Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate SMa2400 SMa2400 diaminobutyrate--2-oxoglutarate aminotransferase
Query= BRENDA::P9WQ77 (449 letters) >FitnessBrowser__Smeli:SMa2400 Length = 470 Score = 119 bits (298), Expect = 2e-31 Identities = 132/435 (30%), Positives = 187/435 (42%), Gaps = 58/435 (13%) Query: 41 RSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNK--PSNS-D 97 +S +V + GR YLD + ALG N P ++ E +Q L P ++ D Sbjct: 54 KSASGCIVTDVDGRSYLDCLAGAGTLALGHNHPEVI-------ETLQQVLGSGLPLHTLD 106 Query: 98 VYSVAMARFVE----TFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGID 153 + + RFV T L D A F G AVE A+K A R Sbjct: 107 LTTPVKDRFVSDIFGTLPAGLRDEAKIQ-FCSPSGTDAVEAAIKLAKTATGR-------- 157 Query: 154 PALGTQVLHLRGAFHGRSGYTLSLTNT---KPTITARFPK---FDWP-RIDAPYMRPGLD 206 T ++ RGA+HG S +LSL + K ++ P F +P P+ R G + Sbjct: 158 ----TDLVSFRGAYHGMSQGSLSLMGSLGPKASVGQLVPGAHFFPYPYAYRCPFGRGGNE 213 Query: 207 EPAMAALEAE-ALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFD 265 +AA E ALR RP A + E +QGEGG E+ A+R + + Sbjct: 214 TATLAAEYFERALRDPEGGIN-RP---AAVILEAVQGEGGVIPAPVEWLRAVRRVTRDLG 269 Query: 266 ALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPS 325 LI DEVQ+G G TG+ +A+Q+ + PD+V K + G + V D P Sbjct: 270 IPLIVDEVQSGVGRTGSFYAFQKAGIIPDVVVLSK--AIGGGLPLAVVIYREDLDLWKPG 327 Query: 326 RLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGR 385 T+ GN M + LE+IE E L ERA G+ LRA L+ +AA P + + RG Sbjct: 328 AHAGTFRGNQLAMAAGSKTLEIIERERLVERAAIAGRRLRANLERIAAQTP-YIGEVRGE 386 Query: 386 GLMCAFSL-------------PTTADRDELIRQLWQRAVIVLPAG---ADTVRFRPPLTV 429 GLM + P + +I+ RA I+L G +R PPL + Sbjct: 387 GLMLGVEVVDPEGLPDALGHPPHGQEIARMIQHEMFRAGIILETGGRFGSVLRLLPPLVI 446 Query: 430 STAEIDAAIAAVRSA 444 S AEID A+ +A Sbjct: 447 SDAEIDQVSGALAAA 461 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: 530 Number of extensions: 33 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: 470 Length adjustment: 33 Effective length of query: 416 Effective length of database: 437 Effective search space: 181792 Effective search space used: 181792 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