Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_001592305.1:WP_068170823.1 Length = 428 Score = 340 bits (873), Expect = 4e-98 Identities = 175/411 (42%), Positives = 249/411 (60%), Gaps = 4/411 (0%) Query: 4 ESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63 ++ + + ++ + H +NAE+WD +G+R+IDF GGI VLN GH +P V AI AQ R Sbjct: 19 DATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQAAIAAQLQR 78 Query: 64 LTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAII 123 TH + P+ Y++L E+++ VP+ ++GAEA ENA+K+AR +TG+ +I Sbjct: 79 FTHSCYQVVPYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIARSSTGRSGVI 138 Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183 AF G FHGR+L ++L GKV PYK G P +YH+P+P+ G + ++ +AMD +F Sbjct: 139 AFGGAFHGRSLFAVSLTGKVQPYKAGFGPFPPEIYHVPFPA--EGASLDETKRAMDHVFK 196 Query: 184 VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243 ++ VAA +FEPVQGEGGF + LR CD+ GIL+I DE+Q+GF RTG+ F Sbjct: 197 CDIEPSRVAAIVFEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQTGFARTGRMF 256 Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 A G+ PDL+ +AKS+AGG L AV G+ +M GGLGGTY+GNP++ AA+ A L Sbjct: 257 AMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNPLAIAASHAVL 316 Query: 304 AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363 M +E L +R +V+ KA P IG + G+GAM EF +A G+P Sbjct: 317 DVMAEEKLPERAQRLGDQLVAHLRAAKAK--YPRIGEVRGLGAMVACEFVDAAGAPDADT 374 Query: 364 LAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 +V AA RGLLL+ G ++IR L PLTIE V E L +L+ +AE Sbjct: 375 TKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAE 425 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: 547 Number of extensions: 15 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: 428 Length adjustment: 32 Effective length of query: 384 Effective length of database: 396 Effective search space: 152064 Effective search space used: 152064 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 09 2024. 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