Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate CA265_RS08140 CA265_RS08140 methionine aminotransferase
Query= BRENDA::Q16773 (422 letters) >FitnessBrowser__Pedo557:CA265_RS08140 Length = 381 Score = 212 bits (540), Expect = 1e-59 Identities = 135/409 (33%), Positives = 202/409 (49%), Gaps = 37/409 (9%) Query: 9 RLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFG 68 +L G+ + KLA+EH+ +NL QGFPD+ VE A+ F NQY G Sbjct: 7 KLPGVSTTIFSVMSKLAAEHNAINLSQGFPDYACDPKLVELVNKAMQDGF--NQYAPMPG 64 Query: 69 YPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCY 128 L + +A L + +P + VT GG A+FTA ++++ GDEVII EP +D Y Sbjct: 65 STFLKETIAEKVENLYNIKYNPETEITVTAGGTQAIFTALASIINAGDEVIIFEPAYDSY 124 Query: 129 EPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLG 188 P + GG L P N+ +D + FT++T+ ++LNTP NP G Sbjct: 125 APTIKLLGGLVKTYELAP-----------PNYAIDWDMVKKLFTAKTRMIILNTPQNPTG 173 Query: 189 KVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKT 248 + S ++++ + L D++ ++DEVY+ ++YD +H S+ P + +R+ I S GK Sbjct: 174 SILSSDDMKSLIKLISGTDILILSDEVYEHLIYDEQKHQSVMLYPELKQRSFIIASFGKL 233 Query: 249 FSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQ 308 ATGWK+G+ L P+ + K R VHQ +VF + Q A+A ++P +Y + Sbjct: 234 LHATGWKLGYCLAPEKLTKEFRKVHQFNVFSVNSPMQQAIAH-------YIKEPKNY-TE 285 Query: 309 FPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVK 368 Q+ RD+ L K + GSYF S ++ + D F Sbjct: 286 IGSFFQQKRDYFRSLLAESRFKLLPCNGSYFQCVSYS-----------SISDEKDTDFSM 334 Query: 369 WMIKNKGLVAIPVSIFYSVPHQKHFDH-YIRFCFVKDEATLQAMDEKLR 416 +IK G+ IPVS FY QK DH IRFCF K+ ATL EKL+ Sbjct: 335 RLIKEFGVATIPVSAFY----QKGIDHKIIRFCFAKENATLALAAEKLK 379 Lambda K H 0.323 0.139 0.435 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: 395 Number of extensions: 25 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: 422 Length of database: 381 Length adjustment: 31 Effective length of query: 391 Effective length of database: 350 Effective search space: 136850 Effective search space used: 136850 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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