Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= BRENDA::P9WQ77 (449 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 156 bits (395), Expect = 1e-42 Identities = 135/418 (32%), Positives = 193/418 (46%), Gaps = 49/418 (11%) Query: 37 LDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNS 96 L R G+YL A GRRYLD VA +ALG P LV L A S Sbjct: 9 LAFERGEGAYLFTA-DGRRYLDFAAGVAVNALGHCHPRLVK------ALTAQAAKVWHTS 61 Query: 97 DVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPAL 156 ++Y VA V A+++ +FF GA A+E ++K A RH+ A G Sbjct: 62 NLYRVAGQESVA--AKLVERSFADTVFFCNSGAEALECSIKMA----RRHHFAAGNPQRY 115 Query: 157 GTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAE 216 +++ GAFHGR+ T++ K + P D G D L A Sbjct: 116 --RIICAEGAFHGRTLATVAAGGQKKHLEGFAPAVD-----------GFDHVPYGNLNA- 161 Query: 217 ALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTG 276 RA+ + A + EP+QGEGG P++ +R DEF LLIFDEVQTG Sbjct: 162 ----LRASIT---EETAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTG 214 Query: 277 CGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFA----VPSRLNSTWG 332 G TGT +A++Q +APDI+ K G+ G V A VP ST+G Sbjct: 215 MGRTGTLFAHEQAGIAPDIMGVAK-----GLGGGFPVGACLATTKAASGMVPGTHGSTFG 269 Query: 333 GNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFS 392 GN M A +L+++ G E LR+++++ AA FP VV + RG GLM Sbjct: 270 GNPLAMAVAGEVLDIMAEPGFLEHVQAMAALLRSKVEDTAARFPGVVEEVRGLGLMLGIK 329 Query: 393 --LPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVV 448 +P T E++ +L + ++ + AG + VR PPL ++ A++D A+ + A V Sbjct: 330 PRMPNT----EMVARLAEGGLLTVGAGDNIVRLLPPLIINDAQVDEAVGILARAFDEV 383 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: 402 Number of extensions: 24 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: 384 Length adjustment: 31 Effective length of query: 418 Effective length of database: 353 Effective search space: 147554 Effective search space used: 147554 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 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