Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate CA265_RS02025 CA265_RS02025 8-amino-7-oxononanoate synthase
Query= reanno::ANA3:7026975 (397 letters) >FitnessBrowser__Pedo557:CA265_RS02025 Length = 413 Score = 203 bits (517), Expect = 6e-57 Identities = 119/366 (32%), Positives = 195/366 (53%), Gaps = 11/366 (3%) Query: 37 IQVNHQEVVNFCANNYLGLANHPELIKAAQQGLDSHGFGMA---SVRFICGTQDIHKQLE 93 +Q +E + + NNYLGLANHPE+ KA ++ FGMA R + G + H+QLE Sbjct: 38 MQFRGKEHLVWSLNNYLGLANHPEVRKADEEAAAK--FGMAYPMGARMMSGNSNYHEQLE 95 Query: 94 ASLSEFLGMEDTILYSSCFDANAGLFETLLDAEDAIISDALNHASIIDGVRLCKAKRFRY 153 L+EF+G D L + + + +TL+D D ++ DA +HA I+DG+RL KRF Y Sbjct: 96 QELAEFVGKPDAFLLNYGYQGMVSIIDTLVDRNDVVVYDAESHACIVDGLRLHMGKRFVY 155 Query: 154 ANNDMADLETQLIAAK---AAGARNILIATDGVFSMDGVIANLQGVCDLADKYGALVMVD 210 +ND+ QL A IL+ T+GVF M G L+ + DL + ++VD Sbjct: 156 KHNDIESARKQLERATKLVEETGGGILLITEGVFGMSGAQGKLKEIVDLKKDFNFRILVD 215 Query: 211 DSHAVGFVGLNGRGSHEHCGVMGRVDIITGTLGKALGGASGGFTSGKKEVIDWLRQRSRP 270 D+H G +G G G+HE + +D+ GT K++ G G F + +++ ++LR R Sbjct: 216 DAHGFGTMGKTGAGTHEAQDCIEGIDVYFGTFAKSMAGI-GAFVASTEQITNFLRYNMRS 274 Query: 271 YLFSNSLAPSIVTASIHVLEMLKSGQALREAVWENSRYFREKMSAAGFTLGGADHAIIPV 330 F+ +L +V + LE+LKS L++ +WE + ++ + GF LG D + PV Sbjct: 275 QTFAKALPMPMVIGLLKRLELLKSKPELKDKLWEIAMTLQKGLRERGFDLGVTDSVVTPV 334 Query: 331 MI-GDAKLASDFANRLLAEH-IYVIGFSFPVVPKGQARIRTQMSAAHTREQLDKAIEAFT 388 + G+ A+ L + I+ +PV+PKG +R +A HT E + + ++AF+ Sbjct: 335 FLKGELSDATAITYDLRENYSIFCSIVVYPVIPKGMIELRLIPTAVHTLEDVQRTLDAFS 394 Query: 389 RIAKEM 394 +A+++ Sbjct: 395 EVAEKL 400 Lambda K H 0.321 0.134 0.385 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: 402 Number of extensions: 23 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: 397 Length of database: 413 Length adjustment: 31 Effective length of query: 366 Effective length of database: 382 Effective search space: 139812 Effective search space used: 139812 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 (21.9 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