Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_106716872.1 CU100_RS12530 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_003010935.1:WP_106716872.1 Length = 493 Score = 459 bits (1180), Expect = e-133 Identities = 245/483 (50%), Positives = 327/483 (67%), Gaps = 11/483 (2%) Query: 8 ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67 I E + + K I ++L + I+ ++ + A++ E+A A AK D + Sbjct: 9 IAEARDQLKAKTISAAELTGAYIEAIENANEALNAYIVTTPEKALAMAKASDARL-ASGN 67 Query: 68 HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127 G L G+P+G+KD T+G+ T +S IL+ F P Y++TV L AV +GKLNMDEF Sbjct: 68 AGALEGIPLGIKDLFGTEGIHTQAASHILDGFKPNYESTVTANLWADGAVMLGKLNMDEF 127 Query: 128 AMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 AMGSS E S Y KNPW N D VPGGSSGGSAAAVAA + +DTGGSIRQP Sbjct: 128 AMGSSNETSYYGAVKNPWRARGSNADLVPGGSSGGSAAAVAARLCAGATATDTGGSIRQP 187 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 A+F G VG+KPTYGR SR+G+VAFASSLDQ GPI R V D A LL++++ VD D+TS + Sbjct: 188 AAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIARDVRDAAILLKSMASVDVKDTTSVD 247 Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302 V VPD+ +++ + GLKI +PKEY +G+ +E ++ L+ GA+ ++SLPH+ Sbjct: 248 VAVPDYEAAIGKPLAGLKIGIPKEYRVDGMPEEIERLWQQGIEWLKDAGASIVDISLPHT 307 Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362 KYAL YY+++ +EAS+NLAR+DG+RYG R D ++++Y++TRA GFG EVKRRIM+G Sbjct: 308 KYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IVEMYEKTRATGFGEEVKRRIMIG 366 Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGEN--TKDPL 419 T+ LS+GYYDAYY +AQKVRTLIKKDFEDVF D I+ P TP+ AF I + DP+ Sbjct: 367 TYVLSAGYYDAYYLQAQKVRTLIKKDFEDVFHAGVDAILTPATPSAAFGIADQDMAADPV 426 Query: 420 TMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478 MY NDI T+ VN+AG+PGI+VP GL A GLPLGLQ+IG+ FDE T+++ A+ EQA Sbjct: 427 KMYLNDIFTVTVNMAGLPGIAVPAGLDARGLPLGLQLIGRPFDEETLFQTAYVIEQAAGK 486 Query: 479 HKA 481 A Sbjct: 487 FNA 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: 617 Number of extensions: 30 Number of successful extensions: 5 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 WP_106716872.1 CU100_RS12530 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.3324385.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-174 566.9 0.0 2e-174 566.6 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106716872.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106716872.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 566.6 0.0 2e-174 2e-174 2 463 .. 13 483 .. 12 486 .. 0.97 Alignments for each domain: == domain 1 score: 566.6 bits; conditional E-value: 2e-174 TIGR00132 2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 +++lk+k++s+ e++ +++e+ie+ ++ +na++ +t+ekal++ak++d+++a + l gip+++Kd + ++ NCBI__GCF_003010935.1:WP_106716872.1 13 RDQLKAKTISAAELTGAYIEAIENANEALNAYIVTTPEKALAMAKASDARLAsGNaGALEGIPLGIKDLFGTE 85 578999*********************************************975536**************** PP TIGR00132 73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGG 140 +i+t +aS+iL+++++ y++tV+ +l ++ga+++Gk N+DEFamGss etS++g++knP n + vpGG NCBI__GCF_003010935.1:WP_106716872.1 86 GIHTQAASHILDGFKPNYESTVTANLWADGAVMLGKLNMDEFAMGSSNETSYYGAVKNPwrargSNADLVPGG 158 ***********************************************************666665899***** PP TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialv 213 SsgGsaaavaa l+ a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G++a++v d+a++ NCBI__GCF_003010935.1:WP_106716872.1 159 SSGGSAAAVAARLCAGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIARDVRDAAIL 231 ************************************************************************* PP TIGR00132 214 ldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevsl 286 l+ ++ +D kD+ts++v+v+++ ++ k l glk+g+ ke++ +++++e+++ +++ +e l++ ga iv++sl NCBI__GCF_003010935.1:WP_106716872.1 232 LKSMASVDVKDTTSVDVAVPDYEAAIGKPLAGLKIGIPKEYRVDGMPEEIERLWQQGIEWLKDAGASIVDISL 304 ************************************************************************* PP TIGR00132 287 psvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyyd 359 p+ k+al++Yyi++p+Eassnlarydg+ryG rv ++ + e+y ktR+ gfgeevkrRim+G+y+ls++yyd NCBI__GCF_003010935.1:WP_106716872.1 305 PHTKYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IVEMYEKTRATGFGEEVKRRIMIGTYVLSAGYYD 376 **********************************9998.********************************** PP TIGR00132 360 kyykkAqkvrtliidefeklfe.evDvivsptaptlafklgek..aedplemylsDvltvpanlaGlpaisvP 429 +yy++Aqkvrtli+++fe++f+ vD i++p++p af ++++ a+dp++myl+D++tv++n+aGlp+i+vP NCBI__GCF_003010935.1:WP_106716872.1 377 AYYLQAQKVRTLIKKDFEDVFHaGVDAILTPATPSAAFGIADQdmAADPVKMYLNDIFTVTVNMAGLPGIAVP 449 *********************637****************87622567************************* PP TIGR00132 430 lgkkekglpiGlqiigkafddkkllsvakaleqa 463 +g + +glp+Glq+ig+ fd+++l++ a+ +eqa NCBI__GCF_003010935.1:WP_106716872.1 450 AGLDARGLPLGLQLIGRPFDEETLFQTAYVIEQA 483 ********************************97 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 28.12 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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