Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__ANA3:7025943 Length = 425 Score = 335 bits (858), Expect = 2e-96 Identities = 173/409 (42%), Positives = 244/409 (59%), Gaps = 3/409 (0%) Query: 3 QESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQAT 62 Q +++ + +HP+ + NA VWD +G+ +IDF GGI VLN GH +P V A+ AQ Sbjct: 13 QAAVAGGVGQIHPVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLE 72 Query: 63 RLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAI 122 +H F + Y+ + E+L+Q VP + L SG+EA ENA+KVAR T + + Sbjct: 73 DFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGV 132 Query: 123 IAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLF 182 IAF G+HGRT+A L L GKVAPY + +G + V+ +P A GV+ + A+ +++R+F Sbjct: 133 IAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVSDDDAMASIERIF 192 Query: 183 SVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242 + ++AA I EPVQGEGGF A P F Q LR CD GI++I DE+Q+G GRTG Sbjct: 193 KNDAEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIADEVQTGAGRTGTF 252 Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS 302 FA ++G+ D+ AKSIAGG PL + G+ E+M A+ GGLGGTY GNP++CAAALA Sbjct: 253 FAMEQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAV 312 Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPA 362 L +E L + I S + P I + G+GAM IE +G PAP Sbjct: 313 LEVFEEEKLLERANAIGERIKSALNTMQVE--HPQIADVRGLGAMIAIELME-EGKPAPQ 369 Query: 363 QLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQC 411 A+++ AR RGL+L+ G +++R+L PLT+ E L GL IL+ C Sbjct: 370 YCAQILAEARNRGLILLSCGTYGNVLRILVPLTVPDEQLAAGLGILKSC 418 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: 480 Number of extensions: 16 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: 416 Length of database: 425 Length adjustment: 32 Effective length of query: 384 Effective length of database: 393 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