Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate 14737 b0600 putative aminotransferase (NCBI)
Query= BRENDA::Q71RI9 (455 letters) >FitnessBrowser__Keio:14737 Length = 386 Score = 212 bits (539), Expect = 2e-59 Identities = 132/404 (32%), Positives = 209/404 (51%), Gaps = 30/404 (7%) Query: 45 RIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGH 104 ++ L + ++ + + LA +NL QGFPD P Y++E L+ NQY G Sbjct: 11 KLPQLGTTIFTQMSALAQQHQAINLSQGFPDFDGPRYLQERLAHHV-AQGANQYAPMTGV 69 Query: 105 PALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYE 164 AL +A++ ++Y Q D + +I V GA +L+ +I LV GDEVI P YD Y Sbjct: 70 QALREAIAQKTERLYGYQPDADSDITVTAGATEALYAAITALVRNGDEVICFDPSYDSYA 129 Query: 165 PMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKV 224 P + ++G + + L+ P + W +E + S +T+ +ILNTPHNP V Sbjct: 130 PAIALSGGIVKRMALQP-PHFRVDW---------QEFAALLSERTRLVILNTPHNPSATV 179 Query: 225 YTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFS 284 + + + + H+ ISDEVYE + ++ H + P + ER + + S GKT+ Sbjct: 180 WQQADFAALWQAIAGHEIFVISDEVYEHINFSQQGHASVLAHPQLRERAVAVSSFGKTYH 239 Query: 285 VTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLP 344 +TGWK+G+ + PA + ++ V Q ++ TP Q ALA+ +PE Y +LP Sbjct: 240 MTGWKVGYCVAPAPISAEIRKVHQYLTFSVNTPAQLALADML------RAEPEHYL-ALP 292 Query: 345 KELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTK 404 KRD +V LN L+ + +G YF++ D S+ +S ++ D +F +W+T+ Sbjct: 293 DFYRQKRDILVNALNESRLEILPCEGTYFLLVDYSA----VSTLD-----DVEFCQWLTQ 343 Query: 405 HKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFR 448 + AIP+S FC + P KL+R CF KK+STL AA E R Sbjct: 344 EHGVAAIPLSVFC---ADPFPHKLIRLCFAKKESTLLAAAERLR 384 Lambda K H 0.320 0.136 0.419 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: 17 Number of successful extensions: 6 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: 455 Length of database: 386 Length adjustment: 32 Effective length of query: 423 Effective length of database: 354 Effective search space: 149742 Effective search space used: 149742 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 Aug 03 2021. The underlying query database was built on Aug 03 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