Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__Putida:PP_4481 Length = 406 Score = 112 bits (279), Expect = 3e-29 Identities = 119/412 (28%), Positives = 176/412 (42%), Gaps = 40/412 (9%) Query: 41 RSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYS 100 R GS + D +GR +D +A +ALG PALV A + N +N Sbjct: 30 RGEGSRVWDQ-SGRELIDFAGGIAVNALGHCHPALVKALTEQANTLWHVSNVFTNEPALR 88 Query: 101 VAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQV 160 +A TFA FF GA + E A K A AH ++ Sbjct: 89 LAHKLVDATFA--------DRAFFCNSGAESNEAAFKLA------RRVAHDRFGPQKHEI 134 Query: 161 LHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQ 220 + +FHGR+ +T+S+ +P + F P+I P D + AL+A+ + Sbjct: 135 IATVNSFHGRTLFTVSVGG-QPKYSDGFG----PKITGISHVPYND---LEALKAQISDK 186 Query: 221 ARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLT 280 A V EPIQGE G + R+LCDE +ALLIFDEVQTG G T Sbjct: 187 TCAV-----------VIEPIQGESGVVPADKAYLEGARKLCDEHNALLIFDEVQTGVGRT 235 Query: 281 GTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVR 340 G+ +AYQ V PDI+ K+ G G + +T+GGN Sbjct: 236 GSLYAYQHYGVIPDILT-SAKSLGGGFPIGAMLTTTELAKHLAVGTHGTTYGGNPLGCAV 294 Query: 341 ARRILEVIEA-EGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLM--CAFSLPTTA 397 A +L+V+ E L +H ++ + RL+++ + + RG GL+ C + Sbjct: 295 ACAVLDVVNTPETLAGIKAKHERF-KTRLEQIGQQY-NLFSQVRGVGLLLGCVLTEAWKG 352 Query: 398 DRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449 +++ + V+VL AG D VRF P L V A+ID + A+ +T Sbjct: 353 KAKDVLNAAEKEGVMVLQAGPDVVRFAPSLVVEDADIDEGLDRFERAVATLT 404 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: 417 Number of extensions: 20 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: 406 Length adjustment: 32 Effective length of query: 417 Effective length of database: 374 Effective search space: 155958 Effective search space used: 155958 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