Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 176 bits (445), Expect = 1e-48 Identities = 130/405 (32%), Positives = 206/405 (50%), Gaps = 47/405 (11%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 + G A + +DG+R++DF G+ V LGH +P +V A++AQA +L H + G Sbjct: 15 VIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPG 74 Query: 76 PYLALMEQLSQ-FVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGG 128 E++++ + S+ N+GAEA E +K+AR G + I+A G Sbjct: 75 -----QERVAERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGS 129 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRT+ATL G Y + G + H+PY E A A+ Sbjct: 130 FHGRTIATLAAAG-TPKYLEGFGPVAQGFDHVPYGDL------EAARGAIG--------- 173 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 + AA + EPVQGEGG DPA+ + LR D+ G+L+++DE+Q+G GRTG+ FA Sbjct: 174 SNTAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWS 233 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 GI PD++ LAK + GG P+GAV+ ++ + + G G T+ GNP++ A A A L D Sbjct: 234 GIAPDVMGLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVL----D 289 Query: 309 ENLATWGERQEQAIVSRYERWKASGLS----PYIGRLTGVGAMRGIEFANADGSPAPAQL 364 E +A + QA+ + R + L+ I ++ G G M G++ P + Sbjct: 290 EVMAPGFLERVQAVAALL-RGRLDDLARRYPGAIAQVRGQGLMLGLKTV-----PVNTEF 343 Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILE 409 + AA GLL + +G +++RL+ PL I +E ++I++ Sbjct: 344 NAKLFAA---GLLAVGAGD--NVVRLVPPLIIGEAEVERAVEIID 383 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: 457 Number of extensions: 24 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: 388 Length adjustment: 31 Effective length of query: 385 Effective length of database: 357 Effective search space: 137445 Effective search space used: 137445 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