Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011876070.1 2-aminoadipate aminotransferase
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >NCBI__GCF_000016205.1:WP_011876070.1 Length = 405 Score = 289 bits (740), Expect = 9e-83 Identities = 156/381 (40%), Positives = 230/381 (60%), Gaps = 6/381 (1%) Query: 16 SAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAFQYGLTEGYPPL 75 S +REL K+ PG+IS GG PA +LFD GL A + QYG T+G L Sbjct: 14 SPIRELFKYLSEPGMISFAGGYPASDLFDVAGLQAAEARAYETPTR-CLQYGPTDGLAEL 72 Query: 76 RQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAALQVFQL 135 ++ + L RGVAC + + +T+GSQQ LD++ R L++PGD ++ E+P Y A LQ +L Sbjct: 73 KKQLVSLMAQRGVACGSDELVVTTGSQQGLDLLLRVLVNPGDTVLTEQPAYPATLQALRL 132 Query: 136 AQANILSVDTDDDGMLVEQLADLLETTRVKA---VYLVPTFGNPGGKTLSEARRRRLVEL 192 QA I++V D DG+ + L+ LL + VK+ +Y VPTF NP G TL+ RR L++L Sbjct: 133 QQAQIVTVPVDGDGLNADMLSSLLASGAVKSPKILYTVPTFANPTGATLTLERRIALLKL 192 Query: 193 AKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVEL-GCEDQVVYTSTFSKILAPGMRIGWI 251 A K+ F+I+EDDPYG++ F E + A E+ G D VV+ ++ SKI+APG+R+GW Sbjct: 193 AVKYRFLIVEDDPYGDLRFAGEKLPSILSLAAEVEGGRDWVVHFASLSKIVAPGLRVGWT 252 Query: 252 VMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALADAL 311 V P + ++ VI KQ DL + +Q AEYLS LE + I + Y++KC L L Sbjct: 253 VGPAEIVRRCVIAKQTVDLCSAPWTQATAAEYLSDGALERHLPRITDMYKRKCDTLCSEL 312 Query: 312 ESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDNPDTRTLR 371 +Q GE +EF +P+GGMF+WAR D + ++++N V++VPG+AF+ D D TLR Sbjct: 313 RAQFGEKVEFQKPEGGMFVWARLE-GIDVSALLARSIDNKVLFVPGKAFFADKFDPCTLR 371 Query: 372 LSYSTVSADGLMTAVERLAKS 392 LS++ D + +RL ++ Sbjct: 372 LSFAAPGVDDIQEGAKRLKRA 392 Lambda K H 0.320 0.136 0.395 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: 400 Number of extensions: 14 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: 393 Length of database: 405 Length adjustment: 31 Effective length of query: 362 Effective length of database: 374 Effective search space: 135388 Effective search space used: 135388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
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