Align glutamyl-tRNA(Gln) amidotransferase subunit E (EC 6.3.5.7) (characterized)
to candidate WP_048062518.1 MAEO_RS05715 Glu-tRNA(Gln) amidotransferase GatDE subunit E
Query= metacyc::MONOMER-14999
(619 letters)
>NCBI__GCF_000017185.1:WP_048062518.1
Length = 637
Score = 578 bits (1490), Expect = e-169
Identities = 307/634 (48%), Positives = 438/634 (69%), Gaps = 18/634 (2%)
Query: 1 MDWEKVGLKMGLEIHQQLDTESKLFCPCRTELTDSEPDHDIVRNLRPTQSELGKFDRAAF 60
+++ ++GLK+GLEIHQQL+T+ KLFC C T + + PD +I R LR +QSE+G+ D+AA
Sbjct: 3 LNYNELGLKVGLEIHQQLNTKRKLFCNCPTLIREDSPDGEIQRTLRTSQSEMGEIDKAAL 62
Query: 61 EEAMRKLHFHYENYHEETCLVEADEEPPHPLNPEALEIAVTIALLLNMRVVDEFHTMRKQ 120
E+ + Y+ Y++ TCLVE DEEPPH + EA++ A+ ++ L+NM V+E TMRK
Sbjct: 63 IESKKGKKNIYQYYNDTTCLVELDEEPPHAPSEEAIKTALEVSYLMNMEAVNEIQTMRKI 122
Query: 121 VIDGSNTGGFQRTGLVATDGHLETPQGTVKIENLCLEEDAARRIRETGDGVVFRLDRLGI 180
VIDGSNT GFQRT ++ DG +ET G V I +LCLEEDA R+I ++R+DRLGI
Sbjct: 123 VIDGSNTSGFQRTAYISQDGFIETEHGRVGITSLCLEEDACRKIEGNDSYTIYRVDRLGI 182
Query: 181 PLVEITTDPSMSDPQQLREVAYQIGQILRST-RVKRGLGTIRQDLNISIRDGARVEVKGV 239
PL+EITT+P +++P+ +E A +IG ILR+T KRGLGTIRQD+N+SI++GAR+E KGV
Sbjct: 183 PLLEITTEPDITNPKMGKESAKRIGSILRATGMAKRGLGTIRQDVNVSIKNGARIEAKGV 242
Query: 240 QDLDLIPEIVEREVKRQLSLVEIRDTLQERGAVVEDKIFDVSEVFADTESRIISSA---- 295
Q+LDLI +++E EV RQ++L+EI TLQER A I D++E+ +T S+++ SA
Sbjct: 243 QNLDLIEKVIENEVIRQMNLIEIAKTLQERNAEAIHNIIDITELLKNTNSKVLKSALKKK 302
Query: 296 -ESVLAVKLRGFDGLIGVEIQPGRRLGTEMADYAK-KRGVSGIFHTDELPAYGITEEEVR 353
+ AV L+GF GL+G EIQ GRRLGTE++D AK GV G+FHTDELP YGIT EEV+
Sbjct: 303 NGKIKAVVLKGFGGLVGKEIQEGRRLGTELSDRAKIIAGVGGLFHTDELPHYGITGEEVK 362
Query: 354 GLRDAVGA----SQGDAVVMVAHERVTAENALREVIRRAEMAIQGVPEETRKALPDGNTQ 409
L++ + + ++ DA+V+VA E +NAL ++ RAE AI GVPEETRKAL +GNT
Sbjct: 363 LLKEYINSIISITEQDAIVLVADENNKVDNALNAILTRAEEAILGVPEETRKALENGNTS 422
Query: 410 YLRPLPTSSRMYLETDIPLFRIEDDLLEGIRRNLPELPSEKKERIMRDYGLSEDLASQLV 469
YLRPL S+RMY ETDIP +E++ ++ I+ NLPE+P K +R +++Y L+EDLA+ +V
Sbjct: 423 YLRPLAGSARMYPETDIPAIYLEEEYIQSIKDNLPEMPETKLKRFIKEYELNEDLANIMV 482
Query: 470 KRNLVDEFEALTEFR--VDTTVIASLLAYTLRELRREGHDVDGLGLDELRDAIKLLEVGK 527
V+ FE L + + T+IA+ L TLRE++REGH+ DGL L K
Sbjct: 483 SSYKVNMFEELCKNHNTIKPTLIATTLEATLREIKREGHNTDGLTKQHFDMVFSGLAEAK 542
Query: 528 ISKDALRDIVACMADEGLAAEDAARKL---NLLLLAEDEIESIIQEIVEGNLDMISERGM 584
SK+A+ DI+ + ED + L L L+++E+E II+ I+ N+++++ +GM
Sbjct: 543 TSKEAIVDILKGFIE--YPNEDLDKILEIKGLKSLSKEEVEEIIENIINQNIEVVNSKGM 600
Query: 585 GAMGPLMGQAMGRLRGRADGKVVNRILREKIQER 618
