVA 144 (144)
T ss_dssp HHHTT----EEEEEEEEEEEEE-----------------------------EEEEEEEEEEEE
T ss_pred HhhcC-CeEEEEEeceEEEEEEEeeccccccccccccccccCccccccCccceEEeeEEEEEC
Confidence 98886 677788999999999998653 456677899999999984
No 7
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=91.72 E-value=0.13 Score=48.57 Aligned_cols=16 Identities=44% Similarity=0.592 Sum_probs=9.8
Q ss_pred CCCCCCCccccCCcCC
Q 028304 155 SGRGRSRGRGILCHYG 170 (210)
Q Consensus 155 gg~g~~~g~~~~~~~~ 170 (210)
||||+|.|+|||+|.+
T Consensus 447 ggrgrgggggrg~y~~ 462 (465)
T KOG3973|consen 447 GGRGRGGGGGRGGYRG 462 (465)
T ss_pred CCCCCCCCCCCcccCC
Confidence 3455556667777654
No 8
>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=91.31 E-value=0.059 Score=53.17 Aligned_cols=35 Identities=20% Similarity=0.233 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHhcCCceeEEEEEEE--Eeeccceecc
Q 028304 59 KTVTIVELIKRRIVGLHQNTVIGST--DITDTWEPLE 93 (210)
Q Consensus 59 KAV~VAEILKrRi~GLhQ~t~I~tv--~i~d~~eP~e 93 (210)
.|+.+++=|-.-+.+|+-..-+-.. .|+=.|.+..
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 4554444444445565544433322 2666787653
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=80.13 E-value=24 Score=26.93 Aligned_cols=51 Identities=16% Similarity=0.359 Sum_probs=34.6
Q ss_pred CEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcC-hhHHHHHHHHHHHHHhc
Q 028304 19 NEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMG-RAINKTVTIVELIKRRI 71 (210)
Q Consensus 19 NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G-~AIsKAV~VAEILKrRi 71 (210)
+.++|+++++....-..-...+.+ ...+.|.|+| .|++.||.-.-|-+.-+
T Consensus 2 e~LKVSs~S~p~~vAgAIa~~lre--~~~v~lqaiGa~AvnqAvKAIAiAR~~l 53 (86)
T PF04232_consen 2 EVLKVSSKSNPNAVAGAIAGVLRE--GGKVELQAIGAGAVNQAVKAIAIARGYL 53 (86)
T ss_dssp -EEEE-TT--HHHHHHHHHHHHHH--TSEEEEEE-SHHHHHHHHHHHHHHHHHH
T ss_pred ceEEEcCCCCHHHHHHHHHHHHhc--CCcEEEEEECHHHHHHHHHHHHHHHHhh
Confidence 468999999986666666667776 3599999999 58888887666666554
No 10
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=78.68 E-value=2.1 Score=34.89 Aligned_cols=23 Identities=39% Similarity=0.593 Sum_probs=10.9
Q ss_pred CCCCCCCCCC-CCCccccCCcCCC
Q 028304 149 GPRRGRSGRG-RSRGRGILCHYGI 171 (210)
Q Consensus 149 g~~rgrgg~g-~~~g~~~~~~~~~ 171 (210)
+||+|+|.++ ++||+++|+..|+
T Consensus 99 grG~gng~~~~~~rg~~~g~~~g~ 122 (134)
T KOG3293|consen 99 GRGRGNGNRGGNRRGGGRGGSMGQ 122 (134)
T ss_pred CcCCCCCCCCCCcCCCCCCCCcCC
Confidence 4444444333 2445555555554
No 11
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=78.35 E-value=1.9 Score=39.01 Aligned_cols=14 Identities=64% Similarity=0.997 Sum_probs=6.8
Q ss_pred CCCCCCCCccccCC
Q 028304 154 RSGRGRSRGRGILC 167 (210)
Q Consensus 154 rgg~g~~~g~~~~~ 167 (210)
||+||+|||+||++
T Consensus 17 ~~~~g~~~~~~~~~ 30 (257)
T PTZ00070 17 RGGRGRGRGRGRGG 30 (257)
T ss_pred CCCCCCCCCCCCCC
Confidence 44455555544443
No 12
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=67.85 E-value=5.2 Score=38.13 Aligned_cols=19 Identities=21% Similarity=0.102 Sum_probs=10.0
Q ss_pred eeeeeeEEEEEEecccCCC
Q 028304 101 TTRHVSMITITLSKKELNR 119 (210)
Q Consensus 101 ~~R~VS~I~ItLSk~~LD~ 119 (210)
++|..|.|+=.+.-...|.
