Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::Q5XPV2 (457 letters) >FitnessBrowser__SB2B:6938908 Length = 404 Score = 117 bits (293), Expect = 7e-31 Identities = 100/339 (29%), Positives = 160/339 (47%), Gaps = 43/339 (12%) Query: 124 RLFFVDGGALAVENALKAALDWKAQKLGLAEPDTDRLQVLHLERSFHGRSGYTMSLTNTE 183 R++F + GA A E ALK A + +K G +++V+ +++FHGR+ +T+S+ Sbjct: 100 RVYFANSGAEANEAALKLARRYAIEKFG-----EHKVEVIAFDKAFHGRTFFTVSVGGQA 154 Query: 184 PSKTARFPKFGWPRISSPALQHPPAEHTGANQEAERRALEAAREAFAAADGMIACFIAEP 243 PK A+ H P A LEAA +D A + EP Sbjct: 155 AYSDGFGPK-------PAAITHLPFNDIAA--------LEAA-----VSDNTCAIML-EP 193 Query: 244 IQGEGGDNHLSAEFLQAMQRLCHENDALFVLDEVQSGCGITGTAWAYQQLGLQPDLVAFG 303 +QGEGG + EFL+A++RL +++AL + DEVQ+G G TG +AY + PD++ Sbjct: 194 LQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPDILTTA 253 Query: 304 KKTQVCGVMGGGRIDEVPENVFAVSSRI-----SSTWGGNLADMVRATRLLETIERTQVF 358 K +GGG ++S + ST+GGN +++ + +V Sbjct: 254 K------ALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVL 307 Query: 359 DTVVQRGKYFRDGLEDLAARHPSVVTNARGRGLMCAVDLPDT---RTRNEVLRLMYTEHQ 415 D V R + FRDGL + ++ V + RG+GL+ L + R+R + L E Sbjct: 308 DGVKHREQLFRDGLAQINEKY-HVFSEIRGKGLLLGAVLNEQFAGRSR-DFLNASVAE-G 364 Query: 416 VIALPCGGRSLRFRPALTIAEHEIDQALQALASSVTAVA 454 ++ L G +RF P+L I E +I + L +V VA Sbjct: 365 LLTLMAGANVVRFTPSLVIPEADIVEGLARFERAVAKVA 403 Lambda K H 0.320 0.135 0.402 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: 17 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: 457 Length of database: 404 Length adjustment: 32 Effective length of query: 425 Effective length of database: 372 Effective search space: 158100 Effective search space used: 158100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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