Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 350971 BT1443 8-amino-7-oxononanoate synthase (NCBI ptt file)
Query= reanno::Koxy:BWI76_RS27255 (397 letters) >FitnessBrowser__Btheta:350971 Length = 384 Score = 193 bits (491), Expect = 6e-54 Identities = 119/353 (33%), Positives = 192/353 (54%), Gaps = 6/353 (1%) Query: 35 DITVGGSQVINFCANNYLGLANHPELIAAAKSGMDSHGF--GMASVRFICGTQDSHKALE 92 D+TV G +++N +N+YLGLAN L A + F +S R + G +++ LE Sbjct: 31 DVTVDGRRMLNLSSNDYLGLANEVSLREAFLKTITPETFLPTSSSSRLLTGNFTAYQELE 90 Query: 93 KKLADFLGMEDAILYSSCFDANGGLFETLLGAEDAIISDALNHASIIDGVRLCKAKRFRY 152 ++LA G E A+L++S + AN G+ + A I++D L HAS+IDG+RL AK RY Sbjct: 91 QQLATMFGAESALLFNSGYHANTGILPAVSDARTLILADKLVHASLIDGIRLSSAKCIRY 150 Query: 153 ANNDMVELEARLKEARDAGARHVLIATDGVFSMDGVIANLKGVCDLADKY-DALVMVDDS 211 +ND+ +L RL E ++I T+ +FSMDG A+L+ + L Y + L+ VD++ Sbjct: 151 RHNDLAQLR-RLLEENHGMYEKIIIVTESIFSMDGDEADLQALVRLKHDYANLLLYVDEA 209 Query: 212 HAVGFVGENGRGSHEYCDVMGRVDIITGTLGKALGGASGGYTAARKEVVEWLRQRSRPYL 271 HA G GE G G E + + +D + GT GKA A G Y R+ + E+L + R ++ Sbjct: 210 HAFGARGEKGLGCAEEQNCINDIDFLVGTFGKAAASA-GAYIICRQTIREYLINKMRTFI 268 Query: 272 FSNSLAPAIVAASIKVLEMVEAGSELRDRLWSNARLFREKMTAAGFILAGADHAIIPVML 331 F+ +L P + + VL+ R+ L +R +E +T G+ H I+P+++ Sbjct: 269 FTTALPPVNIQWTAWVLKHFADFRSKREHLLQISRKLKEALTEKGYNCPSVSH-IVPMVV 327 Query: 332 GEATVAQEFARELQKEGIYVTGFFYPVVPKGQARIRTQMSAAHTPEQIERAVE 384 G + A ELQ++G Y P VP+G +RIR ++A T ++I+ +E Sbjct: 328 GASEDTIRKAEELQRKGFYALPVRPPTVPEGTSRIRFSLTADITEKEIDTLIE 380 Lambda K H 0.321 0.136 0.390 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: 300 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: 397 Length of database: 384 Length adjustment: 31 Effective length of query: 366 Effective length of database: 353 Effective search space: 129198 Effective search space used: 129198 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 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