Query 038777
Match_columns 361
No_of_seqs 184 out of 231
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 03:10:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038777.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038777hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2330 Splicing factor 3b, su 100.0 5E-125 1E-129 930.3 21.5 318 2-324 115-499 (500)
2 COG5182 CUS1 Splicing factor 3 100.0 1.4E-89 3.1E-94 664.6 16.3 235 2-238 122-364 (429)
3 PF04037 DUF382: Domain of unk 100.0 5.7E-76 1.2E-80 505.5 11.2 129 23-151 1-129 (129)
4 smart00581 PSP proline-rich do 99.9 2.1E-28 4.6E-33 184.5 5.6 54 156-209 1-54 (54)
5 PF04046 PSP: PSP; InterPro: 99.9 1.4E-25 3E-30 165.9 5.3 48 160-207 1-48 (48)
6 KOG2673 Uncharacterized conser 99.0 1.5E-10 3.3E-15 117.5 3.9 57 138-196 161-217 (485)
7 KOG2673 Uncharacterized conser 72.0 2.8 6.1E-05 44.2 2.5 56 139-197 29-84 (485)
8 TIGR02697 WPE_wolbac Wolbachia 63.7 2.9 6.3E-05 30.1 0.5 10 51-60 1-10 (36)
9 PRK09350 poxB regulator PoxA; 61.2 2.9 6.2E-05 40.8 0.2 86 109-194 187-283 (306)
10 TIGR00462 genX lysyl-tRNA synt 50.1 7.8 0.00017 37.8 1.1 75 120-194 197-278 (304)
11 cd00776 AsxRS_core Asx tRNA sy 45.6 6.5 0.00014 38.6 -0.2 73 120-194 216-291 (322)
12 TIGR00457 asnS asparaginyl-tRN 39.2 10 0.00022 39.3 0.0 73 120-194 344-418 (453)
13 cd00669 Asp_Lys_Asn_RS_core As 37.0 15 0.00034 35.3 0.9 73 121-194 161-238 (269)
14 PTZ00401 aspartyl-tRNA synthet 34.4 16 0.00035 39.1 0.7 82 111-194 429-515 (550)
15 PLN02850 aspartate-tRNA ligase 29.5 14 0.00029 39.4 -0.9 72 121-194 422-495 (530)
16 TIGR02663 nifX nitrogen fixati 28.4 27 0.00058 29.4 0.9 25 161-185 93-117 (119)
17 PRK06462 asparagine synthetase 27.9 21 0.00046 35.4 0.2 75 118-194 222-300 (335)
18 PRK05159 aspC aspartyl-tRNA sy 27.6 12 0.00026 38.4 -1.6 84 109-194 314-402 (437)
19 TIGR00458 aspS_arch aspartyl-t 27.3 13 0.00029 38.0 -1.3 74 119-194 318-393 (428)
20 COG5033 TFG3 Transcription ini 26.7 22 0.00047 34.6 0.0 43 43-89 8-86 (225)
No 1
>KOG2330 consensus Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=4.9e-125 Score=930.34 Aligned_cols=318 Identities=52% Similarity=0.832 Sum_probs=284.8
Q ss_pred CCChhHHHhhcCCCHHHHHhhcCCCCeEEeecCCCCChHHHHHHhhcCCCccCCccccchhccccCccCCCCCCCCCcHH
Q 038777 2 GLSKKRKKHGRRMRIAEVKRYCSRPDVVEVWDATAADPKLLVFLKAYRNTVPVPRHWCQKRKFLQGKRGIGKQPFHLPDF 81 (361)
Q Consensus 2 ~lSkkk~r~~~r~svaeLK~~v~~PevVE~~D~tA~DP~lLv~lKs~rNtVPVP~HW~~KR~YLsgkrgieKppf~LP~~ 81 (361)
.|||||+|++.|+|||+||++|.||||||||||||.||.|||+||+|+|+||||+|||+||+||||+||||||||+||+|
T Consensus 115 klskrklRk~~r~svaeLK~~v~~pdvvE~~Dvta~dP~ll~~lK~~~n~VPVPrHW~~kr~yl~G~rg~ekppfelP~~ 194 (500)
T KOG2330|consen 115 KLSKRKLRKLLRPSVAELKQLVPYPDVVEWHDVTARDPKLLVHLKAYRNSVPVPRHWNSKRKYLSGKRGIEKPPFELPDF 194 (500)
T ss_pred hhhHHHHHHhhcccHHHHhhcCCccceeeeeccCCCChHHHHHhhhccCCCcCchhhhhhhhhhccccccCCCCccchHH
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhChHHHHhhhhhhhhhHHHHHHHhhhcCCCCCccCCChHHHHHHHhccCCCCCCCCCCcccccchhhhhhhhccCCC
