Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 159 bits (401), Expect = 2e-43 Identities = 126/411 (30%), Positives = 202/411 (49%), Gaps = 26/411 (6%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNP----AVVEAIQAQATRLTHYAFN 70 P+ + +NA ++ DGK Y+DF+ G G LN GH N A++E I+A F Sbjct: 19 PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78 Query: 71 AAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFH 130 A H + + + + Y + +G E ALK+AR G+ II+F GFH Sbjct: 79 TAKHDFMESYKKHILDPRGLDYKMQ-FTGPTGTNCVEAALKLARKVKGRSGIISFTNGFH 137 Query: 131 GRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCE-QALKAMDRLFSV-ELAV 188 G T+ + G K G + P+ ++ + D + + L MD+L S Sbjct: 138 GVTMGAVATTGN----KHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDKLLSDGSSGF 193 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 E AA I E VQGEGG A + + L C + IL+I+D+IQ+G GRTG+ F+F Sbjct: 194 ELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFA 253 Query: 249 GIEPDLLLLAKSIAG-GMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ-M 306 GI+PD++ ++KS++G G+P+ V+ + EL P G GT+ GN ++ A A++ Sbjct: 254 GIKPDIVTVSKSLSGYGLPMALVLFKPELDVWDP-GEHNGTFRGNNMAFITARAAVENYW 312 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIG--RLTGVGAMRGIEFANADGSPAPAQL 364 D+ A + + + + + S Y G ++ G G MRGIE +AD + Sbjct: 313 KDDAFANEVKAKTEVLGDALQ----SICDKYPGQFKMKGRGLMRGIEAKHADIT------ 362 Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 + + A GL++ SG +I+ L PLT E L++G +L + + E+ Sbjct: 363 GPITKRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEI 413 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: 425 Number of extensions: 30 Number of successful extensions: 5 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: 422 Length adjustment: 32 Effective length of query: 384 Effective length of database: 390 Effective search space: 149760 Effective search space used: 149760 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 17 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