GAMG LMG+ M LRG+ADGK++N +L+ K+ E+
Sbjct: 601 GAMGMLMGRCMAELRGKADGKIINTVLKNKLMEK 634
Lambda K H
0.318 0.137 0.380
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1032
Number of extensions: 56
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 619
Length of database: 637
Length adjustment: 38
Effective length of query: 581
Effective length of database: 599
Effective search space: 348019
Effective search space used: 348019
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate WP_048062518.1 MAEO_RS05715 (Glu-tRNA(Gln) amidotransferase GatDE subunit E)
to HMM TIGR00134 (gatE: glutamyl-tRNA(Gln) amidotransferase, subunit E (EC 6.3.5.-))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.aa/TIGR00134.hmm
# target sequence database: /tmp/gapView.30817.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00134 [M=622]
Accession: TIGR00134
Description: gatE_arch: glutamyl-tRNA(Gln) amidotransferase, subunit E
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.4e-283 926.1 18.9 5e-283 925.9 18.9 1.0 1 lcl|NCBI__GCF_000017185.1:WP_048062518.1 MAEO_RS05715 Glu-tRNA(Gln) amido
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_048062518.1 MAEO_RS05715 Glu-tRNA(Gln) amidotransferase GatDE subunit E
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 925.9 18.9 5e-283 5e-283 2 620 .. 3 633 .. 2 635 .. 0.99
Alignments for each domain:
== domain 1 score: 925.9 bits; conditional E-value: 5e-283
TIGR00134 2 ldyekvGlkvGleihqqldtkrklfclcptllrdseedfeivrvlrpkrselGevdraaleeaerkkkf 70
l+y+ +GlkvGleihqql+tkrklfc+cptl+r++ +d+ei r+lr ++se+Ge+d+aal+e +++kk
lcl|NCBI__GCF_000017185.1:WP_048062518.1 3 LNYNELGLKVGLEIHQQLNTKRKLFCNCPTLIREDSPDGEIQRTLRTSQSEMGEIDKAALIESKKGKKN 71
89******************************************************************* PP
TIGR00134 71 iykyyndttclveadeepprelneealeiavevalllnmevvdevhtmrkividGsntsGfqrtalvat 139
iy+yyndttclve+deepp+ ++eea++ a+ev+ l+nme v+e+ tmrkividGsntsGfqrta++++
lcl|NCBI__GCF_000017185.1:WP_048062518.1 72 IYQYYNDTTCLVELDEEPPHAPSEEAIKTALEVSYLMNMEAVNEIQTMRKIVIDGSNTSGFQRTAYISQ 140
********************************************************************* PP
TIGR00134 140 dGyletdegkvgieslcleedaarkiedrgdavvysldrlGiplveistepdikspkmakevaariGei 208
dG++et++g+vgi+slcleeda+rkie ++ + +y++drlGipl+ei+tepdi +pkm ke a+riG i
lcl|NCBI__GCF_000017185.1:WP_048062518.1 141 DGFIETEHGRVGITSLCLEEDACRKIEGNDSYTIYRVDRLGIPLLEITTEPDITNPKMGKESAKRIGSI 209