Q 038777 82 IAATGIEKVRQACNEKEDSKKLKQKQSERMQPRMKKMDIDYPALYDAFFKYQTKPKLTTHGDLYYEGKEFEVKQLMEMKP 161 (361)
Q Consensus 82 I~~TGI~emR~a~~eke~~~sLKqk~RervqPKmGklDIDYqkLhDAFFk~qtKP~Lt~~GDlYYEGKE~e~~~~~~~kP 161 (361)
|+.|||++||+++.|+|+++|||++||||||||||++|||||+||||||+|||||.||.||||||||||+|.. +++++|
T Consensus 195 Ik~TgI~emR~a~~e~e~~~sLk~kmRerv~PkmGkidiDyqkLhdaFFk~qtkp~lt~~Ge~yyegke~e~~-~k~k~P 273 (500)
T KOG2330|consen 195 IKKTGIQEMREALLEREAGKSLKEKMRERVRPKMGKIDIDYQKLHDAFFKWQTKPYLTKFGELYYEGKELEAM-VKEKKP 273 (500)
T ss_pred HHhcCHHHHHHHHHhhhccccHHHHHHHhhCcccccccchHHHHHHHHHhcCCCcceeecceeeecchhHHHH-HhhcCc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999988 999999
Q ss_pred CcccHHHHHHhCCCCCCCchHHHHHhhcCCCCCCCCCccccCCCCCCCCCC-------CCCCCC----------------
Q 038777 162 CTLSYELREALGIPDVASPPYLRNMQRYGAPPSYPNLKIPGFNAPIPQEAD-------KPHVVD---------------- 218 (361)
Q Consensus 162 G~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPsYp~LkIpGLNapip~g~~-------kppvd~---------------- 218 (361)
|.||+|||+||||+.+.|||||++||+||||||||||||||||||||+||+ --|||+
T Consensus 274 G~iS~eLr~aLgmp~g~pPPWl~aMqryGpPpsYPdlkIpGLNapIPeg~s~Gyh~gGWGpVDe~g~PLygDVfG~~~p~ 353 (500)
T KOG2330|consen 274 GDISDELRIALGMPVGTPPPWLIAMQRYGPPPSYPDLKIPGLNAPIPEGCSFGYHAGGWGPVDEFGKPLYGDVFGLNIPE 353 (500)
T ss_pred cchhHHHHHHhCCCCCCCChHHHHhhhcCCCCCCCcccCCCCCCCCCcccccccccCCCccccccCCccchhcccccccc
Confidence 999999999999999999999999999999999999999999999999999 227772
Q ss_pred ------CCccCCCCCCcCCCccchhhhhh-------------hc-------------------cCcccccc--ccc----
Q 038777 219 ------TEPVDKTRHWGDLEEAEDEIEEE-------------LE-------------------DGIESVES--QRK---- 254 (361)
Q Consensus 219 ------~~~v~~~~~WG~l~~eeeeeeee-------------~~-------------------~g~~t~~~--~rk---- 254 (361)
+..+++ .|||+|+++++|++|+ ++ +|++||+. +||
T Consensus 354 ~~~~t~es~~~r-n~wgel~~e~~E~~EEreeee~~d~~~~~e~gg~~dp~d~~~~~~Lts~ptgiEtpd~iELRK~k~e 432 (500)
T KOG2330|consen 354 HHNGTKESEIER-NHWGELESEEEESSEEREEEEREDKNDASENGGAVDPADDIVPSGLTSFPTGIETPDAIELRKKKRE 432 (500)
T ss_pred cccccccccccc-ccccccccccchhhhhhhhhhhhhhhhhhhccccCCccccccccccccCCccccChhHHHHHhhccc
Confidence 223446 5999998654332111 01 13333333 554
Q ss_pred CCCCccceecccccccccCCccccccceecccccccCCCCCCeeeecCchhhccccchhHHHHHHHHHHh
Q 038777 255 EPERTLYQVLEEKEERIAPRTLLVTTHTVKRVDLLKGQQTDRVDAILQPEELEVMDNVLPAKYEEAKQEE 324 (361)
Q Consensus 255 ~~~~~ly~Vl~ek~~~~~~~~~~gs~~~Y~~~~~~~~~~~~~v~v~l~p~el~~~~~~l~~~ye~~~~~~ 324 (361)
+++|.||||||||.+++.||+||||+|+|+...... .+.+||++||||++|+.++.+| +||+++++|
T Consensus 433 e~~r~LYqVLpEK~t~~igg~mmgstH~Ydis~~~a-~k~~GV~~sL~Peeld~d~~~l--~yee~~req 499 (500)
T KOG2330|consen 433 EETRALYQVLPEKRTSRIGGTMMGSTHTYDISTGTA-DKTPGVEFSLDPEELDADGMAL--RYEEQRREQ 499 (500)
T ss_pred cccHHHHHhccccccccccceeeccceEEecccccc-ccCCCceeecChhhhccchhhH--HHHHHHhhc
Confidence 457899999999999988899999999999654332 2345799999999999888888 899999986
No 2
>COG5182 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=1.4e-89 Score=664.60 Aligned_cols=235 Identities=40% Similarity=0.641 Sum_probs=219.4
