Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 201877 SO2739 8-amino-7-oxononanoate synthase (NCBI ptt file)
Query= reanno::Koxy:BWI76_RS27255 (397 letters) >FitnessBrowser__MR1:201877 Length = 401 Score = 198 bits (503), Expect = 3e-55 Identities = 128/376 (34%), Positives = 195/376 (51%), Gaps = 17/376 (4%) Query: 19 EGLFKEERIIT-----SAQQADITVGGSQVINFCANNYLGLANHPELIAAAKSGMDSHGF 73 +GL ++ + ++ S + G +NF +N+YLGL+ PELIAA G +G Sbjct: 23 QGLLRQRQALSIDAVLSDAEPQFCFEGQTYLNFSSNDYLGLSRAPELIAALHRGAQQYGV 82 Query: 74 GMASVRFICGTQDSHKALEKKLADFLGMEDAILYSSCFDANGGLFETLLGAEDAIISDAL 133 G + + G ++H ALE KL G E A+L+SS F AN L +TL +D +++D L Sbjct: 83 GSGASPLVTGYSEAHLALETKLCKITGFEAALLFSSGFSANTTLCKTLFDKQDVVLADKL 142 Query: 134 NHASIIDGVRLCKAKRFRYANNDMVELEARLKEARDAGARHVLIATDGVFSMDGVIANLK 193 HASIIDG+R A R+ +N E RL A + T+ VFSMDG IA +K Sbjct: 143 VHASIIDGLRDSGADFKRFLHNS-TESAERLLAKNTVSA----LITESVFSMDGDIAPIK 197 Query: 194 GVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGTLGKALGGASGGYT 253 + L ++ ++VDD+H G + +DI T GKAL G G Sbjct: 198 ALSSLCRAHNVWLIVDDAHGFGVSDIFNQ------PAANLIDIQIVTFGKAL-GCQGAAI 250 Query: 254 AARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDRLWSNARLFREKMT 313 +E++ +L +R Y++S +L+PA A ++ +E EA ELR +L N LF++ Sbjct: 251 LGSRELIAFLVSNAREYIYSTALSPANAALALAAVEHCEAQPELRQKLQRNISLFKQLCQ 310 Query: 314 AAGFILAGADHAIIPVMLGEATVAQEFARELQKEGIYVTGFFYPVVPKGQARIRTQMSAA 373 A L G+D I P+++G+A A++L+ GI+V P VP G AR+R +SA+ Sbjct: 311 DADIPLLGSDTPIQPLIIGDAKQTLLVAQKLKAMGIWVGAIRPPTVPVGSARLRITLSAS 370 Query: 374 HTPEQIERAVEAFTRI 389 H+ I R V T++ Sbjct: 371 HSEAAIRRCVNGITQV 386 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: 333 Number of extensions: 11 Number of successful extensions: 3 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: 401 Length adjustment: 31 Effective length of query: 366 Effective length of database: 370 Effective search space: 135420 Effective search space used: 135420 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