Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS15580 Length = 394 Score = 281 bits (720), Expect = 2e-80 Identities = 160/382 (41%), Positives = 226/382 (59%), Gaps = 7/382 (1%) Query: 9 NFDEWMIP----VYASAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREAL 64 NF+E+ I + + G+GS L+D GK Y+DF G AVN+LGH + + EAL Sbjct: 2 NFNEYPIESLMYITNRPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEAL 61 Query: 65 NEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRY 124 N+Q+ + + N+P+ +LA L + D+VFF NSGAEANE A+KLARK+ ++ Sbjct: 62 NKQSQLLINPSPAFYNQPMAQLAGLLTQHSCFDKVFFANSGAEANEGAIKLARKWGK-KF 120 Query: 125 GSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDST 184 I+ F ++FHGRTL T+SA G+P + +AP A NDI S LI+ T Sbjct: 121 KDGAFEIITFDHSFHGRTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKT 180 Query: 185 CAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVT 244 AV++EPIQGEGGV+PA+ F+Q LREL +HN LLI DEVQ+G GR G L+AY + Sbjct: 181 VAVMLEPIQGEGGVIPATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIE 240 Query: 245 PDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEM 304 PD++T K +GGG P+ ALLA E A V G G TY GNPL +AV V+ + P Sbjct: 241 PDIMTLGKGIGGGVPLAALLAKAEIA-VFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGF 299 Query: 305 LNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVM 364 L G++ R ++ +L ++ G F RG GLL +L D Q + +++ G++ Sbjct: 300 LEGLRARGEYLRAKLLELSEERG-FEGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLL 358 Query: 365 VLIAGGNVVRFAPALNVSEEEV 386 + A N++RF PALNV+ EE+ Sbjct: 359 LNAARPNLLRFMPALNVTNEEI 380 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: 430 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: 406 Length of database: 394 Length adjustment: 31 Effective length of query: 375 Effective length of database: 363 Effective search space: 136125 Effective search space used: 136125 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 Sep 17 2021. 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