Q ss_pred CCChhHHHhhcCCCHHHHHhhcCCCCeEEeecCCCCChHHHHHHhhcCCCccCCccccchhccccCccCCCCCCCCCcHH
Q 038777 2 GLSKKRKKHGRRMRIAEVKRYCSRPDVVEVWDATAADPKLLVFLKAYRNTVPVPRHWCQKRKFLQGKRGIGKQPFHLPDF 81 (361)
Q Consensus 2 ~lSkkk~r~~~r~svaeLK~~v~~PevVE~~D~tA~DP~lLv~lKs~rNtVPVP~HW~~KR~YLsgkrgieKppf~LP~~ 81 (361)
.||++|+|+..++++++||.+|.+|+|||||||||+||.||.+||++.|+||||+||++|++||||.+++++.||+||++
T Consensus 122 ~ls~~k~Rk~~~~~~~qLK~~vpyp~I~Ew~D~~~~dP~~l~~~K~~~N~VPVPrHW~sk~~ylsg~~~~~~r~felP~~ 201 (429)
T COG5182 122 SLSRQKKRKALQHRYEQLKLVVPYPEIFEWEDATCPDPMSLNRMKGCSNGVPVPRHWRSKSRYLSGHGYHKPRPFELPRH 201 (429)
T ss_pred hhHHHHHHHHhhhhHHHHhccCCccceeeeecCCCCChhhhhhhccCCCCCCCchhhhhhhhcccccccCCCCcccchHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhChHHHHhhhhhhhhhHHHHHHHhhhcCCCCCccCCChHHHHHHHhccCCCCCCCCCCcccccchhhhhhhhccCCC
Q 038777 82 IAATGIEKVRQACNEKEDSKKLKQKQSERMQPRMKKMDIDYPALYDAFFKYQTKPKLTTHGDLYYEGKEFEVKQLMEMKP 161 (361)
Q Consensus 82 I~~TGI~emR~a~~eke~~~sLKqk~RervqPKmGklDIDYqkLhDAFFk~qtKP~Lt~~GDlYYEGKE~e~~~~~~~kP 161 (361)
|..|||.+||+++.|.|++++|++++|||||||||++||||++||||||++|+||.||.|||+||||++.+.- .++++|
T Consensus 202 I~~TgI~qmR~~~~e~ea~msLre~~RervqPkmG~ldvDy~kLhdaFF~~g~kP~L~~fGe~y~e~~n~~~~-vk~krP 280 (429)
T COG5182 202 IIGTGIPQMRRMMREREAGMSLRERIRERVQPKMGGLDVDYRKLHDAFFSLGPKPYLSKFGEFYEEVDNDYRF-VKKKRP 280 (429)
T ss_pred HhhcChHHHHHhhhhccccCcHHHHHHHhhCccccccchhHHHHHHHHHhcCCCcccccccceeeccchHHHH-HhccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999988765 789999
Q ss_pred CcccHHHHHHhCCCCCCCchHHHHHhhcCCCCCCCCCccccCC-CCCC-CCCC----CCCCCC--CCccCCCCCCcCCCc
Q 038777 162 CTLSYELREALGIPDVASPPYLRNMQRYGAPPSYPNLKIPGFN-APIP-QEAD----KPHVVD--TEPVDKTRHWGDLEE 233 (361)
Q Consensus 162 G~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPsYp~LkIpGLN-apip-~g~~----kppvd~--~~~v~~~~~WG~l~~ 233 (361)
|.||.|||+||||++++|||||++||+||+|||||+||||||| ++|| .||. +|-.-+ .+++.. .+||+|.+
T Consensus 281 G~IS~eLrealgi~~g~pPPWlf~Mq~~G~PpsYPDlkIpGlNW~~~pL~GdvyG~~~p~~h~~~~~~~~~-~~~gel~~ 359 (429)
T COG5182 281 GAISAELREALGIDSGTPPPWLFNMQKHGMPPSYPDLKIPGLNWAPIPLEGDVYGYQPPGWHEPLFEVGPE-TAEGELLQ 359 (429)
T ss_pred cchHHHHHHHhCCCCCCCChHHHhhhhcCCCCCCccccCCCCCCCCcccccccccccCCCcCCccCCcCcc-hhhhhhhh
Confidence 9999999999999999999999999999999999999999999 6778 7887 332222 344555 59999976
Q ss_pred cchhh
Q 038777 234 AEDEI 238 (361)
Q Consensus 234 eeeee 238 (361)
.|+||
T Consensus 360 fe~ee 364 (429)
T COG5182 360 FEAEE 364 (429)
T ss_pred ccchh
Confidence 65443
No 3
>PF04037 DUF382: Domain of unknown function (DUF382) ; InterPro: IPR007180 This domain is specific to the human splicing factor 3b subunit 2 and its orthologs.; GO: 0005634 nucleus
Probab=100.00 E-value=5.7e-76 Score=505.51 Aligned_cols=129 Identities=74% Similarity=1.171 Sum_probs=128.0
Q ss_pred cCCCCeEEeecCCCCChHHHHHHhhcCCCccCCccccchhccccCccCCCCCCCCCcHHHHhhChHHHHhhhhhhhhhHH
Q 038777 23 CSRPDVVEVWDATAADPKLLVFLKAYRNTVPVPRHWCQKRKFLQGKRGIGKQPFHLPDFIAATGIEKVRQACNEKEDSKK 102 (361)
