Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= curated2:Q7SI94 (388 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 154 bits (388), Expect = 6e-42 Identities = 118/391 (30%), Positives = 198/391 (50%), Gaps = 29/391 (7%) Query: 17 KGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEIS-TLSLAFDTPIREE 75 + + +++ E +YLD AG G GH N + L + +E + L T + + Sbjct: 24 RAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFTTAKHD 83 Query: 76 MIKELDE--LKPEDLDNL--FLLNSGSEAVELALKIARKITKRRKIVAFKNSFHGRSMGA 131 ++ + L P LD F +G+ VE ALK+ARK+ R I++F N FHG +MGA Sbjct: 84 FMESYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLARKVKGRSGIISFTNGFHGVTMGA 143 Query: 132 LSVTWNKKYREPFEPLIGPVEFLEYN-----NVDSL----------KSITEDTAAVIVEP 176 ++ T NK +R +G V+F+ Y+ +VD+L S E AAVIVE Sbjct: 144 VATTGNKHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDKLLSDGSSGFELPAAVIVEA 203 Query: 177 VQGEGGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILTAG 236 VQGEGG+ + E++K L E+ +K + LLI+D++Q G GRTG+ ++++ IKPDI+T Sbjct: 204 VQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFAGIKPDIVTVS 263 Query: 237 KAIGG-GFPVSAV-FLPNWISEKIEEGDHGSTYGGNPLAAAAVTAACK-VAKSEKIAEQA 293 K++ G G P++ V F P + + G+H T+ GN +A AA + K + A + Sbjct: 264 KSLSGYGLPMALVLFKPE--LDVWDPGEHNGTFRGNNMAFITARAAVENYWKDDAFANEV 321 Query: 294 QKKGELFMRILKEKLEDFKIVREIRGLGLMIGIDLK---VNPSIAIKVLQDEKVLSLKA- 349 + K E+ L+ + + +++G GLM GI+ K + I + + ++ Sbjct: 322 KAKTEVLGDALQSICDKYPGQFKMKGRGLMRGIEAKHADITGPITKRAFEHGLIIETSGP 381 Query: 350 GLTTIRFLPPYLITQSDMEWASDATRKGISE 380 I+ L P ++ D++ + K + E Sbjct: 382 NDEVIKCLMPLTTSEEDLKKGAALLAKSVDE 412 Lambda K H 0.317 0.136 0.386 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: 336 Number of extensions: 19 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: 422 Length adjustment: 31 Effective length of query: 357 Effective length of database: 391 Effective search space: 139587 Effective search space used: 139587 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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