T Consensus 287 Re~Taski~k~~igrvPDR 305 (465)
T KOG3973|consen 287 RERTASKIHKLSIGRVPDR 305 (465)
T ss_pred hhhhhhhhcccccccCCCC
Confidence 4455666665555443353
No 13
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=66.05 E-value=5.8 Score=34.94 Aligned_cols=19 Identities=37% Similarity=0.393 Sum_probs=12.1
Q ss_pred CCCCCCCCccccCCcCCCcc
Q 028304 154 RSGRGRSRGRGILCHYGISC 173 (210)
Q Consensus 154 rgg~g~~~g~~~~~~~~~~~ 173 (210)
++|+|+| |||+++.+|+|+
T Consensus 93 y~gggrg-Ggg~gg~rgpps 111 (241)
T KOG0105|consen 93 YSGGGRG-GGGGGGRRGPPS 111 (241)
T ss_pred cCCCCCC-CCCCCcccCCcc
Confidence 4445544 557788887775
No 14
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=61.84 E-value=8.2 Score=31.44 Aligned_cols=10 Identities=20% Similarity=0.255 Sum_probs=4.9
Q ss_pred ceecccCCCc
Q 028304 89 WEPLEEGLLP 98 (210)
Q Consensus 89 ~eP~eEGl~~ 98 (210)
|-=++||.+.
T Consensus 67 w~LT~eGiey 76 (124)
T PTZ00034 67 YYLTDEGIEY 76 (124)
T ss_pred EEEchHHHHH
Confidence 4444566444
No 15
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=59.50 E-value=4.1 Score=31.11 Aligned_cols=8 Identities=75% Similarity=1.306 Sum_probs=6.8
Q ss_pred hhhhhhHH
Q 028304 188 LFHMHCIG 195 (210)
Q Consensus 188 ~~~~~~~~ 195 (210)
.||||||-
T Consensus 55 ~FH~hCI~ 62 (85)
T PF12861_consen 55 NFHMHCIL 62 (85)
T ss_pred HHHHHHHH
Confidence 69999984
No 16
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=56.84 E-value=13 Score=30.23 Aligned_cols=12 Identities=67% Similarity=1.160 Sum_probs=5.5
Q ss_pred CCCCCCCCcccc
Q 028304 154 RSGRGRSRGRGI 165 (210)
Q Consensus 154 rgg~g~~~g~~~ 165 (210)
|+++|+|||.+|
T Consensus 112 ~~~~~~gr~~~r 123 (124)
T PTZ00034 112 RGGRGRGRGYGR 123 (124)
T ss_pred CCCCCCCCCCCC
Confidence 444445554443
No 17
>PTZ00146 fibrillarin; Provisional
Probab=53.68 E-value=12 Score=34.38 Aligned_cols=6 Identities=50% Similarity=0.446 Sum_probs=2.2
Q ss_pred CccccC
Q 028304 161 RGRGIL 166 (210)
Q Consensus 161 ~g~~~~ 166 (210)
||++++
T Consensus 46 ~~~~~~ 51 (293)
T PTZ00146 46 RGGGGG 51 (293)
T ss_pred CCCCCC
Confidence 333333
No 18
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=53.27 E-value=20 Score=31.46 Aligned_cols=6 Identities=33% Similarity=0.362 Sum_probs=2.4
Q ss_pred EEEEEe
Q 028304 108 ITITLS 113 (210)
Q Consensus 108 I~ItLS 113 (210)
++|+++
T Consensus 106 fsIK~~ 111 (215)
T KOG3262|consen 106 FSIKPS 111 (215)
T ss_pred EEEecC
Confidence 334443
No 19
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=52.31 E-value=13 Score=35.88 Aligned_cols=7 Identities=14% Similarity=-0.211 Sum_probs=2.6
Q ss_pred EEEEcCh
Q 028304 49 VFKAMGR 55 (210)
Q Consensus 49 vIkA~G~ 55 (210)
...+.+.