Q Consensus 23 v~~PevVE~~D~tA~DP~lLv~lKs~rNtVPVP~HW~~KR~YLsgkrgieKppf~LP~~I~~TGI~emR~a~~eke~~~s 102 (361)
|.+|||||||||||+||+|||+|||++||||||+|||+||+|||||||+|||||+||+||++|||++||+|+.|+|+++|
T Consensus 1 V~~PevVE~~D~~a~DP~lLv~lKs~rNtVPVP~HW~~Kr~YL~gkrg~eKppf~LP~~I~~TgI~emR~~~~e~e~~~s 80 (129)
T PF04037_consen 1 VPRPEVVEWHDVTAPDPRLLVHLKSYRNTVPVPRHWSQKRKYLQGKRGIEKPPFQLPDFIKDTGIEEMRQALPEKEDEKS 80 (129)
T ss_pred CCCCceEEeecCCCCChHHHHHHHhcCCCCCCCcchhhhhhhhcccccccCCCCcCCHHHHHHCcHHHHHHhhcccchhh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCCCCCccCCChHHHHHHHhccCCCCCCCCCCcccccchhh
Q 038777 103 LKQKQSERMQPRMKKMDIDYPALYDAFFKYQTKPKLTTHGDLYYEGKEF 151 (361)
Q Consensus 103 LKqk~RervqPKmGklDIDYqkLhDAFFk~qtKP~Lt~~GDlYYEGKE~ 151 (361)
|||+||||||||||+||||||+||||||+|||||.||.|||+|||||||
T Consensus 81 lKqk~RervqPKmGkldIDYq~LhdAFFk~qtKP~l~~~Gd~YyEgkef 129 (129)
T PF04037_consen 81 LKQKQRERVQPKMGKLDIDYQKLHDAFFKFQTKPKLTKFGDLYYEGKEF 129 (129)
T ss_pred HHHHHHHHhCcccCcccccHHHHHHHHHhccCCCCcccccceeeccccC
Confidence 9999999999999999999999999999999999999999999999997
No 4
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=99.95 E-value=2.1e-28 Score=184.54 Aligned_cols=54 Identities=57% Similarity=1.037 Sum_probs=52.2
Q ss_pred hccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCCCCCCccccCCCCCCC
Q 038777 156 LMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPSYPNLKIPGFNAPIPQ 209 (361)
Q Consensus 156 ~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPsYp~LkIpGLNapip~ 209 (361)
+++++||+||++||+||||+++++||||++||++|+|||||+|+||||||+||.
T Consensus 1 ~~~~kPG~lS~~LR~ALG~~~~~pPPWl~~Mq~~G~PPsYp~l~ipglna~ip~ 54 (54)
T smart00581 1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPRLKIPGLNAPIPL 54 (54)
T ss_pred CCCccCCcCCHHHHHHcCCCCCCCChHHHHHHHHCCCCCCcccccCCCCCCCCC
Confidence 468999999999999999999999999999999999999999999999999984
No 5
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=99.92 E-value=1.4e-25 Score=165.85 Aligned_cols=48 Identities=63% Similarity=1.104 Sum_probs=47.4
Q ss_pred CCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCCCCCCccccCCCCC
Q 038777 160 KPCTLSYELREALGIPDVASPPYLRNMQRYGAPPSYPNLKIPGFNAPI 207 (361)
Q Consensus 160 kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPsYp~LkIpGLNapi 207 (361)
|||+||++||+||||+++++||||++||++|+|||||+++|||+|++|
T Consensus 1 kPG~lS~~LR~ALg~~~~~~PPwl~~M~~~G~PP~y~~~ki~g~n~~i 48 (48)
T PF04046_consen 1 KPGKLSDELREALGMQENDPPPWLYRMRRLGYPPGYPDLKIPGLNAPI 48 (48)
T ss_pred CCcccCHHHHHHcCCCCCCCChHHHHHHhcCCCCCCccccccCCCCCC
Confidence 799999999999999999999999999999999999999999999997
No 6
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=99.02 E-value=1.5e-10 Score=117.53 Aligned_cols=57 Identities=32% Similarity=0.517 Sum_probs=48.5
Q ss_pred CCCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCCCC
Q 038777 138 LTTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPSYP 196 (361)
Q Consensus 138 Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPsYp 196 (361)
|+.=-..||---+-- + ..++|||+||.+||.|||+.+++||+|+++|+++||||+|.
