Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_019895362.1 A377_RS0106195 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q8ZV07 (383 letters) >NCBI__GCF_000384235.1:WP_019895362.1 Length = 417 Score = 184 bits (467), Expect = 4e-51 Identities = 132/408 (32%), Positives = 207/408 (50%), Gaps = 35/408 (8%) Query: 4 IAKYYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWA 63 I Y R Y VKG WD+ G+ YID GV+ GH NPK+ A+ + E Sbjct: 11 IRAYSRAYPAVFVKGQNAKQWDETGKEYIDFYAGAGVLNFGHNNPKLKAAMMDYLAEDGV 70 Query: 64 V-PLNFATPARERFIEEFSK-LLPPK---FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIV 118 + L+ T A+ FI+ F + +L P+ + + F+ TGT AVE A+K+A+KVT + ++ Sbjct: 71 LHSLDMMTAAKRDFIQGFVETILQPRKMDYKLQFMGPTGTNAVEAALKLARKVTGRQNVI 130 Query: 119 AFTNSFHGRTMGSLSITWNEKYKKAFEPLYPHVRFGKF--NVPHEVDKLI---------- 166 AF FHG T+G+L+ T N +++A HV F NV + L Sbjct: 131 AFAQGFHGMTLGALACTANGYFRQAAGVPLNHVSHCPFETNVGGGLAMLDTLRALYDNTS 190 Query: 167 --GEDTCCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAF 224 E ++VEPIQ EGGVN A+ E+L+ L + A+ GALLI D++Q G GRTG ++F Sbjct: 191 GGAEKPAAILVEPIQAEGGVNVASAEWLQGLDKLAKDLGALLIVDDIQAGCGRTGQYFSF 250 Query: 225 QKYGVEPDIFTAGKPVAG-GLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASR 283 + G++PDI T K + G G PI + + + + ++PGEH TF G + A A R Sbjct: 251 DEAGIDPDIITLAKGLGGLGTPIAMNLVKPEHDQHWQPGEHTGTFRGQNLSFVAGREALR 310 Query: 284 LLREEDVPGRAE-----RIGA--ELAKALGDTGSRLAVRVKGMGLMLGLELRVKADQFIQ 336 ++ + +GA ++A+ D G +VR KGM L + A + Sbjct: 311 YFEDDQLMNAVHDKGEIMVGALEQMAQTYPDAG--FSVRGKGMMQALDVGDGALAKAVAR 368 Query: 337 PLLERGVMALTAGV--NTLRFLPPYMISKED----VEVVHAAVTEVLK 378 ERG++ GV + ++ +PP I +++ +E++ A+ +K Sbjct: 369 ECFERGMLFGPCGVGGSVIKLIPPLTIPEDELVAGLEILSEALAACMK 416 Lambda K H 0.320 0.138 0.408 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: 378 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: 383 Length of database: 417 Length adjustment: 31 Effective length of query: 352 Effective length of database: 386 Effective search space: 135872 Effective search space used: 135872 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 Jul 25 2024. The underlying query database was built on Jul 25 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