Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__PV4:5208066 Length = 405 Score = 110 bits (276), Expect = 6e-29 Identities = 116/414 (28%), Positives = 178/414 (42%), Gaps = 46/414 (11%) Query: 41 RSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYS 100 R GS + D G ++D +A + LG PALV + E + N +N + Sbjct: 29 RGEGSRVWDQ-EGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLANVMTNEPALA 87 Query: 101 VAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDP--ALGT 158 +A TFA ++F GA A E ALK A + + +D A Sbjct: 88 LATKLVEATFAE--------KVYFANSGAEANEAALKLA--------RRYALDKFGAEKD 131 Query: 159 QVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEAL 218 Q++ AFHGR+ +T+S+ PK P L +AALEAE Sbjct: 132 QIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPK--------PQSITHLPFNDIAALEAEVS 183 Query: 219 RQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCG 278 + A + EP+QGEGG PEF A+R L D+ +AL+IFDEVQTG G Sbjct: 184 DKTCA-----------IMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVG 232 Query: 279 LTGTAWAYQQLDVAPDIVAFGKKT-QVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTD 337 G +AY + +V PDI+ K + A E+A ++ ST+GGN Sbjct: 233 RLGELYAYMRTEVTPDILTTAKALGGGFPIAAMLTTTEIASHLKI--GTHGSTYGGNPLA 290 Query: 338 MVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTT- 396 +L+V+ + + + + LR L+++ + V + RG+GL+ L Sbjct: 291 CAIGNAVLDVVNTPEVLDGVKRREQLLRDGLNQINEKY-HVFTEVRGQGLLLGAVLNEQY 349 Query: 397 --ADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVV 448 +D L+ ++ L AG + +RF P L + A+I +A A+ V Sbjct: 350 QGRSKDFLVAGT-SEGLMCLIAGPNVIRFTPSLVIPEADIAEGLARFERAVAKV 402 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: 421 Number of extensions: 27 Number of successful extensions: 4 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: 405 Length adjustment: 32 Effective length of query: 417 Effective length of database: 373 Effective search space: 155541 Effective search space used: 155541 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