Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PfGW456L13_2521 Long-chain fatty-acid-CoA ligase (EC 6.2.1.3), Mycobacterial subgroup FadD3
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2521 Length = 526 Score = 283 bits (725), Expect = 9e-81 Identities = 181/539 (33%), Positives = 277/539 (51%), Gaps = 32/539 (5%) Query: 30 TIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSH 89 TI FA+ +R A+ +Y QL + A ALL + + GDRV IW+ Sbjct: 9 TIAQLFANAAQAYGDRPAIEDADH--TISYRQLDQLRRQAARALLALDVQVGDRVAIWAP 66 Query: 90 NNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRE 149 N EW++ A VG LV +N + +E Y L + G +L ++ F +DY GML Sbjct: 67 NVWEWIVAAGALQSVGAALVPLNTRMKGSEAGYILRESGTCVLFAIGEFLGADYPGML-- 124 Query: 150 LAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLL--RFTELIARGNAADPRLA 207 PE LP L+ +V + +GA+ L RF +L A R Sbjct: 125 -TPE------------DLPALRHIVSV-----RGANSGTLAWERFMDLAADVPQLALRTR 166 Query: 208 QVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLY 267 + + G QA ++ FTSGTTG PKG +H L + + L DR I P + Sbjct: 167 EQSVGPQALS--DVLFTSGTTGKPKGVMTSHGQNLRIVRDWSDIVGLREGDRYLIVNPFF 224 Query: 268 HCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFA 327 H FG G LA G T++ P FD VL+ VQ ER T L G PT++ + L HP+ + Sbjct: 225 HSFGYKAGWLAALMRGCTLL-PQQVFDVQAVLECVQRERITVLPGPPTLYQSLLAHPQRS 283 Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS--CQSSTDTPLSK 385 EF+LS+LR + + P E++ R+ +++ I AYG+TE + C+S L Sbjct: 284 EFDLSSLRVAVTGAAAIPVEMIHRMRDELGFATIVTAYGLTEVCGFATICRSGDSAELV- 342 Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445 +T G+ P ++V+ V ++G P GE +GY++M GY + ++E +D GW Sbjct: 343 -ANTSGRAMPGVQVRCVG-NSGRSQPANIPGEVQIRGYNLMQGYLNNPEASQEILDADGW 400 Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505 +HTGD+ +D +GY+ I R+KDM I GG N+YP EIE+ L +P V V+G+PD++ Sbjct: 401 LHTGDIGMLDEQGYLRITDRLKDMFITGGFNVYPAEIEQCLLTYPGVAQAAVIGIPDERL 460 Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 GE A+++ PG + + A+C+ Q+A+YKVPR ++ + P+ GK+ K +R+ Sbjct: 461 GEVAMAFLLPAPGMEIEQTRFLAWCREQMANYKVPRRVQVLQKMPINAAGKVTKNVLRE 519 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: 688 Number of extensions: 35 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: 526 Length adjustment: 36 Effective length of query: 542 Effective length of database: 490 Effective search space: 265580 Effective search space used: 265580 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