T Consensus 161 ~~~rnqry~~~teq~-r-e~h~KPG~lS~~~R~al~l~~~d~P~~~yRMR~lGYPPg~L 217 (485)
T KOG2673|consen 161 MVFRNQRYYQDTEQG-R-EDHFKPGVLSGNTRSALGLSPGDPPEWKYRMRRLGYPPGYL 217 (485)
T ss_pred ccccceeeeeecchh-h-hcccCCcccchhHHHhhcCCCCCchHHHHHHhhccCCchhh
Confidence 444444677665543 4 78999999999999999999999999999999999999997
No 7
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=71.99 E-value=2.8 Score=44.25 Aligned_cols=56 Identities=21% Similarity=0.311 Sum_probs=46.4
Q ss_pred CCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCCCCC
Q 038777 139 TTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPSYPN 197 (361)
Q Consensus 139 t~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPsYp~ 197 (361)
..+++.|-++--.+. +..+.+|.|| ++-++|+-.+.+.||+.++||+.|.|+.|-+
T Consensus 29 q~~~e~~~d~~~d~~--~~r~esg~i~-~qqd~l~~te~a~~~fr~~~qe~~t~s~wl~ 84 (485)
T KOG2673|consen 29 QNFQERLHDELVDER--RGRFESGVIS-EQQDLLGVTEKAFPPFRYRMQELGTPSFWLK 84 (485)
T ss_pred cchhhhccchhhhhh--hccccccccc-hHHHHhhcccccccchhhhHHhhcCchhhhh
Confidence 345555666555554 5789999999 8899999999999999999999999999984
No 8
>TIGR02697 WPE_wolbac Wolbachia palindromic element (WPE) domain. This domain conceptually resembles TIGR01045, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure. Note that this model appears to work better in fragment mode.
Probab=63.68 E-value=2.9 Score=30.12 Aligned_cols=10 Identities=60% Similarity=1.438 Sum_probs=8.4
Q ss_pred CccCCccccc
Q 038777 51 TVPVPRHWCQ 60 (361)
Q Consensus 51 tVPVP~HW~~ 60 (361)
+||||+||--
T Consensus 1 vIPV~~hwDp 10 (36)
T TIGR02697 1 VIPVPRHWDP 10 (36)
T ss_pred CcccccccCc
Confidence 5899999974
No 9
>PRK09350 poxB regulator PoxA; Provisional
Probab=61.17 E-value=2.9 Score=40.82 Aligned_cols=86 Identities=17% Similarity=0.235 Sum_probs=56.0
Q ss_pred hhcCCCCCc----cCCChHHHHHHHhccC-CCCCCCCCCcccccchhhhhhhhccCCCCcccHHHH------HHhCCCCC
Q 038777 109 ERMQPRMKK----MDIDYPALYDAFFKYQ-TKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYELR------EALGIPDV 177 (361)
Q Consensus 109 ervqPKmGk----lDIDYqkLhDAFFk~q-tKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR------~ALGm~~~ 177 (361)
..|.|++|+ +-+||-.--.+|.+-. ..|.++.==|+|+.|.|.-...-....|..+...++ ++.|+.+.
T Consensus 187 ~~ve~~l~~~~p~fi~~yP~~~~~~a~~~~~~~~~~~rfdl~i~G~Ei~nG~~el~d~~~~~~r~~~~~~~~~~~g~~~~ 266 (306)
T PRK09350 187 FGVEPNIGKEKPTFVYHFPASQAALAKISTEDHRVAERFEVYFKGIELANGFHELTDAREQRQRFEQDNRKRAARGLPQQ 266 (306)
T ss_pred HHHHHhcCCCCCEEEEcCccccCccccccCCCCCeeEEEEEEECCEEEecchhhcCCHHHHHHHHHHHHHHHHhCCCCcc
Confidence 566777764 3346665555554421 356666556999999986432122345666666654 47888877
Q ss_pred CCchHHHHHhhcCCCCC
Q 038777 178 ASPPYLRNMQRYGAPPS 194 (361)
Q Consensus 178 ~pPPWl~~Mqr~G~PPs 194 (361)
...-|+..+.++|+||.
T Consensus 267 ~~d~~~l~a~~~G~pp~ 283 (306)
T PRK09350 267 PIDENLIAALEAGLPDC 283 (306)
T ss_pred cCcHHHHHHHHcCCCCC
Confidence 76677889999999996
No 10
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=50.09 E-value=7.8 Score=37.82 Aligned_cols=75 Identities=23% Similarity=0.326 Sum_probs=45.3
Q ss_pred CChHHHHHHHhcc-CCCCCCCCCCcccccchhhhhhhhccCCCCcccHHH------HHHhCCCCCCCchHHHHHhhcCCC
Q 038777 120 IDYPALYDAFFKY-QTKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYEL------REALGIPDVASPPYLRNMQRYGAP 192 (361)
Q Consensus 120 IDYqkLhDAFFk~-qtKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eL------R~ALGm~~~~pPPWl~~Mqr~G~P 192 (361)
+||-.-..+|.+- ...|.++.==|+|+.|.|.-...-.-..|..+-..+ +++.|+.+....-|...+.++|+|
T Consensus 197 ~~yP~~~~~~~~~~~~~~~~~~rfdl~~~G~Ei~~G~~el~d~~~~~~r~~~~~~~~~~~g~~~~~~d~~yl~~~~~G~p 276 (304)
T TIGR00462 197 YDYPASQAALARISPDDPRVAERFELYIKGLELANGFHELTDAAEQRRRFEADNAERKALGLPRYPLDERFLAALEAGLP 276 (304)
T ss_pred EcCccccCcCccccCCCCCeeEEEEEEECCEEEeeceeecCCHHHHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHcCCC
Confidence 4555555554432 124566654588888877532201123344444433 345788877776799999999999
Q ss_pred CC
Q 038777 193 PS 194 (361)
Q Consensus 193 Ps 194 (361)
|.
