Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_010961322.1 MCA_RS10180 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_000008325.1:WP_010961322.1 Length = 391 Score = 206 bits (523), Expect = 1e-57 Identities = 142/391 (36%), Positives = 206/391 (52%), Gaps = 45/391 (11%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+T +HG A ++DT+GKRY+D V G+ V +LGH +PAV +A+ QA RL H + N Sbjct: 13 PVTFTHGEGAWLFDTEGKRYLDAVSGVAVCSLGHAHPAVAKALCDQAGRLVHCS-NLYRI 71 Query: 75 GPYLALMEQLSQFVPVSYPLAGM----LTNSGAEAAENALKVARGATGKRAI-----IAF 125 G L +QL L+GM NSGAEA E ALK+AR R I + Sbjct: 72 GLQEDLAKQLCD-------LSGMDNAFFCNSGAEANEAALKIARRYGHHRGIDTPKIVVM 124 Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE 185 +G FHGRTLATL+ G ++ L G LPY A+ A+ A+D Sbjct: 125 EGSFHGRTLATLSATGN-PKVQEGFAPLVGGFVRLPYGDAE-------AVAAVDD----- 171 Query: 186 LAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245 DV A + EPVQGEGG + L+ C+ RG L+++DE+Q+G GRTG+ F Sbjct: 172 ---PDVVAVLVEPVQGEGGVRIPPDDYLARLKSLCERRGWLLMLDEVQTGMGRTGRMFGH 228 Query: 246 PRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ 305 G+ PD++ LAK++ G+P+GA + R L G G T+ GNP++CAAALA + Sbjct: 229 QHTGVTPDVMALAKALGNGVPIGACLARGVAAEMLTAGKHGSTFGGNPLACAAALAVIDT 288 Query: 306 MTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLA 365 +T ++LA E Q ++ + R + SG P + + G+G M G+E Sbjct: 289 LTRQSLAQRAEILGQRLLDGF-RTRLSG-RPGVIEIRGLGLMIGLELER--------PCT 338 Query: 366 KVMEAARARGLLLMPSGKARHIIRLLAPLTI 396 +++ A +GLL+ + A +RLL PL + Sbjct: 339 RLVGMALEQGLLI--NVTAERTVRLLPPLIL 367 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: 422 Number of extensions: 22 Number of successful extensions: 4 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: 391 Length adjustment: 31 Effective length of query: 385 Effective length of database: 360 Effective search space: 138600 Effective search space used: 138600 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 24 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