Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 176 bits (445), Expect = 2e-48 Identities = 133/402 (33%), Positives = 194/402 (48%), Gaps = 26/402 (6%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL-THYAFNAAP 73 P+ + G +WD G+RY+D + ++GHC+P VV+AI QA L TH + Sbjct: 23 PLHIVRGEGVWLWDAGGRRYLDCYNNVP--HVGHCHPRVVDAIARQARVLNTHTRYL--- 77 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRT 133 H L +E+L+ + A +L +G+EA + AL++AR ATGK +IA D +HG T Sbjct: 78 HEGVLDYIERLTGTMDNGLDQA-LLVCTGSEAVDVALRMARAATGKTGLIATDNTYHGNT 136 Query: 134 LATLNLNGKVAP---YKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED 190 A L+ + P Y V +P P P D +A L E A Sbjct: 137 TAVAQLSTRRPPIGGYSDHVRLVPA-----PEPGTDGAAFGAHVARAAAEL---ETAGHG 188 Query: 191 VAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF-AFPRLG 249 VAA I P+ G L F + RG L+I DE+Q GFGR G F + LG Sbjct: 189 VAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGYQALG 248 Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKG-GLGGTYSGNPISCAAALASLAQMTD 308 I PD++ L KS+ G P+ VV R E+M A + G T+ G+P++ AAA+A L + D Sbjct: 249 IAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAMAVLDVLED 308 Query: 309 ENLATWGERQEQAIVSRYERWKASGL-SPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367 E L +R V RY + L P I + G G ++ + DG+P A A V Sbjct: 309 EGLVENAKR-----VGRYTLERLQALRHPAIDGVRGYGLAFALDLVDTDGAPNTALAAAV 363 Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILE 409 E A+ R +L+ G+ HI+++ PL E + D+L+ Sbjct: 364 TEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGDRLGDVLQ 405 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: 475 Number of extensions: 28 Number of successful extensions: 7 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: 413 Length adjustment: 31 Effective length of query: 385 Effective length of database: 382 Effective search space: 147070 Effective search space used: 147070 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 Apr 09 2024.
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