********************************************************************* PP
TIGR00134 209 lrstgkvkrGlGtirqdvnisirdGarvevkGvqdldliekiverevlrqlnllkirdelkergaevee 277
lr+tg krGlGtirqdvn+si++Gar+e kGvq+ldliek++e+ev+rq+nl++i ++l+er+ae +
lcl|NCBI__GCF_000017185.1:WP_048062518.1 210 LRATGMAKRGLGTIRQDVNVSIKNGARIEAKGVQNLDLIEKVIENEVIRQMNLIEIAKTLQERNAEAIH 278
********************************************************************* PP
TIGR00134 278 kifdvtevfkdtkskiirnaek.....vkavllrGfdGlvGkeiqpGrrlGteladiakki.GvgGvfh 340
i d+te++k+t+sk++++a+k +kav l+Gf+GlvGkeiq GrrlGtel+d+ak i GvgG+fh
lcl|NCBI__GCF_000017185.1:WP_048062518.1 279 NIIDITELLKNTNSKVLKSALKkkngkIKAVVLKGFGGLVGKEIQEGRRLGTELSDRAKIIaGVGGLFH 347
*******************99889999*********************************99******* PP
TIGR00134 341 tdelpayGiteeevkklrdavga....eegdavvlvadeevkveralrevierakealvGvpeetrkal 405
tdelp yGit eevk l++++++ e+da+vlvade+ kv++al++++ ra+ea++Gvpeetrkal
lcl|NCBI__GCF_000017185.1:WP_048062518.1 348 TDELPHYGITGEEVKLLKEYINSiisiTEQDAIVLVADENNKVDNALNAILTRAEEAILGVPEETRKAL 416
*******************9875333389**************************************** PP
TIGR00134 406 edGntaylrplpgaarmypetdippvvikeelleeiranlpelpeekaerlkkeyklsedlakklvksn 474
e+Gnt+ylrpl g+armypetdip + ++ee +++i+ nlpe+pe k +r+ key+l+edla+ +v+s+
lcl|NCBI__GCF_000017185.1:WP_048062518.1 417 ENGNTSYLRPLAGSARMYPETDIPAIYLEEEYIQSIKDNLPEMPETKLKRFIKEYELNEDLANIMVSSY 485
********************************************************************* PP
TIGR00134 475 yvdvfeelskklk.vdptviasvleltlkelrreGvdidkleerelrevlklleeGkiakegleevlkl 542
v++feel+k+ + ++pt+ia++le tl+e++reG++ d+l ++++ v+ l e k +ke+++++lk+
lcl|NCBI__GCF_000017185.1:WP_048062518.1 486 KVNMFEELCKNHNtIKPTLIATTLEATLREIKREGHNTDGLTKQHFDMVFSGLAEAKTSKEAIVDILKG 554
**********9999******************************************************* PP
TIGR00134 543 laeepdkaedearklk.lkllakeeiekiieeiieekldlikerGegafgplmGrvmkklrGkadGkvv 610
+ e p++ d+++++k lk l+kee+e+iie+ii++++++++ +G+ga+g+lmGr+m++lrGkadGk++
lcl|NCBI__GCF_000017185.1:WP_048062518.1 555 FIEYPNEDLDKILEIKgLKSLSKEEVEEIIENIINQNIEVVNSKGMGAMGMLMGRCMAELRGKADGKII 623
********************************************************************* PP
TIGR00134 611 neilrkklke 620
n +l++kl e
lcl|NCBI__GCF_000017185.1:WP_048062518.1 624 NTVLKNKLME 633
*******987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (622 nodes)
Target sequences: 1 (637 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.33
//
[ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory