Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_054256827.1 BN2503_RS11430 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_001298675.1:WP_054256827.1 Length = 398 Score = 175 bits (443), Expect = 2e-48 Identities = 129/399 (32%), Positives = 191/399 (47%), Gaps = 45/399 (11%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAP 73 PI L G+ VWD +GK Y+D +GGI V LGH + +V A+Q Q +L H + + P Sbjct: 20 PIALERGQGCRVWDVNGKEYLDALGGIAVNTLGHNHAKLVPALQEQIAKLIHTSNYYHVP 79 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-----ATGKRAIIAFDGG 128 LA ++ V +S NSG EA E A+K+AR I+ ++ Sbjct: 80 GQERLA-----AKLVELSGMSKVFFCNSGLEANEAAIKIARKFGVDKGIANPEIVVYEKA 134 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGR++AT++ G + G L +P L +D + Sbjct: 135 FHGRSIATMSATGN-PKIRSGFGPLVEGFIRVP-------------LNDIDAIKQATEGN 180 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 +V A FE +QGEGG + + LR+ CDER L++IDE+Q G GRTG+ FA Sbjct: 181 PNVVAVFFETIQGEGGINPARSEYLRDLRKLCDERDWLMMIDEVQCGMGRTGKWFAHQWA 240 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 GI PD++ LAK + G+P+GAVV + L G G T+ GNP++ A + ++ M + Sbjct: 241 GIVPDVMPLAKGLGSGVPIGAVVAGPKAADVLQPGNHGTTFGGNPLAMRAGVETIRIMEE 300 Query: 309 ----ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQL 364 EN AT G + ++ +A G P + + G G M G+E P A + Sbjct: 301 DGLLENAATVGAHLKASLE------RALGSLPGVKEIRGQGLMLGVEL----DRPCGALI 350 Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEE 403 + EA GLLL S A +IR++ PL + +E Sbjct: 351 GQAAEA----GLLL--SVTADSVIRIVPPLILTTAEADE 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: 431 Number of extensions: 15 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: 398 Length adjustment: 31 Effective length of query: 385 Effective length of database: 367 Effective search space: 141295 Effective search space used: 141295 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