Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_041098563.1 SUTH_RS08535 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000828635.1:WP_041098563.1 Length = 545 Score = 226 bits (576), Expect = 2e-63 Identities = 173/545 (31%), Positives = 253/545 (46%), Gaps = 46/545 (8%) Query: 43 PEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATA 102 PER A S+H RRYT+ Q + RLASAL G+ GD V + +N E Sbjct: 33 PERVA--SIHGSRRYTWGQEYERSRRLASALAMRGVGAGDTVAVMLNNTPEMFECHFGVP 90 Query: 103 QVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHL 162 G VL +N + + LN ++L++ +Y GM+++ Sbjct: 91 MCGAVLNTLNTRLDPESIAFMLNHGEARVLIT-----DREYSGMVKKAL----------- 134 Query: 163 QAAKLPQLKTVVWIDDEAGQGADEP-GLLRFTELIARGNAADPRLAQVAAGLQATDPINI 221 A+L + VV +DD G E G + F L+A G P A D I++ Sbjct: 135 --AELGREILVVDVDDPEYTGPGERVGSIDFETLLASGR---PDYAWKTPA-DEWDAISL 188 Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFT 281 +TSGTTG PKG HR N + P +P++HC G Sbjct: 189 NYTSGTTGNPKGVVYHHRGAYLNALSNIVSWGMPPQSVYLWTLPMFHCNGWCFPWTVAAN 248 Query: 282 HGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAG 341 G + DP +L +++ + T G P + + P + + ++A Sbjct: 249 SGTNVCLRR--VDPKLILDAIREHKVTHYCGAPIVHSMLISAPAEWRKGIEHKVSALVAA 306 Query: 342 SPCPTEVMKRVVEQMNLR--EITIAYGMTET-SPVSCQSSTDT----PLSKRVSTVGQ-- 392 +P P V +E M IT YG+TET P + + D PL ++V G+ Sbjct: 307 APPPAAV----IEGMGKIGFNITHVYGLTETYGPAAVCAKHDEWLELPLDEQVRMNGRQG 362 Query: 393 VQPHLE--VKIVDPDTGAVVPIGQR--GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448 V+ H + V ++DP+T VP + GE +G VM GY + T EA GGW HT Sbjct: 363 VRYHCQEGVTVMDPETMQPVPWDDQTMGEIMFRGNIVMKGYLKNPKATEEAF-HGGWYHT 421 Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508 GDLA M +GY+ I R KD++I GGENI E+E+ LYRHP V VV PD K+GE Sbjct: 422 GDLAVMQPDGYIKIKDRSKDVIISGGENISSIEVEDTLYRHPAVMGAAVVATPDPKWGEV 481 Query: 509 LCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568 CA+I + G+ T +++ FC+ ++A +KVP++ F + P T TGKIQKF +R++ K Sbjct: 482 PCAFIELREGSSVTAEELTEFCRERMARFKVPKHFIF-EALPKTSTGKIQKFVLREKAKS 540 Query: 569 QLGLE 573 E Sbjct: 541 AASFE 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: 733 Number of extensions: 41 Number of successful extensions: 6 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: 545 Length adjustment: 36 Effective length of query: 542 Effective length of database: 509 Effective search space: 275878 Effective search space used: 275878 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 24 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