Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_028950007.1 Q385_RS0101715 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_000619805.1:WP_028950007.1 Length = 388 Score = 162 bits (410), Expect = 2e-44 Identities = 118/403 (29%), Positives = 192/403 (47%), Gaps = 41/403 (10%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P G ++D GK+Y+D + GI V LG+ +P + +AI Q +++ H + N Sbjct: 19 PYFFEKGEGCYLYDEKGKKYLDMLSGIAVNALGYNHPKLTDAICQQVSKIIHIS-NLFYI 77 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-----ATGKRAIIAFDGGF 129 P + + + LS+ S+ NSGAE+ E +K+ R K II F+G F Sbjct: 78 KPQIEVAKILSEN---SFGGKVFFCNSGAESNEALIKLVRRYFYDKKQDKYEIITFEGSF 134 Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189 HGRTLAT+ + P YH + G + K D L + Sbjct: 135 HGRTLATVTATAQ-------------PKYHEGFYPLVGGF---KYAKFNDINSVKNLITD 178 Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249 AA + E VQGEGG D F + L C E+ IL +DE+Q+G GRTG+ FA+ Sbjct: 179 KTAAILIELVQGEGGVNPADKEFIKDLYNLCKEKDILFTVDEVQTGIGRTGKLFAYQHFE 238 Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDE 309 I+PD++ LAK + GG+P+GA++ + ++ + G T+ GN +S AA L ++ E Sbjct: 239 IQPDIISLAKGLGGGVPIGAIIAKDKIAKSFVPGTHASTFGGNYLSTVAAKVVLEEVLSE 298 Query: 310 NLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369 V + + L + + G+G M G++ P +VM+ Sbjct: 299 GFLD--------KVQKVGDYLKESLKVFGYPVKGLGLMVGMDL------PKDIPAKEVMK 344 Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 A +GL++ +G+ + +R + PL I + ++E +DIL++ L Sbjct: 345 KALEKGLIVGTAGE--NTLRFVPPLIITEKQVDEAVDILKEVL 385 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: 367 Number of extensions: 13 Number of successful extensions: 3 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 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