Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__Keio:17148 Length = 459 Score = 131 bits (330), Expect = 4e-35 Identities = 120/403 (29%), Positives = 178/403 (44%), Gaps = 33/403 (8%) Query: 47 LVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARF 106 LVD G+ ++D +G P +V A Q A + ++ A Sbjct: 76 LVDT-QGQEFIDCLGGFGIFNVGHRNPVVVS-----AVQNQLAKQPLHSQELLDPLRAML 129 Query: 107 VETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGA 166 +T A L L + FF G +VE ALK A ++S + I + GA Sbjct: 130 AKTLA-ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATS---------GA 179 Query: 167 FHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFE 226 FHG+S LS T K T F + PG +EA +R A + Sbjct: 180 FHGKSLGALSAT-AKSTFRKPFMP----------LLPGFRHVPFGNIEA--MRTALNECK 226 Query: 227 TRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAY 286 D+A + EPIQGEGG P + A+R+LCDEF AL+I DEVQTG G TG +A Sbjct: 227 KTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFAC 286 Query: 287 QQLDVAPDIVAFGKKT--QVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRI 344 + +V PDI+ K V + A +EV +F P +T+GGN A Sbjct: 287 EHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALAT 346 Query: 345 LEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIR 404 + V+ + L +A Q G L +LA ++P +V + RG+G++ A Sbjct: 347 INVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFAS 406 Query: 405 QLWQRAVIVLPA--GADTVRFRPPLTVSTAEIDAAIAAVRSAL 445 +++++ V+V A T+R PPLT++ + + I A R AL Sbjct: 407 EMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKAL 449 Lambda K H 0.323 0.137 0.412 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: 419 Number of extensions: 23 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: 449 Length of database: 459 Length adjustment: 33 Effective length of query: 416 Effective length of database: 426 Effective search space: 177216 Effective search space used: 177216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 51 (24.3 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