Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_084198647.1 C0029_RS18740 aspartate aminotransferase family protein
Query= BRENDA::P9WQ77 (449 letters) >NCBI__GCF_002869505.1:WP_084198647.1 Length = 387 Score = 137 bits (345), Expect = 6e-37 Identities = 127/395 (32%), Positives = 173/395 (43%), Gaps = 47/395 (11%) Query: 44 GSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVA- 102 G YL D GRRYLD + +A + LG N P + A + A S++Y V Sbjct: 20 GVYLFDT-EGRRYLDGISGIAVNGLGHNHPGVT------AAIQDQAGKLVHTSNLYGVGP 72 Query: 103 MARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLH 162 E + G + FF GA A E A+K A H D T ++ Sbjct: 73 QEALAERLTEISG---MERCFFGNSGAEANEAAIKIA------RLHGHNRDVEKPT-IIV 122 Query: 163 LRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQAR 222 L GAFHGR+ TLS T + I A F + AP + EA+RQ Sbjct: 123 LEGAFHGRTLATLSATGNRQ-IQAGFEPLVSGFVRAPRN------------DLEAIRQIA 169 Query: 223 AAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGT 282 A D+ F+AEPIQGEGG ++ +RE+CD L++ DEVQTG G TGT Sbjct: 170 A----NNPDVVAFLAEPIQGEGGVNPLDEDYLRGVREICDAQGWLMMLDEVQTGNGRTGT 225 Query: 283 AWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRAR 342 +AYQ + PD+V K + A N F P ST+GGN A Sbjct: 226 WFAYQGMGFIPDVVTTAKGLGNGVPIGACLARGEAANTFG-PGHHGSTYGGNPLVCAAAL 284 Query: 343 RILEVIEAEGLFERAVQHGKYLRARLDELAADFPAV--VLDPRGRGLMCAFSLPTTADRD 400 ++E + E + + +R D ++AD A + D RGRGLM F L DRD Sbjct: 285 AVVEAVNGEDILTNVERMSALIR---DTISADPAAAPRIKDIRGRGLMLGFQL----DRD 337 Query: 401 --ELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAE 433 EL++ +++ +TVR PPL +S E Sbjct: 338 CPELVKAALDAGLLINVTAGNTVRLLPPLIISEDE 372 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: 405 Number of extensions: 29 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: 449 Length of database: 387 Length adjustment: 31 Effective length of query: 418 Effective length of database: 356 Effective search space: 148808 Effective search space used: 148808 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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