Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_011813801.1 HHAL_RS05115 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_000015585.1:WP_011813801.1 Length = 479 Score = 509 bits (1312), Expect = e-149 Identities = 256/477 (53%), Positives = 347/477 (72%), Gaps = 4/477 (0%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M +ETVIGLE+H +L T +K+FS +P +GAEPN+ +DL PGVLPV+N+ V A+ Sbjct: 1 MKWETVIGLEIHAQLATRTKIFSGAPTAYGAEPNTQACPVDLGLPGVLPVLNREVVRMAI 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119 + +A++ IA S F RKNYFYPD PK YQISQ+D PI E G++DIE+ DG +KRIGIT Sbjct: 61 KFGLAVDARIAPRSVFARKNYFYPDLPKGYQISQYDLPIVEGGHLDIELEDGASKRIGIT 120 Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177 R H+EEDAGKS H+ + + VDLNR GTPL+EIVSEPD+RSP EA AY++KL ++++Y Sbjct: 121 RAHLEEDAGKSLHEDFHGMTGVDLNRAGTPLMEIVSEPDLRSPAEAAAYMKKLHALVRYL 180 Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237 + D M+EGS RCDAN+S+RP GQE FGT+AELKNLNSF +V + LEYE +RQ + L S Sbjct: 181 EICDGNMQEGSFRCDANVSVRPVGQEAFGTRAELKNLNSFRFVERALEYEVERQIDLLES 240 Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297 GGE+ QETR +D G T MR KE ++DYRYFPEPD++P+ +D A + VR+T+PELPD Sbjct: 241 GGEVVQETRLYDVDKGVTRSMRTKEEANDYRYFPEPDLLPVEVDAALVDEVRETLPELPD 300 Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTI-EHGADVKLTSNWLMGGVNEYLNKNQ 356 E++ ++ E GLPAYDA VLT T++M+DFFE + E G K T+N LM + YLNK+ Sbjct: 301 EKRRRFEEEYGLPAYDAGVLTATRDMADFFEHAVSESGGFAKRTANLLMSELLAYLNKDG 360 Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416 +E+ ++ +TPE L ++ +ED T+SS+ AK VF + A G +++E GL Q++D + Sbjct: 361 LEIAESPVTPEMLGKLVARVEDETLSSRGAKDVFEAMWAGEGEPDEVIEKKGLKQVTDTS 420 Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473 + V+EA+ NN Q +E Y+ GK K GF VGQ+MKAS G+ANPQ VN+LLK++LD Sbjct: 421 AIEALVDEAIANNPQQLEQYRAGKEKLFGFFVGQVMKASGGKANPQQVNELLKKKLD 477 Lambda K H 0.313 0.133 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: 646 Number of extensions: 19 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: 475 Length of database: 479 Length adjustment: 33 Effective length of query: 442 Effective length of database: 446 Effective search space: 197132 Effective search space used: 197132 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_011813801.1 HHAL_RS05115 (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.22341.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-184 597.3 0.0 1.1e-183 597.1 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011813801.1 HHAL_RS05115 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011813801.1 HHAL_RS05115 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 ! 597.1 0.0 1.1e-183 1.1e-183 3 480 .. 2 476 .. 1 477 [. 0.98 Alignments for each domain: == domain 1 score: 597.1 bits; conditional E-value: 1.1e-183 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 ++e viGlE+H ql t++K+F+ +++ + +pNt+ cpv+lglPG+lPvlN+e+v++A+k +la++++ lcl|NCBI__GCF_000015585.1:WP_011813801.1 2 KWETVIGLEIHAQLATRTKIFSGAPTAYGA-EPNTQACPVDLGLPGVLPVLNREVVRMAIKFGLAVDAR 69 7899************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139 +++ svF+RK+YfYpDlPkgyqi+q+dlPi+e+G+l+iele+++ k+igi+r hlEeD+gks ++ lcl|NCBI__GCF_000015585.1:WP_011813801.1 70 -IAPRSVFARKNYFYPDLPKGYQISQYDLPIVEGGHLDIELEDGAsKRIGITRAHLEEDAGKSLHEDF- 136 .668*************************************99877*******************944. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 + ++ vD+NR+g+PL+EiV++Pdl+s+ ea+a++kkl++++rylei dg+++eGs+R+D+Nvs+r++G lcl|NCBI__GCF_000015585.1:WP_011813801.1 137 -HGMTGVDLNRAGTPLMEIVSEPDLRSPAEAAAYMKKLHALVRYLEICDGNMQEGSFRCDANVSVRPVG 204 .589***************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 qe++gtr+E+KNlns++ +e+a+eyE+eRq++ll++g ev+qetr +d k +t s+R Kee++DYRYf lcl|NCBI__GCF_000015585.1:WP_011813801.1 205 QEAFGTRAELKNLNSFRFVERALEYEVERQIDLLESGGEVVQETRLYDVDKGVTRSMRTKEEANDYRYF 273 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkli.kep 345 pePdl p+e+d +v+e v+e+lpelP++kr r+++eygl ++da vl++ ++++d fe++v+ + + + lcl|NCBI__GCF_000015585.1:WP_011813801.1 274 PEPDLLPVEVDAALVDE-VRETLPELPDEKRRRFEEEYGLPAYDAGVLTATRDMADFFEHAVSESgGFA 341 ****************9.*****************************************9876651567 PP TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414 k ++n +++ell++Lnk +++ae+ ++pe+l +l++ ++++++s++ ak+++e + +++p+++iek lcl|NCBI__GCF_000015585.1:WP_011813801.1 342 KRTANLLMSELLAYLNKDGLEIAESPVTPEMLGKLVARVEDETLSSRGAKDVFEAMWAGEGEPDEVIEK 410 ********************************************************************* PP TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 +gl q++d++++ ++v+e+i++np+++e+y++gkek+++f+vGqvmk + g+a+p++v++llk++l lcl|NCBI__GCF_000015585.1:WP_011813801.1 411 KGLKQVTDTSAIEALVDEAIANNPQQLEQYRAGKEKLFGFFVGQVMKASGGKANPQQVNELLKKKL 476 ****************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (479 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: 00:00:00.01 # Mc/sec: 11.67 // [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