T Consensus 241 ~~~~~p~ 247 (419)
T KOG0116|consen 241 QSKGSPP 247 (419)
T ss_pred eeccCCC
Confidence 3333333
No 20
>KOG2945 consensus Predicted RNA-binding protein [General function prediction only]
Probab=49.84 E-value=13 Score=35.36 Aligned_cols=8 Identities=75% Similarity=1.386 Sum_probs=3.0
Q ss_pred CCCCCCCC
Q 028304 151 RRGRSGRG 158 (210)
Q Consensus 151 ~rgrgg~g 158 (210)
||||||||
T Consensus 331 grGrGgRg 338 (365)
T KOG2945|consen 331 GRGRGGRG 338 (365)
T ss_pred cCCCCCCC
Confidence 33333333
No 21
>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=47.17 E-value=48 Score=29.08 Aligned_cols=42 Identities=14% Similarity=0.288 Sum_probs=31.7
Q ss_pred CCCeEEEEEcCh-hHHHHHHHHHHHHHhcCCceeEEEEEEEEeeccc
Q 028304 44 GSNEIVFKAMGR-AINKTVTIVELIKRRIVGLHQNTVIGSTDITDTW 89 (210)
Q Consensus 44 g~~eVvIkA~G~-AIsKAV~VAEILKrRi~GLhQ~t~I~tv~i~d~~ 89 (210)
....|||-+.|- ..--+++.|.+|++.+|+| +|..|.|.|-.
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 467899999995 6667899999999999999 99999998753
No 22
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=44.26 E-value=29 Score=32.69 Aligned_cols=10 Identities=10% Similarity=0.311 Sum_probs=4.6
Q ss_pred HHHHHHHHHH
Q 028304 60 TVTIVELIKR 69 (210)
Q Consensus 60 AV~VAEILKr 69 (210)
|-.+++.|+.
T Consensus 258 ~~~l~~~L~~ 267 (456)
T PRK10590 258 ANHLAEQLNK 267 (456)
T ss_pred HHHHHHHHHH
Confidence 3444555543
No 23
>PRK05261 putative phosphoketolase; Provisional
Probab=43.23 E-value=39 Score=35.14 Aligned_cols=30 Identities=17% Similarity=0.366 Sum_probs=28.2
Q ss_pred CCeEEEEEcChhHHH-HHHHHHHHHHhcCCc
Q 028304 45 SNEIVFKAMGRAINK-TVTIVELIKRRIVGL 74 (210)
Q Consensus 45 ~~eVvIkA~G~AIsK-AV~VAEILKrRi~GL 74 (210)
...|+|-|.|.-+.. |+..|++|++++||+
T Consensus 613 ~pDvvL~atGsev~leAlaAa~~L~~~~pgi 643 (785)
T PRK05261 613 EPDVVLACAGDVPTLETLAAADLLREHFPDL 643 (785)
T ss_pred CCCEEEEEeCcHhhHHHHHHHHHHHhhCCCC
Confidence 358999999999999 999999999999998
No 24
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=39.46 E-value=19 Score=31.29 Aligned_cols=6 Identities=33% Similarity=0.058 Sum_probs=3.3
Q ss_pred CccccC
Q 028304 161 RGRGIL 166 (210)
Q Consensus 161 ~g~~~~ 166 (210)
-||+++
T Consensus 18 l~~~~~ 23 (233)
T PF11705_consen 18 LGFGRG 23 (233)
T ss_pred CccccC
Confidence 356655
No 25
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=35.85 E-value=37 Score=27.22 Aligned_cols=8 Identities=50% Similarity=0.621 Sum_probs=3.5
Q ss_pred CCccccCC
Q 028304 160 SRGRGILC 167 (210)
Q Consensus 160 ~~g~~~~~ 167 (210)
.+|+|+|+
T Consensus 103 ~~grg~g~ 110 (119)
T KOG3172|consen 103 ARGRGRGG 110 (119)
T ss_pred ccCCCCCC
Confidence 34444444
No 26
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=33.98 E-value=68 Score=30.23 Aligned_cols=23 Identities=9% Similarity=0.042 Sum_probs=13.3
Q ss_pred HHHHHHHHhhCCCCeEEEEEcCh
Q 028304 33 ITYAMTLLQERGSNEIVFKAMGR 55 (210)
Q Consensus 33 V~~A~~lL~~~g~~eVvIkA~G~ 55 (210)
+......|.+.+.....++|-=.
T Consensus 258 ~~~l~~~L~~~g~~~~~lhg~~~ 280 (456)
T PRK10590 258 ANHLAEQLNKDGIRSAAIHGNKS 280 (456)
T ss_pred HHHHHHHHHHCCCCEEEEECCCC
Confidence 34444555555677777776433
No 27
>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=32.91 E-value=64 Score=24.86 Aligned_cols=16 Identities=31% Similarity=0.729 Sum_probs=13.4
Q ss_pred hhhHHHHHHHHHHhhh
Q 028304 191 MHCIGFIFLLYSLHFL 206 (210)
Q Consensus 191 ~~~~~~~~~~~~~~~~ 206 (210)
.-.+||||..+.||.+
T Consensus 65 vmSvgFIasV~~LHi~ 80 (88)
T KOG3457|consen 65 VMSVGFIASVFALHIW 80 (88)
T ss_pred hhhHHHHHHHHHHHHH
Confidence 3468999999999965
No 28
>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=32.35 E-value=1.3e+02 Score=22.83 Aligned_cols=28 Identities=18% Similarity=0.423 Sum_probs=25.7
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHHHhcCCc
Q 028304 45 SNEIVFKAMGRAINKTVTIVELIKRRIVGL 74 (210)
Q Consensus 45 ~~eVvIkA~G~AIsKAV~VAEILKrRi~GL 74 (210)
-+.|.|-++|..+..|+..|+.|+.+ |+
T Consensus 9 g~di~iia~G~~~~~al~A~~~L~~~--Gi 36 (124)
T PF02780_consen 9 GADITIIAYGSMVEEALEAAEELEEE--GI 36 (124)
T ss_dssp SSSEEEEEETTHHHHHHHHHHHHHHT--TC
T ss_pred CCCEEEEeehHHHHHHHHHHHHHHHc--CC
Confidence 46899999999999999999999998 65
No 29
>KOG0523 consensus Transketolase [Carbohydrate transport and metabolism]
Probab=30.98 E-value=81 Score=32.08 Aligned_cols=64 Identities=22% Similarity=0.404 Sum_probs=42.4
Q ss_pred CCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcChhHHHHHHHHHHHHHhcCCceeEEEEEEEEeec--cceecc
Q 028304 18 ENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVGLHQNTVIGSTDITD--TWEPLE 93 (210)
Q Consensus 18 ~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G~AIsKAV~VAEILKrRi~GLhQ~t~I~tv~i~d--~~eP~e 93 (210)
.|-+.++.... .-+..+...|++ +.+.|+|-|.|.++..|+..||.|..+ || + +++.| .|+|++
T Consensus 481 ~~~~~~~~~~~--~~igkg~~vl~~-~~~dV~LiG~Gs~v~~cl~AA~~L~~~--gi----~---vrVvd~~~~kplD 546 (632)
T KOG0523|consen 481 QNLPIYNNTEI--EEIGKGKYVLQE-VEPDVILIGTGSEVQECLEAAELLSED--GI----K---VRVVDPFTWKPLD 546 (632)
T ss_pred ccccccCCCch--hhhccccEEEec-CCCCEEEEeccHHHHHHHHHHHHHHhc--Cc----e---EEEecccceeecc
Confidence 34444444332 234444445555 458999999999999999999999966 66 2 33333 478876
No 30
>PF07794 DUF1633: Protein of unknown function (DUF1633); InterPro: IPR012436 This family contains sequences derived from a group of hypothetical proteins expressed by Arabidopsis thaliana (Mouse-ear cress). These sequences are highly similar and the region concerned is about 100 residues long.
Probab=29.19 E-value=95 Score=31.30 Aligned_cols=25 Identities=28% Similarity=0.329 Sum_probs=13.4
Q ss_pred CcCCCcccccccccCcc---------hhhhhhhh
Q 028304 167 CHYGISCYTCASTHGHD---------TYKLLFHM 191 (210)
Q Consensus 167 ~~~~~~~~~~~~~~~~~---------~~~~~~~~ 191 (210)
|.-|--.+.-.-||-.| +-+||.|.
