Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 6938794 Sama_2897 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__SB2B:6938794 Length = 531 Score = 219 bits (558), Expect = 2e-61 Identities = 155/493 (31%), Positives = 241/493 (48%), Gaps = 32/493 (6%) Query: 78 LTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMAR 137 L PGD+V I N ++V+ + G+VLVN NP Y E+ + G K+LV + Sbjct: 63 LQPGDKVAIQLPNLTQFVIAAYGVLKAGMVLVNTNPLYTERELIHQFKDSGAKVLVVL-- 120 Query: 138 FKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIA 197 SD L L ++ E + + + +D + Q + GL L A Sbjct: 121 ---SDLLPTLAKVVAE-----------TPIELVISTHALDLVSPQIQPKTGLKNIEFLKA 166 Query: 198 RGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK--LT 255 + VAA +Q+T GTTG KGA L+H N++ N + + +T Sbjct: 167 LNLGSQESWQPVAANHSTL--AALQYTGGTTGLSKGAMLSHGNLIANALQCRDRLANVIT 224 Query: 256 PADRLCI-PVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 P + + + P+P+YH + ++ + GA V + D ++++T+ TG G+ Sbjct: 225 PGEDIFVAPLPIYHIYAFLVNLVLFVEQGACSVLIPNPRDIPSLIKTLAKYPFTGFAGLN 284 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 T+F+A F + S L+ I G+ TE + +Q I+ YG++ETSPV Sbjct: 285 TLFVALCHQEEFRALDFSHLKLTISGGTAL-TEAAAGLWQQTTGCTISEGYGLSETSPV- 342 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 + + P ++R+ T+G+ EV+I+D D VP+GQ GE +G VM GYW Sbjct: 343 --ITLNQPGAERLGTIGRPVLATEVQILDEDE-TPVPMGQAGELAVRGPQVMSGYWQQAG 399 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 +T + G+ TGD+A + +G IV R KDM+I G N+YP E+E L HP V + Sbjct: 400 ETERVFSKDGFFKTGDIAIAEPDGCYRIVDRKKDMIIVSGFNVYPNEVENVLASHPAVLE 459 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIR----AFCKGQIAHYKVPRYIRFVTSFP 550 V+GV D++ GE + A I+ KP + DD R A C+ +A YK PR+I FV S P Sbjct: 460 CAVIGVADERSGEAVKAVIVLKPSVE--ADDARAAITAHCQANLAGYKQPRHIEFVASLP 517 Query: 551 MTVTGKIQKFKIR 563 + GKI + +R Sbjct: 518 KSTVGKILRRALR 530 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: 705 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 578 Length of database: 531 Length adjustment: 36 Effective length of query: 542 Effective length of database: 495 Effective search space: 268290 Effective search space used: 268290 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