Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate BPHYT_RS17295 BPHYT_RS17295 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__BFirm:BPHYT_RS17295 Length = 557 Score = 228 bits (581), Expect = 5e-64 Identities = 168/523 (32%), Positives = 252/523 (48%), Gaps = 20/523 (3%) Query: 51 VHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 V G+ +Y +L + +LA+ GL G R+ I N ++ + A + G V+VN Sbjct: 43 VCMGKEISYGELDALSRKLAAWFQSKGLARGARIAIMMPNVLQYPVAIAAILRAGYVVVN 102 Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170 +NP Y E+E+ L G + ++ + F + + G L K + Sbjct: 103 VNPLYTPRELEHQLKDSGAEAIILLENFAVTLQAIVRNTSIKHVVVAAMGDLMGIKGTLV 162 Query: 171 KTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGF 230 VV + PG ++F IA G A V G + D +Q+T GTTG Sbjct: 163 NFVVRKVKKMVPAWSLPGHVKFNTAIAEG--ARQNFKPVQQGPE--DVAFLQYTGGTTGV 218 Query: 231 PKGATLTHRNILNNGFFIGECMKLTPADR-------LCIPVPLYHCFGM-VLGNLACFTH 282 KGATL HRN++ N + A+R + +PLYH F + V G L T Sbjct: 219 AKGATLLHRNLIANVLQSEIWLDPVRANRKDIDQFVTVVALPLYHVFALTVCGLLTIRTG 278 Query: 283 GATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGS 342 G ++ PN P +++ ++ T + V T++ A L+ P F + + S L G Sbjct: 279 GLGVLIPNPRDIP-GMIKALEGYPITTIPAVNTLYNALLNSPDFHKLDFSKLIAANGGGM 337 Query: 343 PCPTEVMKRVVEQMNLREITIAYGMTETSP-VSCQSSTDTPLSKRVSTVGQVQPHLEVKI 401 V KR EQ + I YG++ETSP V+C T T S T+G P E+ I Sbjct: 338 AVQEAVAKRWYEQTHT-PIIEGYGLSETSPCVTCNPVTVTEYS---GTIGLPLPSTEISI 393 Query: 402 VDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVN 461 D D G VP+GQ GE C +G VM GYW +T + + G+ +GD+ M+ G+V Sbjct: 394 RD-DEGNEVPLGQPGEICIRGPQVMAGYWNRPDETAKVMTADGFFKSGDVGLMNDGGFVK 452 Query: 462 IVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQP 521 IV R KDM++ G N+YP EIE+ + + P V +V VGVPDQ GE + +++ K Sbjct: 453 IVDRKKDMILVSGFNVYPNEIEDVVAKLPGVFEVAAVGVPDQHSGEAVKLFVVKKDQAL- 511 Query: 522 TEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 T+ DI A+CK Q+ YK P+ + F T P + GKI + ++RD Sbjct: 512 TDADIFAYCKQQLTGYKRPKIVEFRTELPKSNVGKILRRELRD 554 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: 741 Number of extensions: 40 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: 578 Length of database: 557 Length adjustment: 36 Effective length of query: 542 Effective length of database: 521 Effective search space: 282382 Effective search space used: 282382 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