T Consensus 277 P~ 278 (304)
T TIGR00462 277 EC 278 (304)
T ss_pred CC
Confidence 96
No 11
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=45.65 E-value=6.5 Score=38.62 Aligned_cols=73 Identities=22% Similarity=0.368 Sum_probs=47.1
Q ss_pred CChHHHHHHHhcc--CCCCCCCCCCcccccc-hhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCC
Q 038777 120 IDYPALYDAFFKY--QTKPKLTTHGDLYYEG-KEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPS 194 (361)
Q Consensus 120 IDYqkLhDAFFk~--qtKP~Lt~~GDlYYEG-KE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPs 194 (361)
+||-.-..+|+.- ...|.++.-=|+|+.| .|.-....+...|-.+-..+.+ .|+++... .|+..+.++|+||.
T Consensus 216 ~~~P~~~~pfy~~~~~~~~~~~~~fdl~~~G~~El~~g~~r~~d~~~l~~r~~~-~g~~~~~~-~~yl~a~~~G~pp~ 291 (322)
T cd00776 216 TDYPKEIKPFYMKPDDDNPETVESFDLLMPGVGEIVGGSQRIHDYDELEERIKE-HGLDPESF-EWYLDLRKYGMPPH 291 (322)
T ss_pred ECCccccCCceeeecCCCCCeeEEEEEEcCCCeEEeeceeecCCHHHHHHHHHH-cCCChHHH-HHHHHHHHCCCCCC
Confidence 4666555666332 2356677777899999 8764322234455555555554 67776544 89999999999985
No 12
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=39.22 E-value=10 Score=39.33 Aligned_cols=73 Identities=21% Similarity=0.326 Sum_probs=44.8
Q ss_pred CChHHHHHHHhc-cCCCCCCCCCCcccccc-hhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCC
Q 038777 120 IDYPALYDAFFK-YQTKPKLTTHGDLYYEG-KEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPS 194 (361)
Q Consensus 120 IDYqkLhDAFFk-~qtKP~Lt~~GDlYYEG-KE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPs 194 (361)
+||-+-...|+. ....|.++.-=|+|+.| .|.-...-++..+-.|-..++ +.||.+. .-.|.+.+.+||+||.
T Consensus 344 t~~P~~~~pfy~~~~~~~~~~~~fDL~~~g~gEi~~gsere~~~~~l~~~~~-~~g~d~~-~~~~Yl~~~~~G~pPh 418 (453)
T TIGR00457 344 TNYPKDIKAFYMKLNDDGKTVAAMDLLAPGIGEIIGGSEREDDLDKLENRMK-EMGLDTD-ALNWYLDLRKYGSVPH 418 (453)
T ss_pred ECCCcccChhhcccCCCcCceeeeeeccCCceEEeehhccCCCHHHHHHHHH-HcCCCHH-HHHHHHHHHHcCCCCC
Confidence 355555555553 22566666666888888 365322233444444444444 5687765 3569999999999984
No 13
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=36.98 E-value=15 Score=35.31 Aligned_cols=73 Identities=23% Similarity=0.333 Sum_probs=43.6
Q ss_pred ChHHHHHHHhccC--CCCCCCCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCC---CCchHHHHHhhcCCCCC
Q 038777 121 DYPALYDAFFKYQ--TKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDV---ASPPYLRNMQRYGAPPS 194 (361)
Q Consensus 121 DYqkLhDAFFk~q--tKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~---~pPPWl~~Mqr~G~PPs 194 (361)
||-..--+||... ..|.++.-=|+|+.|.|.-....+...|-.+-..+++. |+.+. .+=.|+..+.++|+||.
T Consensus 161 d~P~~~~~fy~~~~~~~~~~~~~fdl~~~g~Ei~~G~~r~~d~~~l~~~~~~~-~~~~~~~~~~~~~yl~a~~~G~pp~ 238 (269)
T cd00669 161 DYPAEMHSPLASPHDVNPEIADAFDLFINGVEVGNGSSRLHDPDIQAEVFQEQ-GINKEAGMEYFEFYLKALEYGLPPH 238 (269)
T ss_pred CCCcccCCCCCCcCCCCCCeEEEEEEeeCCEEEeeCchhcCCHHHHHHHHHHh-CcChhhccccHHHHHHHHHcCCCCC
Confidence 4444433444322 24556555589999987633223344554444554444 55544 36789999999999985
No 14
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=34.36 E-value=16 Score=39.06 Aligned_cols=82 Identities=18% Similarity=0.258 Sum_probs=54.9
Q ss_pred cCCCCCc--cCCC-hHHHHHHHhc--cCCCCCCCCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHH
Q 038777 111 MQPRMKK--MDID-YPALYDAFFK--YQTKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRN 185 (361)
Q Consensus 111 vqPKmGk--lDID-YqkLhDAFFk--~qtKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~ 185 (361)
|.|+.|+ .-+| |-.---+|+. ....|.++.-=|+|+.|-|.-...-+...|-.|-..++ +.||++... -|.+.
