Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 339 bits (870), Expect = 8e-98 Identities = 172/413 (41%), Positives = 256/413 (61%), Gaps = 4/413 (0%) Query: 5 SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64 ++ + + +HPI H +N+ V D +G+ +IDF GGI VLN GH +P +++A++ Q +L Sbjct: 15 AVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKL 74 Query: 65 THYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIA 124 TH F + PY+ L E+++ VP + +L +G+EA ENA+K+AR ATG+ +IA Sbjct: 75 THTCFQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIA 134 Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184 F G +HGRT+ TL L GKVAPY +G +PG ++ YP A GV+ + ++ +++R+F Sbjct: 135 FTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVSVDDSIASIERIFKN 194 Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244 + D+AA I EPVQGEGGF F LR CDE GIL+I DE+Q+G GRTG FA Sbjct: 195 DAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTFFA 254 Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304 ++G+ DL AKS+ GG P+ V G+ E+M A+ GGLGGTY+GNP+SCAAALA L Sbjct: 255 MEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVLE 314 Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANAD-GSPAPA 362 +E L + + + + + + IG + G+GAM IE F + D PA A Sbjct: 315 VFEEEKLLDRCKAVAERLTTGLKAIQTK--HKEIGEVRGLGAMIAIELFEDGDHARPAAA 372 Query: 363 QLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 ++++ AR +GL+L+ G +++R+L PLT E E+L+ GL I+ +C EL Sbjct: 373 LTSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGECFDEL 425 Lambda K H 0.320 0.137 0.402 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: 512 Number of extensions: 25 Number of successful extensions: 3 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: 416 Length of database: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 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 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