Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 149 bits (377), Expect = 1e-40 Identities = 124/418 (29%), Positives = 202/418 (48%), Gaps = 35/418 (8%) Query: 15 IPVYASA-PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQ-----A 68 + VY+ A P I R + + L+ + GKEY+DF G GH + L++AL E Sbjct: 11 VRVYSRAFPVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGV 70 Query: 69 SKFWHTGNGYTNEPVLRLAKKLIDATFAD--RVFFCNSGAEANEAALKLARKFAHDRYGS 126 S+ ++ + K ++D D F +G EAALKLARK Sbjct: 71 SQGLDMFTTAKHDFMESYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLARKV------K 124 Query: 127 HKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYN-----DINSASA--- 178 +SGI++F N FHG T+ V+ G + ++ Y+ D+++ + Sbjct: 125 GRSGIISFTNGFHGVTMGAVATTGNKHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDK 184 Query: 179 LIDDST------CAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRT 232 L+ D + AVIVE +QGEGG+ +L+GL ELC +H+ LLI D++Q G GRT Sbjct: 185 LLSDGSSGFELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRT 244 Query: 233 GELYAYMHYGVTPDLLTTAKALGG-GFPVGALLATEECARVMTVGTHGTTYGGNPLASAV 291 GE +++ G+ PD++T +K+L G G P+ +L E V G H T+ GN +A Sbjct: 245 GEFFSFEFAGIKPDIVTVSKSLSGYGLPMALVLFKPE-LDVWDPGEHNGTFRGNNMAFIT 303 Query: 292 AGKVLE-LINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ 350 A +E N VK + + + L +I +Y +++G GL+ G + A +A Sbjct: 304 ARAAVENYWKDDAFANEVKAKTEVLGDALQSICDKYPGQFKMKGRGLMRG--IEAKHADI 361 Query: 351 AKQISQEAAKAGVMVLIAGGN--VVRFAPALNVSEEEVTTGLDRFAAACEHFVSRGSS 406 I++ A + G+++ +G N V++ L SEE++ G A + + + G S Sbjct: 362 TGPITKRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEIMQEGLS 419 Lambda K H 0.319 0.135 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: 416 Number of extensions: 27 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: 406 Length of database: 422 Length adjustment: 31 Effective length of query: 375 Effective length of database: 391 Effective search space: 146625 Effective search space used: 146625 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 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