Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_011383994.1 AMB_RS07990 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000009985.1:WP_011383994.1 Length = 485 Score = 431 bits (1108), Expect = e-125 Identities = 220/474 (46%), Positives = 318/474 (67%), Gaps = 3/474 (0%) Query: 2 NFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMK 61 ++E VIGLEVH ++ +K+K+FS + T FGAE NTQ S ID G+PG+LPV+N+ VE A++ Sbjct: 11 DWEIVIGLEVHAQVISKAKLFSGAATEFGAEPNTQVSFIDAGFPGMLPVINEVCVEQAVR 70 Query: 62 AAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGITR 120 + L +I + F RKNYFY D P+ YQISQ+D+PI G + +++ G T+ +GI R Sbjct: 71 TGLGLKAKINLTSVFARKNYFYADLPQGYQISQYDQPIVGEGELILDLPDGGTRTVGIER 130 Query: 121 LHLEEDAGKLTHT-GDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179 LHLE+DAGK H S +D NR G L+EIVS+PD+R+PEEA YL KL+SI++Y Sbjct: 131 LHLEQDAGKSIHDMHPSKSFIDLNRSGVALMEIVSKPDLRSPEEAGLYLTKLRSILRYLE 190 Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239 D M+EGS+RCDAN+S+RP+G E T+ E+KN+NS FVQ+ +E E +R V SG Sbjct: 191 TCDGNMQEGSMRCDANVSVRPVGSTELRTRCEIKNVNSIRFVQQAIEFEARRHIDVYESG 250 Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299 I+QETR +D +T MR KE + DYRYFP+PDL+ L I+ + + +K+ +PELPDE Sbjct: 251 GEIRQETRLFDSVKGETRSMRSKEHAHDYRYFPDPDLLPLVIEQSFVDGIKSGLPELPDE 310 Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359 ++ R++ E G AYDA VL K A+FF ETV KG ++K A NW+MG+ A LNA K Sbjct: 311 KKARFMAEYGLNAYDAGVLVAEKASAEFF-ETVAKGRDSKMACNWVMGDFFASLNATGKT 369 Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419 + + +T L +I LI+ GT+S ++AK VF ++E G +V+E+GL Q++D G + Sbjct: 370 IENPPVTAANLGQLIDLIKDGTLSGRLAKDVFALMVETGKAPAVLVEERGLKQVTDTGAI 429 Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473 V + NP ++ K+GK +G+ GQ+MK+++G+ANP MVN++L ++I Sbjct: 430 EAAVDAVISANPDKVQQVKDGKTALLGWFTGQVMKSTQGKANPAMVNEMLSKKI 483 Lambda K H 0.314 0.134 0.373 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: 599 Number of extensions: 24 Number of successful extensions: 4 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: 476 Length of database: 485 Length adjustment: 34 Effective length of query: 442 Effective length of database: 451 Effective search space: 199342 Effective search space used: 199342 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 bits)
Align candidate WP_011383994.1 AMB_RS07990 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm # target sequence database: /tmp/gapView.14796.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-164 533.4 0.0 2.7e-164 533.1 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383994.1 AMB_RS07990 Asp-tRNA(Asn)/Glu-tR Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011383994.1 AMB_RS07990 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 533.1 0.0 2.7e-164 2.7e-164 3 480 .. 11 483 .. 9 484 .. 0.98 Alignments for each domain: == domain 1 score: 533.1 bits; conditional E-value: 2.7e-164 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 ++e+viGlEvH q+ k+KlF+ + +e+ +pNt+v+ ++ g+PG lPv+N+ v++A+ +l l++k lcl|NCBI__GCF_000009985.1:WP_011383994.1 11 DWEIVIGLEVHAQVISKAKLFSGAATEFGA-EPNTQVSFIDAGFPGMLPVINEVCVEQAVRTGLGLKAK 78 5799************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139 i+ +svF+RK+YfY DlP+gyqi+q+d+Pi+ +G+l ++l ++ +++gierlhlE+D+gks + + lcl|NCBI__GCF_000009985.1:WP_011383994.1 79 IN-LTSVFARKNYFYADLPQGYQISQYDQPIVGEGELILDLPDGGtRTVGIERLHLEQDAGKSIHDMH- 145 77.59***********************************9875449******************977. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 ++ s++D+NRsgv L+EiV+kPdl+s++ea +l klr+ilryle dg+++eGsmR+D+Nvs+r++G lcl|NCBI__GCF_000009985.1:WP_011383994.1 146 -PSKSFIDLNRSGVALMEIVSKPDLRSPEEAGLYLTKLRSILRYLETCDGNMQEGSMRCDANVSVRPVG 213 .79****************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 +++ tr EiKN+ns++ +++aie+E R +++ ++g e+ qetr fd k t s+R+Ke+++DYRYf lcl|NCBI__GCF_000009985.1:WP_011383994.1 214 STELRTRCEIKNVNSIRFVQQAIEFEARRHIDVYESGGEIRQETRLFDSVKGETRSMRSKEHAHDYRYF 282 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl p++i++++v++ ++ lpelP++k++r++ eygl+++da vlv+++ ++ fe+v+k ++ k lcl|NCBI__GCF_000009985.1:WP_011383994.1 283 PDPDLLPLVIEQSFVDG-IKSGLPELPDEKKARFMAEYGLNAYDAGVLVAEKASAEFFETVAKGRDS-K 349 *****************.99*****************************************998887.* PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 a nW++ ++ ++Ln++ ++++ +++ +l +li+lik+g++s++ ak+++ ++e++k p l+e++ lcl|NCBI__GCF_000009985.1:WP_011383994.1 350 MACNWVMGDFFASLNATGKTIENPPVTAANLGQLIDLIKDGTLSGRLAKDVFALMVETGKAPAVLVEER 418 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gl q++d+ ++ ++v++vi+ np++v++ k+gk ++l+++ Gqvmk t+g+a+p+ v+++l +++ lcl|NCBI__GCF_000009985.1:WP_011383994.1 419 GLKQVTDTGAIEAAVDAVISANPDKVQQVKDGKTALLGWFTGQVMKSTQGKANPAMVNEMLSKKI 483 ************************************************************98865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (485 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.29 // [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