Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate SMc01352 SMc01352 aspartyl/glutamyl-tRNA amidotransferase subunit A
Query= SwissProt::O06491 (485 letters) >FitnessBrowser__Smeli:SMc01352 Length = 493 Score = 466 bits (1199), Expect = e-136 Identities = 247/483 (51%), Positives = 329/483 (68%), Gaps = 11/483 (2%) Query: 8 ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67 I E + + KEI +L D I+A ++ + A++A+ E+AR AK D + Sbjct: 9 IAEARAKLSAKEITAVELTDAYLGAIEAANETINAYVAVTPEKAREMAKASDARI-AAGN 67 Query: 68 HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127 L G+P+G+KD T+G+ T S IL+ F+P Y++TV Q L + AV +GKLNMDEF Sbjct: 68 AAALEGIPLGIKDLFGTEGIHTQACSHILDGFEPRYESTVTQNLWNDGAVMLGKLNMDEF 127 Query: 128 AMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 AMGSS E S Y KNPW NLD VPGGSSGGSAAAVAA + +DTGGSIRQP Sbjct: 128 AMGSSNETSYYGPVKNPWRAKGSNLDLVPGGSSGGSAAAVAARLCAGATATDTGGSIRQP 187 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 A+F G VG+KPTYGR SR+G+VAFASSLDQ GPI R V D A LL++++ +D D+TS + Sbjct: 188 AAFTGTVGIKPTYGRCSRWGVVAFASSLDQAGPIARDVRDAAILLKSMASIDPKDTTSVD 247 Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302 + VPD+ +++ IKG++I +PKEY +G+ ++ + L GA ++SLPH+ Sbjct: 248 LPVPDYEAAIGQSIKGMRIGIPKEYRVDGMPEDIEALWQQGIAWLRDAGAEIVDISLPHT 307 Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362 KYAL YY+++ +EAS+NLAR+DG+RYG R D D +ID+Y++TRA GFG EVKRRIM+G Sbjct: 308 KYALPAYYIVAPAEASSNLARYDGVRYGLRVDGKD-IIDMYEKTRAAGFGQEVKRRIMIG 366 Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGEN--TKDPL 419 T+ LS+GYYDAYY +AQKVRTLIK+DFE F+ D I+ P TP+ AF I + DP+ Sbjct: 367 TYVLSAGYYDAYYLRAQKVRTLIKRDFELAFQAGVDAILTPATPSSAFGIADEDLASDPV 426 Query: 420 TMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478 MY NDI T+ VN+AG+PGI+VP GL GLPLGLQ+IGK F+E T+++ AH EQA Sbjct: 427 KMYLNDIFTVTVNMAGLPGIAVPGGLDRKGLPLGLQLIGKPFEEETLFKTAHVIEQAAGR 486 Query: 479 HKA 481 A Sbjct: 487 FTA 489 Lambda K H 0.315 0.134 0.381 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: 610 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 485 Length of database: 493 Length adjustment: 34 Effective length of query: 451 Effective length of database: 459 Effective search space: 207009 Effective search space used: 207009 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 (21.6 bits) S2: 52 (24.6 bits)
Align candidate SMc01352 SMc01352 (aspartyl/glutamyl-tRNA amidotransferase subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (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/TIGR00132.hmm # target sequence database: /tmp/gapView.2885.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00132 [M=466] Accession: TIGR00132 Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-175 570.9 0.0 1.2e-175 570.7 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc01352 SMc01352 aspartyl/glutamyl-tRNA Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01352 SMc01352 aspartyl/glutamyl-tRNA amidotransferase subunit A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 570.7 0.0 1.2e-175 1.2e-175 3 463 .. 14 483 .. 12 486 .. 0.97 Alignments for each domain: == domain 1 score: 570.7 bits; conditional E-value: 1.2e-175 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdie 75 ++l +ke++++e+++++l +iea +++ina+++vt+eka ++ak++d+++a + l gip+++Kd + +++i+ lcl|FitnessBrowser__Smeli:SMc01352 14 AKLSAKEITAVELTDAYLGAIEAANETINAYVAVTPEKAREMAKASDARIAaGNaAALEGIPLGIKDLFGTEGIH 88 67899*********************************************975546******************* PP TIGR00132 76 ttcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGGSsgGs 145 t + S+iL+++ + y++tV+++l ++ga+++Gk N+DEFamGss etS++g++knP n + vpGGSsgGs lcl|FitnessBrowser__Smeli:SMc01352 89 TQACSHILDGFEPRYESTVTQNLWNDGAVMLGKLNMDEFAMGSSNETSYYGPVKNPwrakgSNLDLVPGGSSGGS 163 ********************************************************655555889********** PP TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgk 220 aaavaa l+ a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G++a++v d+a++l+ ++ lcl|FitnessBrowser__Smeli:SMc01352 164 AAAVAARLCAGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGVVAFASSLDQAGPIARDVRDAAILLKSMASI 238 *************************************************************************** PP TIGR00132 221 DkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalai 295 D kD+ts++ +v+++ ++ + +kg+++g+ ke++ +++++++++ +++ + l++ gaeiv++slp+ k+al++ lcl|FitnessBrowser__Smeli:SMc01352 239 DPKDTTSVDLPVPDYEAAIGQSIKGMRIGIPKEYRVDGMPEDIEALWQQGIAWLRDAGAEIVDISLPHTKYALPA 313 *************************************************************************** PP TIGR00132 296 YyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrt 370 Yyi++p+Eassnlarydg+ryG rv+ ++ + ++y ktR++gfg+evkrRim+G+y+ls++yyd+yy++Aqkvrt lcl|FitnessBrowser__Smeli:SMc01352 314 YYIVAPAEASSNLARYDGVRYGLRVDGKD-IIDMYEKTRAAGFGQEVKRRIMIGTYVLSAGYYDAYYLRAQKVRT 387 *************************9888.********************************************* PP TIGR00132 371 liidefeklfe.evDvivsptaptlafklgek..aedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlq 442 li+++fe +f+ vD i++p++p +af ++++ a+dp++myl+D++tv++n+aGlp+i+vP g ++kglp+Glq lcl|FitnessBrowser__Smeli:SMc01352 388 LIKRDFELAFQaGVDAILTPATPSSAFGIADEdlASDPVKMYLNDIFTVTVNMAGLPGIAVPGGLDRKGLPLGLQ 462 **********737****************87633678************************************** PP TIGR00132 443 iigkafddkkllsvakaleqa 463 +igk f++++l++ a+ +eqa lcl|FitnessBrowser__Smeli:SMc01352 463 LIGKPFEEETLFKTAHVIEQA 483 ******************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (493 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: 00:00:00.02 # Mc/sec: 7.71 // [ok]
This GapMind analysis is from Apr 09 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