T Consensus 429 v~~~~~~~~fI~d~yP~~~rpFY~~~~~~dp~~s~~fDlf~~G~EI~sG~qR~~d~~~l~~r~~-~~G~d~~~~-~~Yl~ 506 (550)
T PTZ00401 429 VKERYGTDFFISDRFPSSARPFYTMECKDDERFTNSYDMFIRGEEISSGAQRIHDPDLLLARAK-MLNVDLTPI-KEYVD 506 (550)
T ss_pred HHHhcCCCEEEECCCChhhCchhcCcCCCCCCEEEEEEEEeCCEEEccchhhcCCHHHHHHHHH-HcCCCchhh-HHHHH
Confidence 4555554 2235 6666677764 22467777777999999876443234556666666665 479887644 78899
Q ss_pred HhhcCCCCC
Q 038777 186 MQRYGAPPS 194 (361)
Q Consensus 186 Mqr~G~PPs 194 (361)
+.+||+||.
T Consensus 507 a~~~G~PPh 515 (550)
T PTZ00401 507 SFRLGAWPH 515 (550)
T ss_pred HHHcCCCCC
Confidence 999999985
No 15
>PLN02850 aspartate-tRNA ligase
Probab=29.49 E-value=14 Score=39.37 Aligned_cols=72 Identities=25% Similarity=0.381 Sum_probs=50.8
Q ss_pred ChHHHHHHHhc--cCCCCCCCCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCC
Q 038777 121 DYPALYDAFFK--YQTKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPS 194 (361)
Q Consensus 121 DYqkLhDAFFk--~qtKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPs 194 (361)
||-.-.-+|+. ....|.++.==|+|+.|-|.-...-+...|-.|-..++ +.|+++... -|++.+.+||+||.
T Consensus 422 ~yP~~~~pfY~~~~~~d~~~~~~fDl~i~G~EI~~G~qr~~d~~~l~~r~~-~~g~d~~~~-~~Yl~a~~~G~pPh 495 (530)
T PLN02850 422 RYPLAVRPFYTMPCPDDPKYSNSFDVFIRGEEIISGAQRVHDPELLEKRAE-ECGIDVKTI-STYIDSFRYGAPPH 495 (530)
T ss_pred CCccccCchhccccCCCCCeEEEEEEEeCCEEEeccceecCCHHHHHHHHH-HcCCChHHH-HHHHHHHHcCCCCC
Confidence 56666677754 33567777666999999876433233455555555554 489988766 99999999999985
No 16
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=28.36 E-value=27 Score=29.39 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=16.6
Q ss_pred CCcccHHHHHHhCCCCCCCchHHHH
Q 038777 161 PCTLSYELREALGIPDVASPPYLRN 185 (361)
Q Consensus 161 PG~LS~eLR~ALGm~~~~pPPWl~~ 185 (361)
+|.+.+.|..-..+=.+.|||||.+
T Consensus 93 ~~~v~eal~~l~~~~~~~~~~w~~~ 117 (119)
T TIGR02663 93 PESISELLERLQKMLKGNPPPWLRK 117 (119)
T ss_pred CccHHHHHHHHHHHHcCCCCHHHHh
Confidence 3455555555555556899999976
No 17
>PRK06462 asparagine synthetase A; Reviewed
Probab=27.94 E-value=21 Score=35.41 Aligned_cols=75 Identities=20% Similarity=0.176 Sum_probs=46.6
Q ss_pred cCCChHHHHHHHhccC--CCCCCCCCCcccc--cchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCC
Q 038777 118 MDIDYPALYDAFFKYQ--TKPKLTTHGDLYY--EGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPP 193 (361)
Q Consensus 118 lDIDYqkLhDAFFk~q--tKP~Lt~~GDlYY--EGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PP 193 (361)
.-+||-..-.+|+... ..|.++.==|+|+ .+.|.-...-...++=.| .+.+.+.|+++. ...|+..+.++|+||
T Consensus 222 fi~~yP~~~~pfy~~~~~~~~~~~~rFdL~~~~g~gEl~~g~er~~~~~~l-~~~~~~~g~~~~-~~~~yl~a~~~G~pp 299 (335)
T PRK06462 222 WIIDIPKGSREFYDREDPERPGVLRNYDLLLPEGYGEAVSGGEREYEYEEI-VERIREHGVDPE-KYKWYLEMAKEGPLP 299 (335)
T ss_pred EEECCChhhCCcccccCCCCCCEEEEEEEEeeCCCcEEeeeEEEecCHHHH-HHHHHHcCCChH-HHHHHHHHHHCCCCC
Confidence 4468888777888643 4677775668888 333331110111122112 234567898876 568999999999998
Q ss_pred C
Q 038777 194 S 194 (361)
Q Consensus 194 s 194 (361)
.
