Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013819183.1 METME_RS12875 acetylornithine transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000214665.1:WP_013819183.1 Length = 390 Score = 196 bits (497), Expect = 1e-54 Identities = 140/409 (34%), Positives = 213/409 (52%), Gaps = 47/409 (11%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 +T G A +WD++GKRY+D + GI V NLGH +PAV +A+ Q+ L H + N Sbjct: 14 VTFDRGEGAWLWDSNGKRYLDALAGIAVCNLGHAHPAVHQALCKQSQTLIHTS-NLYGVK 72 Query: 76 PYLALMEQLSQFVPVSYPLAGM----LTNSGAEAAENALKVARGATGKRAI-----IAFD 126 L ++L + L+GM NSGAEA E A+K+AR ++ I + D Sbjct: 73 LQAELADKLCR-------LSGMDNVFFCNSGAEANEAAIKIARKYGHEQGIDAPVILTMD 125 Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186 FHGRT+ L+ G + LPG V H+PY + +D + S Sbjct: 126 KSFHGRTMGALSATGNTKIKQGFAPLLPGFV-HVPYNN-------------IDAIISAIH 171 Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 A +++ A + EPVQGEGG D + +R CDE +L+++DEIQ+G GRTG+ A+ Sbjct: 172 ADKNIVAILVEPVQGEGGVNIPDADYLNRIRALCDEHQLLLMLDEIQTGIGRTGEFLAYQ 231 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 R I PD+ LAK++ G+P+GA + R + A L G G T+ GNP++C+AALA L + Sbjct: 232 RNQILPDVCTLAKALGNGVPIGACMARGKAAAILTAGNHGSTFGGNPLACSAALAVLDTL 291 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366 +L +R+ + I R +P+I + +G M GIE +P + K Sbjct: 292 CSTDLIADADRKGKRICDAVTRQLEG--NPHIVSIRHLGLMIGIEL----DAPCGELVGK 345 Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 +E +GLL+ + A + IRLL PL I+ + +D+L + L+ L Sbjct: 346 ALE----QGLLI--NVTADNTIRLLPPLLID----DAQIDLLTETLSAL 384 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: 358 Number of extensions: 14 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: 390 Length adjustment: 31 Effective length of query: 385 Effective length of database: 359 Effective search space: 138215 Effective search space used: 138215 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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