Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_110806203.1 C8J30_RS11905 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_003217355.1:WP_110806203.1 Length = 393 Score = 178 bits (451), Expect = 3e-49 Identities = 132/409 (32%), Positives = 186/409 (45%), Gaps = 41/409 (10%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAP 73 P+ G + +W DG RY+D GI V LGH P +V + QA +L H + P Sbjct: 13 PLAFVRGEGSWLWTEDGSRYLDLGAGIAVNALGHAAPELVATLTEQAGKLWHVSNLYRIP 72 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDG 127 LA M + F + TNSG EA E A+K+ R G + I+ F G Sbjct: 73 EQERLADMLVANTFADTVF-----FTNSGTEACELAVKMVRKYFYEKGQPERSDILTFSG 127 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGR+ A + G K LPG HLP+ + +V+ A Sbjct: 128 AFHGRSSAAIAAAGTEKMVKGFGPLLPG-FKHLPWGDLE----------------AVKAA 170 Query: 188 VEDV-AAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 V D AA + EP+QGEGG F +ALR CD G L++ DE+Q G RTG+ FA Sbjct: 171 VTDTTAAILIEPIQGEGGIRPAPEGFLKALREICDATGTLLVFDEVQCGVARTGRLFAHE 230 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 G+ PD++++AK I GG PLGAV+ + + G G TY GNP+ CA + + Sbjct: 231 WAGVTPDVMMVAKGIGGGFPLGAVLATANAASGMTAGTHGSTYGGNPLGCAIGAKMIEIV 290 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366 T R+ + R E A+ + G G M G+ G Sbjct: 291 TAPGFLEEVSRKAGFLRQRLEGLVAAH-PDIFEEVRGQGLMLGLRCKLPPGD-------- 341 Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 V++AA A+ LL +P+ A +++RLL LTI + + E + LE L Sbjct: 342 VVKAAYAQNLLTVPA--ADNVLRLLPALTITEDDMAEAVRRLEAAATAL 388 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: 387 Number of extensions: 20 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: 393 Length adjustment: 31 Effective length of query: 385 Effective length of database: 362 Effective search space: 139370 Effective search space used: 139370 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