Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein
Query= BRENDA::P9WQ77 (449 letters) >NCBI__GCF_900105005.1:WP_090273343.1 Length = 404 Score = 140 bits (352), Expect = 1e-37 Identities = 135/414 (32%), Positives = 194/414 (46%), Gaps = 52/414 (12%) Query: 41 RSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYS 100 R GS L D GR Y+D+ +A ++LG P LV+ A+ + N +N Sbjct: 29 RGDGSRLWDQ-QGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVSNIMTNEPALR 87 Query: 101 VAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQV 160 +A TFA + FV GA A E A K A W H+Q+ G D ++ Sbjct: 88 LADKLVAATFA--------DKVLFVNSGAEANEAAFKLARRWA--HDQS-GPDKH---EI 133 Query: 161 LHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQ 220 + +FHGR+ +T+S+ +P + F P I P D +AALEA+ + Sbjct: 134 IACSNSFHGRTLFTVSVGG-QPKYSQGFG----PAISGISHVPYND---IAALEAQISER 185 Query: 221 ARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLT 280 A V EP+QGEGG E+ A+R LCD+++ALLIFDEVQ+G G T Sbjct: 186 TCAV-----------VVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRT 234 Query: 281 GTAWAYQQLDVAPDIVAFGKKTQVCG---VMAGRRVDEVADNVFAVPSRLNSTWGGNLTD 337 G +AY VAPDI+ K + G + A +D VA + ST+GGN Sbjct: 235 GKLYAYMHSGVAPDILTSAK--GIGGGFPIAAMLTIDRVAPALSV--GTHGSTYGGNPLG 290 Query: 338 MVRARRILEVIEA----EGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSL 393 A R+L++I +G+ ER Q LR DEL V + RG+GL+ L Sbjct: 291 CAVAERVLDIINTPQVLDGVGERQAQLTAGLRILADEL-----GVFSEIRGQGLLIGAVL 345 Query: 394 PT--TADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSAL 445 +++R + ++VL AGAD VR P L + A+I A+ +R+AL Sbjct: 346 AERWRGQAGQVMRLAQEEGLLVLQAGADVVRLAPSLIIPEADIREALGRMRAAL 399 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: 383 Number of extensions: 23 Number of successful extensions: 3 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: 404 Length adjustment: 32 Effective length of query: 417 Effective length of database: 372 Effective search space: 155124 Effective search space used: 155124 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 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