T Consensus 485 gsag~~pfh~s~t~drdh~ived~A~~~nLl~h~ 518 (790)
T PF07794_consen 485 GSAGSRPFHWSYTHDRDHPIVEDEAGLANLLRHI 518 (790)
T ss_pred CccCCCccccccccCCCCccchhhhHHHHHHHHH
Confidence 33344445555666654 45666664
No 31
>PRK02399 hypothetical protein; Provisional
Probab=28.27 E-value=1.7e+02 Score=28.29 Aligned_cols=64 Identities=25% Similarity=0.314 Sum_probs=46.1
Q ss_pred CCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcC---hhHHHHHHHHHHHHHhcCCceeEEEEEEEEeeccc
Q 028304 18 ENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMG---RAINKTVTIVELIKRRIVGLHQNTVIGSTDITDTW 89 (210)
Q Consensus 18 ~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G---~AIsKAV~VAEILKrRi~GLhQ~t~I~tv~i~d~~ 89 (210)
.-.|=+|.=+.--.+|..+...|++++++.+|+||.| +|+.+-|. .. -++-...+.+.++.|++
T Consensus 186 kp~Ig~TmfGvTtp~v~~~~~~Le~~GyEvlVFHATG~GGraME~Li~------~G--~~~gVlDlTttEv~d~l 252 (406)
T PRK02399 186 KPLIGLTMFGVTTPCVQAAREELEARGYEVLVFHATGTGGRAMEKLID------SG--LIAGVLDLTTTEVCDEL 252 (406)
T ss_pred CceEEEecCCCcHHHHHHHHHHHHhCCCeEEEEcCCCCchHHHHHHHH------cC--CceEEEEcchHHHHHHH
Confidence 4467777766666999999999999899999999986 57765442 11 14444567777776664
No 32
>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=27.03 E-value=77 Score=28.98 Aligned_cols=41 Identities=22% Similarity=0.320 Sum_probs=24.0
Q ss_pred CCCeEEEEEcChhHH---HHHHHHHHHHHhcCCceeEEEEEEEEeecc
Q 028304 44 GSNEIVFKAMGRAIN---KTVTIVELIKRRIVGLHQNTVIGSTDITDT 88 (210)
Q Consensus 44 g~~eVvIkA~G~AIs---KAV~VAEILKrRi~GLhQ~t~I~tv~i~d~ 88 (210)
..+.|+|||||.... -.-.+.+.|++.+||. .+.++++.+.
T Consensus 5 ~~PvViwHGmGD~~~~~~~m~~i~~~i~~~~PG~----yV~si~ig~~ 48 (279)
T PF02089_consen 5 PLPVVIWHGMGDSCCNPSSMGSIKELIEEQHPGT----YVHSIEIGND 48 (279)
T ss_dssp S--EEEE--TT--S--TTTHHHHHHHHHHHSTT------EEE--SSSS
T ss_pred CCcEEEEEcCccccCChhHHHHHHHHHHHhCCCc----eEEEEEECCC
Confidence 357899999997653 3567889999999997 6777887654
No 33
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=27.00 E-value=1.8e+02 Score=28.10 Aligned_cols=65 Identities=25% Similarity=0.333 Sum_probs=46.6
Q ss_pred CCCEEEEcCCCchHHHHHHHHHHHhhCCCCeEEEEEcC---hhHHHHHHHHHHHHHhcCCceeEEEEEEEEeeccc
Q 028304 17 DENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMG---RAINKTVTIVELIKRRIVGLHQNTVIGSTDITDTW 89 (210)
Q Consensus 17 ~~NeIrVt~k~~irnYV~~A~~lL~~~g~~eVvIkA~G---~AIsKAV~VAEILKrRi~GLhQ~t~I~tv~i~d~~ 89 (210)
..-.|=||.=+.--..|..+...|++.|++.+++||.| +|+.+-|. . .-+.-...+.+.++.|++
T Consensus 184 ~kp~I~iTmfGvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li~-------~-G~~~~VlDlTttEl~d~l 251 (403)
T PF06792_consen 184 DKPLIGITMFGVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLIR-------E-GQFDGVLDLTTTELADEL 251 (403)
T ss_pred CCcEEEEECCCCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHHH-------c-CCcEEEEECcHHHHHHHH
