Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_245300308.1 B1812_RS21480 diaminobutyrate--2-oxoglutarate transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_002117405.1:WP_245300308.1 Length = 454 Score = 184 bits (468), Expect = 4e-51 Identities = 135/412 (32%), Positives = 198/412 (48%), Gaps = 31/412 (7%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 PI L G V D + + YID + G G LGH + VV+A++ + P Sbjct: 31 PIALKSGGGVRVRDVEDREYIDCLSGAGTQPLGHNHEVVVDAVRDALSGAVPLQTLDLPT 90 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLT---NSGAEAAENALKVARGATGKRAIIAFDGGFHG 131 + L +P +P + SGA+A E ALK+ R ATG+R I++F G +HG Sbjct: 91 PLKDRFIGDLFDSLPAEFPNNFKIQFCGPSGADAIEAALKLVRTATGRRGILSFRGAYHG 150 Query: 132 RTLATLNLNGKVAPYKQRVGELPGPVYHLPYPS-------ADTGVTCEQALKAMDRLFSV 184 T L+L G+ P K + V LPYPS E + + ++ L Sbjct: 151 MTSGALSLTGESGP-KAAINGGAAEVQFLPYPSDYRCPFGLGGHAGSEMSARYIENLLED 209 Query: 185 ELA-VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243 L+ V AA I E VQGEGG ++ + +R + RGI +I+DE+Q+G GRTG+ + Sbjct: 210 PLSGVPLPAAMILEVVQGEGGINPAPDSWLRKIREITEFRGIPLILDEVQTGLGRTGRLY 269 Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 AF GI PD+L+L+K+I GG+PL V+ R+EL P G GT+ GN ++ AA A++ Sbjct: 270 AFQHAGITPDVLVLSKAIGGGLPLSVVIYRRELDHWQP-GAHAGTFRGNQLAFAAGAATI 328 Query: 304 ----AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANAD--- 356 AQ + N G R + A+ S + IG + G G M G+E AD Sbjct: 329 RFISAQRLECNAEEMGCRLQDALRSIQSETRC------IGHVRGRGLMVGVEIVRADHTD 382 Query: 357 -----GSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEE 403 S +P K+ RGL+L G+ +IR L PL + ++E Sbjct: 383 RLAGPPSSSPQMAQKLQNECLRRGLILERGGRLGSVIRFLPPLIVTPAEIDE 434 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: 503 Number of extensions: 24 Number of successful extensions: 5 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: 454 Length adjustment: 32 Effective length of query: 384 Effective length of database: 422 Effective search space: 162048 Effective search space used: 162048 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: 51 (24.3 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