Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF4563 PS417_23355 4-aminobutyrate aminotransferase
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__WCS417:GFF4563 Length = 416 Score = 348 bits (894), Expect = e-100 Identities = 175/412 (42%), Positives = 256/412 (62%), Gaps = 4/412 (0%) Query: 16 VPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKLT 75 + + + +HPI H KN+ V D G+ +IDF GGI VLN GH HP V+ A+ +Q +LT Sbjct: 6 ISQSISIVHPISLSHGKNAEVWDTSGKRYIDFVGGIGVLNLGHCHPGVVDAIRDQATRLT 65 Query: 76 HTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIAF 135 H F + PYVEL +++ A +P D+ +L +G+EA EN++KI R ATGR VIAF Sbjct: 66 HYAFNAAPHAPYVELMDRLTAFIPVDYPISGMLTNSGAEAAENALKIVRGATGRTAVIAF 125 Query: 136 TGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKND 195 GA+HGRT+ TL L GKV PY +G++PG ++ YP+ +GV+ +++ +++R+F + Sbjct: 126 DGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVYHLPYPSADNGVTCAEALKAMDRLFSVE 185 Query: 196 AEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255 + D+A IIEPVQGEGGF EF + LR C+++ ILLIADE+Q+G GRTG FA Sbjct: 186 IDVSDVACFIIEPVQGEGGFLALDIEFAQALRRFCNENNILLIADEIQSGFGRTGERFAF 245 Query: 256 EQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEV 315 ++G+ DL KSIAGG PL V G+ MD + GGLGGTY+G+PIACAAALA ++ Sbjct: 246 SRLGIEPDLILLGKSIAGGVPLGAVVGRKALMDNLPKGGLGGTYSGNPIACAAALATLDA 305 Query: 316 FEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFENGDSHKPNAAA 373 +EHL E +V+ + +A P +G + +G+M +EL N D P Sbjct: 306 MTDEHLSAWGSQQEEAIVSRYQTWRAHGLTPYLGRLTGVGSMRGIEL-ANADG-TPAPKQ 363 Query: 374 VAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEECFSEL 425 + +++ ARD GL+L+ G +++R+L PLT L++GL + E C +L Sbjct: 364 LTQLLGLARDAGLLLMPSGKSRHIIRLLAPLTIEPAVLEEGLTMFEACLKQL 415 Lambda K H 0.320 0.137 0.395 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: 482 Number of extensions: 17 Number of successful extensions: 2 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: 416 Length adjustment: 32 Effective length of query: 393 Effective length of database: 384 Effective search space: 150912 Effective search space used: 150912 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