Confidence 44588899877777999999999999999999999986 57766542 1 113334455555555543
No 34
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=25.91 E-value=52 Score=35.39 Aligned_cols=14 Identities=43% Similarity=0.653 Sum_probs=6.5
Q ss_pred CCCCCccccCCcCC
Q 028304 157 RGRSRGRGILCHYG 170 (210)
Q Consensus 157 ~g~~~g~~~~~~~~ 170 (210)
||+|||+|++||.|
T Consensus 1258 rgggrgagggGgfg 1271 (1282)
T KOG0921|consen 1258 RGGGRGAGGGGGFG 1271 (1282)
T ss_pred CCCCCCCCCCCCCC
Confidence 44444444455544
No 35
>KOG4298 consensus CAP-binding protein complex interacting protein 2 [RNA processing and modification]
Probab=25.11 E-value=45 Score=29.53 Aligned_cols=20 Identities=35% Similarity=0.878 Sum_probs=16.4
Q ss_pred hhhhHHHHHHHHHHhhhhcc
Q 028304 190 HMHCIGFIFLLYSLHFLRSF 209 (210)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~ 209 (210)
-|=-.|.||..++.||-||.
T Consensus 188 ilvPvgliFvvFa~hfyrsl 207 (245)
T KOG4298|consen 188 ILVPVGLIFVVFAIHFYRSL 207 (245)
T ss_pred hhhhhhHHHHHHHHHHHHHH
Confidence 34557999999999999974
No 36
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=24.86 E-value=33 Score=26.30 Aligned_cols=11 Identities=45% Similarity=0.748 Sum_probs=8.4
Q ss_pred hhhhhhhhhHH
Q 028304 185 YKLLFHMHCIG 195 (210)
Q Consensus 185 ~~~~~~~~~~~ 195 (210)
-+-.||.|||-
T Consensus 54 CnHaFH~HCI~ 64 (88)
T COG5194 54 CNHAFHDHCIY 64 (88)
T ss_pred cchHHHHHHHH
Confidence 34579999985
No 37
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=21.47 E-value=1.2e+02 Score=24.48 Aligned_cols=6 Identities=17% Similarity=0.230 Sum_probs=2.6
Q ss_pred EEEEcC
Q 028304 20 EIRITS 25 (210)
Q Consensus 20 eIrVt~ 25 (210)
.|+|++
T Consensus 36 ~lfVgn 41 (144)
T PLN03134 36 KLFIGG 41 (144)
T ss_pred EEEEeC
Confidence 344443
No 38
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=21.02 E-value=43 Score=26.80 Aligned_cols=10 Identities=50% Similarity=1.006 Sum_probs=7.9
Q ss_pred hhhhhhhHHH
Q 028304 187 LLFHMHCIGF 196 (210)
Q Consensus 187 ~~~~~~~~~~ 196 (210)
--||.|||.-
T Consensus 83 HaFH~hCisr 92 (114)
T KOG2930|consen 83 HAFHFHCISR 92 (114)
T ss_pred hHHHHHHHHH
Confidence 4699999963
No 39
>PF06692 MNSV_P7B: Melon necrotic spot virus P7B protein; InterPro: IPR009575 This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown.
Probab=21.02 E-value=1.1e+02 Score=21.93 Aligned_cols=31 Identities=35% Similarity=0.605 Sum_probs=18.1
Q ss_pred cccccccccCcchhhhhhhhhhHHHHHHHHHH
Q 028304 172 SCYTCASTHGHDTYKLLFHMHCIGFIFLLYSL 203 (210)
Q Consensus 172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 (210)
.||.|-|.-|.-.--||.-.=|+-| |++|+|
T Consensus 2 ~c~rc~~~p~d~~~~lLiliis~~f-~lI~~l 32 (61)
T PF06692_consen 2 ACCRCDSAPGDYSGPLLILIISFVF-FLITSL 32 (61)
T ss_pred cccccCCCCccchhHHHHHHHHHHH-HHHhhh
Confidence 4899999887554455554444443 234443
Done!