Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Koxy:BWI76_RS14020 Length = 461 Score = 198 bits (504), Expect = 2e-55 Identities = 142/426 (33%), Positives = 216/426 (50%), Gaps = 42/426 (9%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR--LTHYAFNAA 72 P+ ++ + D D K+Y+D + G G L LGH +P V+++IQ+ T H Sbjct: 42 PLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTT 101 Query: 73 PHGPYLALMEQLSQFVPVSYPLAG------MLTNSGAEAAENALKVARGATGKRAIIAFD 126 P L ++ S+++ P G SGA+A E ALK+A+ TG+ ++I+F Sbjct: 102 P------LKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFS 155 Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPS---ADTGVTCEQALKAMDRLFS 183 GG+HG T L++ G ++P G +P V +PYP G+ E +KA+ F Sbjct: 156 GGYHGMTHGALSVTGNLSPKAAVNGMMP-EVQFMPYPHQYRCPLGIGGEAGVKALTYYFE 214 Query: 184 -----VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGR 238 VE V AA I E VQGEGG + Q +R+ E GIL+IIDE+Q+GF R Sbjct: 215 NLINDVESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAGFAR 274 Query: 239 TGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAA 298 TG+ FAF GIEPD+++++K++ GG+PL AV+G K+ A G GT+ GN ++ A Sbjct: 275 TGKFFAFEHAGIEPDIIVMSKAVGGGLPL-AVLGIKKQFDAWEPGHHTGTFRGNQLAMAT 333 Query: 299 ALASLAQMTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFAN 354 L +L + D + A GE + + +R+ P IG + G+G M GIE Sbjct: 334 GLTTLRHLKDNKIADKTAAQGEWLKGKLAEMQKRY------PVIGHVRGLGLMIGIEIVK 387 Query: 355 ADGS-------PAPAQLAKVME-AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLD 406 + + PA +L+ +++ GL+L G+ ++RLL L I LE D Sbjct: 388 PNEAPDHMGCYPADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELEIFFD 447 Query: 407 ILEQCL 412 EQ L Sbjct: 448 KFEQAL 453 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: 502 Number of extensions: 22 Number of successful extensions: 6 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: 461 Length adjustment: 32 Effective length of query: 384 Effective length of database: 429 Effective search space: 164736 Effective search space used: 164736 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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