Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 168 bits (426), Expect = 2e-46 Identities = 128/409 (31%), Positives = 203/409 (49%), Gaps = 36/409 (8%) Query: 9 YARA-DIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTA--QAHKLWHT 65 Y+RA ++F R + +LY DG+ +LDF AG GH N L +AL +A + Sbjct: 14 YSRAFPVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQG 73 Query: 66 SNLFRVAGQ---ESLAKRLTEATFAD--TVFFTNSGAEAWECGAKLIRKYHYEKGDKART 120 ++F A ES K + + D F +G E KL RK K R+ Sbjct: 74 LDMFTTAKHDFMESYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLARKV------KGRS 127 Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPF----GD----LEAVRNAVT 172 II+F FHG T+ AV+ + G G L D + + GD L + ++ Sbjct: 128 GIISFTNGFHGVTMGAVATTGNKHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDKLLS 187 Query: 173 DETAG------ICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKL 226 D ++G + +E +QGEGG+ A E+L+GL E+C +H +LL LD+IQ G GRTG+ Sbjct: 188 DGSSGFELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEF 247 Query: 227 FAHEWAGITPDVMAVAKGIGG-GFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNA 285 F+ E+AGI PD++ V+K + G G P+ A + + G H T+ GN +A A Sbjct: 248 FSFEFAGIKPDIVTVSKSLSGYGLPM-ALVLFKPELDVWDPGEHNGTFRGNNMAFITARA 306 Query: 286 VLDKV-LEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPA--VGDV 342 ++ + F + V+ +L D L + + P FK ++G+GLM G+ A G + Sbjct: 307 AVENYWKDDAFANEVKAKTEVLGDALQSICDKYPGQFK-MKGRGLMRGIEAKHADITGPI 365 Query: 343 VVALRANGLLSVPAG--DNVVRLLPPLNIGEAEVEEAVAILAKTAKELV 389 +GL+ +G D V++ L PL E ++++ A+LAK+ E++ Sbjct: 366 TKRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEIM 414 Lambda K H 0.321 0.139 0.414 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: 427 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: 389 Length of database: 422 Length adjustment: 31 Effective length of query: 358 Effective length of database: 391 Effective search space: 139978 Effective search space used: 139978 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