Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate BWI76_RS17800 BWI76_RS17800 long-chain-fatty-acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Koxy:BWI76_RS17800 Length = 572 Score = 234 bits (598), Expect = 5e-66 Identities = 164/544 (30%), Positives = 266/544 (48%), Gaps = 17/544 (3%) Query: 29 QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALL-GMGLTPGDRVGIW 87 Q++ F V R ++ A +++ G TY +L+ + A+ L G+GL GDRV + Sbjct: 34 QSLVELFEHAVRRYADQPAFINM--GEVMTYRKLEERSRAFAAYLQEGLGLQKGDRVALM 91 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFK-TSDYLGM 146 N ++ + + G+++VN+NP Y E+E+ LN G +V ++ F T + + Sbjct: 92 MPNLLQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGAAAIVIVSNFAHTLEKVVD 151 Query: 147 LRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRL 206 ++ + L AK + VV P + F + G R+ Sbjct: 152 KTQVKHVILTRMGDQLSPAKGTVVNFVVKYIKRLVPKYHLPDAISFRSALQHGY----RM 207 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGEC---MKLTPADRLCIP 263 + + D +Q+T GTTG KGA LTHRN+L N + + + + Sbjct: 208 QYIKPEIVPQDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNGTYGPLLHRGKELVVTA 267 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323 +PLYH F + + L G + + D +++ + T + GV T+F A L++ Sbjct: 268 LPLYHIFALTMNCLLFIELGGQNLLITNPRDIPGLVKELAKYPFTAMTGVNTLFNALLNN 327 Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383 F + + S+L G P V +R V+ + + + YG+TE +P+ + D + Sbjct: 328 KEFQQLDFSSLHLSAGGGMPVQQVVAERWVK-LTGQYLLEGYGLTECAPLVSVNPHD--I 384 Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEG 443 ++G P E K+VD D V P G+ GE C KG VM GYW T E I +G Sbjct: 385 DYHSGSIGLPVPSTEAKLVDDDDNEVPP-GEPGELCVKGPQVMLGYWQRPDATAEIIKDG 443 Query: 444 GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQ 503 W+HTGD+A MD EG++ IV R KDM++ G N+YP EIE+ + +H VQ+V VGVP Sbjct: 444 -WLHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHAGVQEVAAVGVPSG 502 Query: 504 KYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 GE + +++ K T TE+ + FC+ Q+ YKVP+++ F P + GKI + ++R Sbjct: 503 SSGEAVKIFVVKKDPTL-TEEMLITFCRRQLTGYKVPKHVEFRDELPKSNVGKILRRELR 561 Query: 564 DEMK 567 DE + Sbjct: 562 DEAR 565 Lambda K H 0.320 0.136 0.412 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: 772 Number of extensions: 38 Number of successful extensions: 8 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: 578 Length of database: 572 Length adjustment: 36 Effective length of query: 542 Effective length of database: 536 Effective search space: 290512 Effective search space used: 290512 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: 53 (25.0 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