Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate PP_0858 PP_0858 putative methionine/glutamine aminotransferase
Query= BRENDA::Q6YP21 (454 letters) >FitnessBrowser__Putida:PP_0858 Length = 382 Score = 220 bits (560), Expect = 7e-62 Identities = 134/401 (33%), Positives = 205/401 (51%), Gaps = 28/401 (6%) Query: 44 RIEGLDSNVWIEFTKLAADPSVVNLGQGFPDISPPTYVKEELSKIAAIDSLNQYTRGFGH 103 ++ + + ++ ++LA +NL QGFPD + P + + + + A NQY+ G Sbjct: 5 KLPNVGTTIFTTMSQLAVQTGALNLSQGFPDFNGPQALLDAVGRHVAAGH-NQYSPMTGL 63 Query: 104 PSLVKALSYLYEKLYQKQIDSNKEILVTVGAYGSLFNTIQALIDEGDEVILIVPFYDCYE 163 P+L + ++ E+LY ++D+++E+ +T GA ++F IQA++ GDEVI+ P YD YE Sbjct: 64 PALRQQVAAKVERLYGARVDADQEVTITPGATEAIFCAIQAVVHAGDEVIVFDPCYDSYE 123 Query: 164 PMVRMAGATPVFIPLRSKPVYGKRWSSSDWTLDPQELESKFNSKTKAIILNTPHNPLGKV 223 P V +AG V + L S D+ +D Q+ + +T+ +ILN+PHNP G + Sbjct: 124 PSVELAGGRCVHVQL----------SDGDFRIDWQKFSDALSPRTRMVILNSPHNPSGAL 173 Query: 224 YNREELQVIADLCIKYDTLCISDEVYEWLVYSGNKHLKIATFPGMWERTITIGSAGKTFS 283 RE+L +A L D +SDEVYE LVY G +H + ++ R + S GKT+ Sbjct: 174 ITREDLDQLAALIADRDIYLVSDEVYEHLVYDGVRHASVLAHEQLYSRAFVVSSFGKTYH 233 Query: 284 VTGWKLGWSIGPNHLIKHLQTVQQNTIYTCATPLQEALAQAFWIDIKRMDDPECYFNSLP 343 VTGWK G+ I P L L+ V Q + TPLQ ALA PE + + LP Sbjct: 234 VTGWKTGYVIAPPALSAELRKVHQYVNFCGVTPLQCALADFM------AGHPE-HIDELP 286 Query: 344 KELEVKRDRMVRLLESVGLKPIVPDGGYFIIADVSLLDPDLSDMKNNEPYDYKFVKWMTK 403 + KRD LL+ G YF + D S + PDL+D+ + W+T+ Sbjct: 287 AFYQAKRDLFCGLLDGSRFNFTRTTGTYFQLVDYSQIRPDLNDVDMS--------LWLTR 338 Query: 404 HKKLSAIPVSAFCNSETKSQFEKFVRFCFIKKDSTLDAAEE 444 ++ IPVS F Q + VR CF K++ TL A E Sbjct: 339 EHGVATIPVSVFYQQPIPEQ--RLVRLCFAKREETLRQAAE 377 Lambda K H 0.319 0.135 0.407 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: 435 Number of extensions: 16 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: 454 Length of database: 382 Length adjustment: 31 Effective length of query: 423 Effective length of database: 351 Effective search space: 148473 Effective search space used: 148473 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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