Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS31975 RR42_RS31975 fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Cup4G11:RR42_RS31975 Length = 546 Score = 292 bits (748), Expect = 2e-83 Identities = 188/542 (34%), Positives = 279/542 (51%), Gaps = 23/542 (4%) Query: 27 IEQTIGAFFADMVARQPERE-ALVSVHQ-GRRYTYAQLQTEAHRLASALLGMGLTPGDRV 84 I TI A ++V R A +++ + G R ++ +L T + ALL +GL PGDRV Sbjct: 23 IPATIPATIPELVRTAAARHGARIAIQEDGLRLSFTELDTLRAQAGRALLALGLLPGDRV 82 Query: 85 GIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYL 144 +W+ N +EW++ LA +G LV IN + E L G ++L + F Y Sbjct: 83 AVWAPNLSEWIVAALAAHSIGAALVPINTRMKGMEAGAILADSGARVLFCIDNFLGESYP 142 Query: 145 GMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQ--GADEPGLLRFTELIARGNAA 202 ML AP +PG L+ +V + AG+ DE F L A+ A Sbjct: 143 EML---APH----RPGTLER--------IVVLRGRAGRQMAPDELAWADFLALAAQTGEA 187 Query: 203 DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCI 262 R + A + ++I FTSGTTG PKG H L + DR I Sbjct: 188 AFRACESA--VSGDTLMDIMFTSGTTGRPKGVMTAHAQNLQAIHGWASITGVEAGDRYLI 245 Query: 263 PVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322 P +H FG G LA GATI+ P+ FD V+ +++ER T L G PT++ L+ Sbjct: 246 VNPFFHTFGYKAGWLAALASGATIL-PHLVFDAEAVMTRIENERITVLPGPPTLYQTLLN 304 Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382 HPR EF+LS+LR + S P +++R+ ++ R+I YG+TE+ + + Sbjct: 305 HPRLREFDLSSLRVAVTGASAIPPVLIQRMRRELGFRDIFTGYGLTESCGFATLTRAADD 364 Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442 T G+ P +E++ VD G VP G+ GE +GY+VM GY+ T EAID Sbjct: 365 ADIVALTSGRAMPGVELRCVD-GAGYPVPAGEPGEVTVRGYNVMRGYFQLPEATTEAIDA 423 Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502 GGW+ TGD+ T+D G + I RIKDM I GG N YP EIE+ L HP + V VVGVP Sbjct: 424 GGWLRTGDIGTLDVRGNLRITDRIKDMFIVGGFNCYPAEIEKLLVSHPAIAQVAVVGVPH 483 Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562 ++ GE A+++ + G++ D++ + + +A+YKVPR + FV + P + GKI K+++ Sbjct: 484 ERLGEAGKAFVVLRHGSKVGADELIDWARRHMANYKVPREVVFVQTLPTSAAGKILKYRL 543 Query: 563 RD 564 R+ Sbjct: 544 RE 545 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: 738 Number of extensions: 34 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: 546 Length adjustment: 36 Effective length of query: 542 Effective length of database: 510 Effective search space: 276420 Effective search space used: 276420 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