Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__azobra:AZOBR_RS19025 Length = 389 Score = 125 bits (313), Expect = 3e-33 Identities = 123/407 (30%), Positives = 174/407 (42%), Gaps = 41/407 (10%) Query: 34 DIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKP 93 DIV + R G YL A GRR+LD VA + LG P LV+ A + N Sbjct: 13 DIVFE--RGEGPYLY-ATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLF 69 Query: 94 SNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGID 153 + S+A TFA + FF GA A E K +++ G D Sbjct: 70 RVAGQESLAKRLTEATFADTV--------FFTNSGAEAWECGAKLI----RKYHYEKG-D 116 Query: 154 PALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAAL 213 A T+++ AFHGR+ +S + I P D G D L Sbjct: 117 KAR-TRIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLD-----------GFDLVPFGDL 164 Query: 214 EAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEV 273 EA +R A + A EPIQGEGG R EF +RE+CDE LL DE+ Sbjct: 165 EA--VRNAVT------DETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEI 216 Query: 274 QTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGG 333 Q G G TG +A++ + PD++A K + E A + + ST+GG Sbjct: 217 QCGMGRTGKLFAHEWAGITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTH-GSTYGG 275 Query: 334 NLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSL 393 N +L+ + G + + G L+ RL L A+ PAV RG+GLM + Sbjct: 276 NPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLAC 335 Query: 394 -PTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIA 439 P D ++ L ++ +PAG + VR PPL + AE++ A+A Sbjct: 336 GPAVGD---VVVALRANGLLSVPAGDNVVRLLPPLNIGEAEVEEAVA 379 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: 384 Number of extensions: 23 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: 389 Length adjustment: 32 Effective length of query: 417 Effective length of database: 357 Effective search space: 148869 Effective search space used: 148869 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