Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::Marino:GFF3099 (404 letters) >NCBI__GCF_900115975.1:WP_207545101.1 Length = 434 Score = 213 bits (542), Expect = 9e-60 Identities = 141/411 (34%), Positives = 222/411 (54%), Gaps = 42/411 (10%) Query: 28 RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTN-EPALR 86 + +G+ I D EG+E+ID GGI GH +V A+ +QAEK+ H ++T EP L Sbjct: 30 KAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVVEAIKNQAEKLLHTCFMVTMYEPYLD 89 Query: 87 LAKTLCDLT---FAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143 LA+ L +LT F +RV F NSGAE E A K+AR YA ++ IISF+ +FHGRT Sbjct: 90 LAEKLIELTPGNFDKRVMFVNSGAECVENAVKIARSYA------KRTGIISFECAFHGRT 143 Query: 144 LFTVSVGGQPK-YLEGFEP-APG---------------------GIHHAEFNDLESVKKL 180 L T+S+ + K Y GF P AP G+H E D + Sbjct: 144 LMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTYRSTYPECGLHCLEQFDRMFAAE- 202 Query: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240 + E A+++EP+QGEGG + FL GLR +CD++ +L+ DEVQ+G GR+G +A Sbjct: 203 VPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKHGIILIADEVQTGFGRTGKMFAC 262 Query: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300 + +G+ PD+++ AK + G P++A++ A + + G G TY GN ++CA +D Sbjct: 263 EHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEIGGTYSGNPVSCAAGLATIDF 322 Query: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGK--AKD--- 355 + Q +++ DK ++ M+ + E+Y + +VRG G + L + K AK+ Sbjct: 323 MQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLGAMNAMELVKDRNTKEPAKEETA 382 Query: 356 -FLNAGLEEGVMVLVAG--ANVIRLAPSLIIPEPDIELALERFEAAVKKLT 403 + ++ GV+V+ AG +NV+R L+I + +E L+ E AV ++ Sbjct: 383 AVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLDVLEQAVASVS 433 Lambda K H 0.318 0.137 0.406 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: 464 Number of extensions: 27 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: 404 Length of database: 434 Length adjustment: 32 Effective length of query: 372 Effective length of database: 402 Effective search space: 149544 Effective search space used: 149544 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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