T Consensus 300 ~ 300 (335)
T PRK06462 300 S 300 (335)
T ss_pred C
Confidence 5
No 18
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=27.61 E-value=12 Score=38.40 Aligned_cols=84 Identities=20% Similarity=0.348 Sum_probs=53.3
Q ss_pred hhcCCCCCc---cCCChHHHHHHHhcc--CCCCCCCCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHH
Q 038777 109 ERMQPRMKK---MDIDYPALYDAFFKY--QTKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYL 183 (361)
Q Consensus 109 ervqPKmGk---lDIDYqkLhDAFFk~--qtKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl 183 (361)
+.+.|++|. +-+||-.--.+|+.. ..+|.++.-=|+|+.|.|.-........|=.+-..++ +.|+++. .--|+
T Consensus 314 ~~~~~~~~~~p~fi~~~P~~~~pfy~~~~~~~~~~~~~fdl~~~g~Ei~~g~~r~~d~~~~~~~~~-~~g~~~~-~~~~y 391 (437)
T PRK05159 314 EYVKEEYGSDFYFITDYPSEKRPFYTMPDEDDPEISKSFDLLFRGLEITSGGQRIHRYDMLVESIK-EKGLNPE-SFEFY 391 (437)
T ss_pred HHHhhhcCCceEEEecCchhcCcceeeecCCCCCEEEEEEEEECCEEEeeCeEEcCCHHHHHHHHH-HcCCCHH-HHHHH
Confidence 445666665 235777666677542 3467777666999999876332122333434444444 4577665 44899
Q ss_pred HHHhhcCCCCC
Q 038777 184 RNMQRYGAPPS 194 (361)
Q Consensus 184 ~~Mqr~G~PPs 194 (361)
..+.+||+||.
T Consensus 392 l~a~~~G~pp~ 402 (437)
T PRK05159 392 LEAFKYGMPPH 402 (437)
T ss_pred HHHHHCCCCCC
Confidence 99999999986
No 19
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=27.26 E-value=13 Score=38.03 Aligned_cols=74 Identities=20% Similarity=0.267 Sum_probs=48.1
Q ss_pred CCChHHHHHHHhc--cCCCCCCCCCCcccccchhhhhhhhccCCCCcccHHHHHHhCCCCCCCchHHHHHhhcCCCCC
Q 038777 119 DIDYPALYDAFFK--YQTKPKLTTHGDLYYEGKEFEVKQLMEMKPCTLSYELREALGIPDVASPPYLRNMQRYGAPPS 194 (361)
Q Consensus 119 DIDYqkLhDAFFk--~qtKP~Lt~~GDlYYEGKE~e~~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~Mqr~G~PPs 194 (361)
-+||-.-..+|+. ....|.++.==|+|+.|.|.-...-+...+-.|-..+ .+.|+++. .-.|+..+.+||+||.
T Consensus 318 i~d~P~~~~pfy~~~~~~~p~~~~~fdl~~~g~Ei~~g~~r~~~~~~l~~~~-~~~g~~~~-~~~~yl~a~~~G~pP~ 393 (428)
T TIGR00458 318 ITDWPTEIRPFYTMPDEDNPEISKSFDLMYRDLEISSGAQRIHLHDLLVERI-KAKGLNPE-GFKDYLEAFSYGMPPH 393 (428)
T ss_pred EEeCchhcCcccccccCCCCCEEEEEEEEeCCeEEeeCchhcCCHHHHHHHH-HHcCCChH-HHHHHHHHHHCCCCCc
Confidence 4577776667753 3356777766689999987633212233333444444 35677665 4589999999999995
No 20
>COG5033 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=26.72 E-value=22 Score=34.58 Aligned_cols=43 Identities=33% Similarity=0.393 Sum_probs=31.6
Q ss_pred HHHhhcCCCcc------------CCccccchhccccC------------------------ccCCCCCCCCCcHHHHhhC
Q 038777 43 VFLKAYRNTVP------------VPRHWCQKRKFLQG------------------------KRGIGKQPFHLPDFIAATG 86 (361)
Q Consensus 43 v~lKs~rNtVP------------VP~HW~~KR~YLsg------------------------krgieKppf~LP~~I~~TG 86 (361)
+.+|++++++| .++||+..+-||-+ .|.|+.|||+ |..||
T Consensus 8 ~r~~t~r~Iipgea~~~~~e~~~P~r~th~w~v~v~~~g~E~~~~iv~KVifkLH~Tf~NP~Rti~~pPFe----I~EtG 83 (225)
T COG5033 8 ERLKTQRVIIPGEAKPLGNEERFPVRHTHIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPPFE----IKETG 83 (225)
T ss_pred EeeeeeceeccCccccCCccccCCchhhEEEEEEEeCCCCcchhhhhheeeEEeccccCCCcccccCCCcE----EEecc
Confidence 34677788877 35799998888765 4778888886 57787
Q ss_pred hHH
Q 038777 87 IEK 89 (361)
Q Consensus 87 I~e 89 (361)
-.|
T Consensus 84 WGE 86 (225)
T COG5033 84 WGE 86 (225)
T ss_pred ccc
Confidence 744
Done!