Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= uniprot:A1S8Y2 (425 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 184 bits (467), Expect = 4e-51 Identities = 128/407 (31%), Positives = 215/407 (52%), Gaps = 19/407 (4%) Query: 25 PVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEK--FSHTCFMVL 82 PV RA+NA ++ +G+EY+DF G LN GH + +K A+ E +E S M Sbjct: 19 PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78 Query: 83 GYESYVAVCEKLNQLVPGDFAKKSALFT--SGSEAVENAIKVARAYTKRAGVIAFTSGYH 140 + K + L P K FT +G+ VE A+K+AR R+G+I+FT+G+H Sbjct: 79 TAKHDFMESYKKHILDPRGLDYKMQ-FTGPTGTNCVEAALKLARKVKGRSGIISFTNGFH 137 Query: 141 GRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSED-DAMASIERIFKNDAEPS 199 G TM A+A TG + G+G NV +F + +D D +A ++++ + + Sbjct: 138 GVTMGAVATTGN-KHHRGGVGTPLGNV---DFMFYDGYLGDDVDTLAIMDKLLSDGSSGF 193 Query: 200 DI-AAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQM 258 ++ AA+I+E VQGEGG A ++K L ELC + I+LI D++Q G GRTG FF+ E Sbjct: 194 ELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFA 253 Query: 259 GVAADITTFAKSIAG-GFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIE-VF 316 G+ DI T +KS++G G P++ + + E +D PG GT+ G+ +A A A +E + Sbjct: 254 GIKPDIVTVSKSLSGYGLPMALVLFKPE-LDVWDPGEHNGTFRGNNMAFITARAAVENYW 312 Query: 317 EEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLT 376 +++ A + + A+ + +YP +++G G M IE P + Sbjct: 313 KDDAFANEVKAKTEVLGDALQSICDKYPGQFKMKGRGLMRGIEAKHADITGP-----ITK 367 Query: 377 EARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423 A GLI+ + G V++ L+P+T +E +++G ++A+ + ++ Sbjct: 368 RAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEIM 414 Lambda K H 0.319 0.136 0.391 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: 440 Number of extensions: 23 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: 425 Length of database: 422 Length adjustment: 32 Effective length of query: 393 Effective length of database: 390 Effective search space: 153270 Effective search space used: 153270 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: 51 (24.3 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