Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate AO353_11510 AO353_11510 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11510 Length = 425 Score = 343 bits (881), Expect = 4e-99 Identities = 174/415 (41%), Positives = 259/415 (62%), Gaps = 4/415 (0%) Query: 3 QESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQAT 62 + ++ + + +HPI H +N+ V D +G+ +IDF GGI VLN GH +P V+ A+ Q Sbjct: 13 EAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLN 72 Query: 63 RLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAI 122 +LTH F + PY+ L E+++ VP + +L +G+EA EN++K+AR ATG+ + Sbjct: 73 KLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGV 132 Query: 123 IAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLF 182 IAF G +HGRT+ TL L GKV PY +G +PG ++ YP+ GV+ + ++ +++R+F Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIF 192 Query: 183 SVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242 + D+AA I EPVQGEGGF F + LR CD+ GIL+I DE+Q+G GRTG Sbjct: 193 KNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTF 252 Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS 302 FA ++G+ DL AKSIAGG PL V G+ E M A+ GGLGGTY+G+PI+CAAALA Sbjct: 253 FAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAV 312 Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANADG-SPA 360 + +E+L + + +V+ + +A P IG + +GAM +E F N D P Sbjct: 313 MEVFEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFENGDSHKPN 370 Query: 361 PAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 A +AKV+ AR +GL+L+ G +++R+L PLT E L++GL I+E+C +EL Sbjct: 371 AAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEECFSEL 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: 500 Number of extensions: 21 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: 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 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