Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_000182725.1:WP_008507916.1 Length = 403 Score = 181 bits (459), Expect = 4e-50 Identities = 136/424 (32%), Positives = 206/424 (48%), Gaps = 56/424 (13%) Query: 13 VHPITLSHGRNA-------EVW--DTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63 VHP+ ++ R A +W DG+RYIDF GI V +LGH +P +VE ++ QA + Sbjct: 7 VHPLYDTYNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEK 66 Query: 64 LTHYAFNAAPHGPYLALMEQLSQ-FVPVSYPLAGMLTNSGAEAAENALKVAR------GA 116 L H + + + E+L + V ++ TNSGAEA E A+K AR G Sbjct: 67 LWHLS-----NIYEIPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGH 121 Query: 117 TGKRAIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALK 176 + II F+G FHGRTLAT+ G+ A Y + G +P+ E AL+ Sbjct: 122 PERFRIITFEGAFHGRTLATIAAGGQ-AKYLEGFGPKVEGFDQVPFGD-------EAALR 173 Query: 177 AMDRLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGF 236 A + A + EP+QGEGG A F + +R+ CDE G+L+++DE+Q+G Sbjct: 174 AA--------ITPETAGILLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGV 225 Query: 237 GRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISC 296 GRTG+ FA GI PD++ +AK I GG P+GA + E + G G TY GNP+ Sbjct: 226 GRTGKFFAHEWAGIRPDIMAIAKGIGGGFPIGACLATAEAAKGMTAGMHGTTYGGNPLGM 285 Query: 297 AAALA----SLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEF 352 A A LA EN+ +Q + S +R+ + + G G + G++ Sbjct: 286 AVGNAVLDVVLADGFMENVQATALVMKQGLASLVDRY-----PNVVSEIRGRGLLMGLKC 340 Query: 353 ANADGSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 + S +++A R +L + +G +++RLL PL E E L +E + Sbjct: 341 VVPNTS--------LIQALRDEHVLSVGAGD--NVVRLLPPLITTPEEAREALKHIETAV 390 Query: 413 AELN 416 L+ Sbjct: 391 ERLS 394 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: 430 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: 403 Length adjustment: 31 Effective length of query: 385 Effective length of database: 372 Effective search space: 143220 Effective search space used: 143220 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