Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase
Query= curated2:Q9YBY6 (388 letters) >FitnessBrowser__Putida:PP_4108 Length = 416 Score = 200 bits (508), Expect = 7e-56 Identities = 148/391 (37%), Positives = 208/391 (53%), Gaps = 38/391 (9%) Query: 26 VWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELV--AASSSFSTP--SLEEALT 81 VWD G++Y+D G G LGH NPA+VEA+ QA L A +++ P +L E L+ Sbjct: 26 VWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALMEQLS 85 Query: 82 EFSRIAPPWAEEIVFLNTGTEAVEAALKAAWLATGKRGIVALKNSFHGRTLASLSVTWNP 141 +F ++ P A + N+G EA E ALK A ATGKR I+A FHGRTLA+L++ Sbjct: 86 QFVPVSYPLAGMLT--NSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGKV 143 Query: 142 R-YRRGV-----PVLDTRFLSPSTDPGEV-------------EKLVPEDTAAIIVEPIQG 182 Y++ V PV + PS D G +L ED AA I EP+QG Sbjct: 144 APYKQRVGELPGPVYHLPY--PSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQG 201 Query: 183 EGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHESLGVEPDIMTAGKSI 242 EGG + A+ALR D G L+I DEIQ+GFGRTG+ +A LG+EPD++ KSI Sbjct: 202 EGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSI 261 Query: 243 AGGLPASAVLSREGVLATLASGRHGSTHAANPLSMAAVAAASRFLREEGVPD-KARAAGA 301 AGG+P AV+ R+ ++A L G G T++ NP+S AA A+ + +E + R A Sbjct: 262 AGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQA 321 Query: 302 LLEGLLRDRIEGLRLVRG-VRGEGLMLGVEL-RLDPGPV---LRCLQESER---VLALRS 353 ++ R + GL G + G G M G+E D P L + E+ R +L + S Sbjct: 322 IVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLMPS 381 Query: 354 GAT--VVRLLPPYSISREDAEMVVYGLERCI 382 G ++RLL P +I E E + LE+C+ Sbjct: 382 GKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 Lambda K H 0.319 0.136 0.398 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: 18 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: 388 Length of database: 416 Length adjustment: 31 Effective length of query: 357 Effective length of database: 385 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 Apr 09 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