Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_048039578.1 MM_RS06350 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000007065.1:WP_048039578.1 Length = 475 Score = 523 bits (1347), Expect = e-153 Identities = 261/468 (55%), Positives = 341/468 (72%), Gaps = 8/468 (1%) Query: 17 KKEIKISDLVDESYKRIQAVD-DKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMP 75 K++IK S + + + ++ + K+ +L + ++ A E + +D G L G+P Sbjct: 11 KEKIKESSAEEVTSRYLEVIKKSKINGYLTISDK-----ALEQAKKIDKEGHEGPLAGVP 65 Query: 76 IGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTEN 135 I +KDNI GL +C SKILE + P ++A V+++L A AV +GK NMDEFAMGSSTE Sbjct: 66 IAIKDNISVVGLPNSCGSKILEGYVPPFNAHVIEKLLSAGAVILGKTNMDEFAMGSSTET 125 Query: 136 SAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTY 195 S + T NPW+L+ VPGGSSGGSAA VAAGE PF+LGSDTGGS+R PASFCGVVGLKPTY Sbjct: 126 SHFGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSVRCPASFCGVVGLKPTY 185 Query: 196 GRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGD 255 G VSRYG+VA+A+SL+Q+GP+ VED A L+ I+G D+ DSTS + ++ +L D Sbjct: 186 GAVSRYGVVAYANSLEQVGPLANNVEDIAVLMDVIAGYDRRDSTSID-SKTEYQKALVDD 244 Query: 256 IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSS 315 +KGLKI VPKE+ GEG+ + ++V A+ E LGATWEEVS+PH KYALA+YY+++ S Sbjct: 245 VKGLKIGVPKEFFGEGIHPDVEKAVWDAIHKCESLGATWEEVSMPHIKYALASYYIIAMS 304 Query: 316 EASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYY 375 EAS+NLARFDG RYG+R +N + +TRAEGFG EVKRRI+LGT+ALS+GY+D YY Sbjct: 305 EASSNLARFDGTRYGFRA-GGENWHAMVSKTRAEGFGTEVKRRILLGTYALSAGYHDKYY 363 Query: 376 KKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAG 435 KA KVRTL+K+DF+ K D+++ PT P PAFKIGE +DPLT+Y +DI T P+NLAG Sbjct: 364 LKALKVRTLVKQDFDKALSKVDLLMAPTMPNPAFKIGEKIEDPLTLYLSDINTCPINLAG 423 Query: 436 VPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 VP ISVPCG DGLP+GLQI+GK FDE TV R A+ FE+ TD+H +P Sbjct: 424 VPSISVPCGFTDGLPIGLQIMGKPFDEETVLRAAYTFEKNTDYHTKRP 471 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: 624 Number of extensions: 30 Number of successful extensions: 3 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: 475 Length adjustment: 34 Effective length of query: 451 Effective length of database: 441 Effective search space: 198891 Effective search space used: 198891 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: 51 (24.3 bits)
Align candidate WP_048039578.1 MM_RS06350 (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.31407.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-197 640.4 0.0 1.1e-196 640.1 0.0 1.0 1 lcl|NCBI__GCF_000007065.1:WP_048039578.1 MM_RS06350 Asp-tRNA(Asn)/Glu-tRN Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_048039578.1 MM_RS06350 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 640.1 0.0 1.1e-196 1.1e-196 7 465 .. 14 465 .. 7 466 .. 0.96 Alignments for each domain: == domain 1 score: 640.1 bits; conditional E-value: 1.1e-196 TIGR00132 7 kkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvakekklagipiavKdniavkdie 75 ke s++ev++++le i+ k+kin +l+++++ al++akk+dk+ +e +lag+pia+Kdni+v +++ lcl|NCBI__GCF_000007065.1:WP_048039578.1 14 IKESSAEEVTSRYLEVIK--KSKINGYLTISDK-ALEQAKKIDKEG-HEGPLAGVPIAIKDNISVVGLP 78 355566666666666664..4589*****9876.**********77.678******************* PP TIGR00132 76 ttcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgG 144 +c+SkiLe+yv+p++a+V+e+l +aga+i+GktN+DEFamGsstetS fg+t+nP++ ervpGGSsgG lcl|NCBI__GCF_000007065.1:WP_048039578.1 79 NSCGSKILEGYVPPFNAHVIEKLLSAGAVILGKTNMDEFAMGSSTETSHFGPTANPWDLERVPGGSSGG 147 ********************************************************************* PP TIGR00132 145 saaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialv 213 saa+vaa+++p+algsDTGgS+R+PAsfcgvvGlKPtYG+vSRyG+vaya+Sl+q+G+la++vedia++ lcl|NCBI__GCF_000007065.1:WP_048039578.1 148 SAAVVAAGEAPFALGSDTGGSVRCPASFCGVVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVEDIAVL 216 ********************************************************************* PP TIGR00132 214 ldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeiv 282 +dvi+g+D +Dsts+++k+ e+ ++l +d+kglk+gv ke+++e+++ +v++++ ++++k e+lga+++ lcl|NCBI__GCF_000007065.1:WP_048039578.1 217 MDVIAGYDRRDSTSIDSKT-EYQKALVDDVKGLKIGVPKEFFGEGIHPDVEKAVWDAIHKCESLGATWE 284 *****************77.7999**9****************************************** PP TIGR00132 283 evslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGay 351 evs+p++k+ala Yyii++sEassnlar+dg ryG r+ + ++ +++ktR+egfg+evkrRi+lG+y lcl|NCBI__GCF_000007065.1:WP_048039578.1 285 EVSMPHIKYALASYYIIAMSEASSNLARFDGTRYGFRAGGEN-WHAMVSKTRAEGFGTEVKRRILLGTY 352 ***************************************999.************************** PP TIGR00132 352 alskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanl 420 als++y dkyy+kA kvrtl++++f+k++++vD++++pt+p afk+gek edpl+ ylsD+ t p+nl lcl|NCBI__GCF_000007065.1:WP_048039578.1 353 ALSAGYHDKYYLKALKVRTLVKQDFDKALSKVDLLMAPTMPNPAFKIGEKIEDPLTLYLSDINTCPINL 421 ********************************************************************* PP TIGR00132 421 aGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 aG+p+isvP+g + +glpiGlqi+gk fd++++l++a+++e+++d lcl|NCBI__GCF_000007065.1:WP_048039578.1 422 AGVPSISVPCGFT-DGLPIGLQIMGKPFDEETVLRAAYTFEKNTD 465 *************.8**************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (475 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: 7.82 // [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