Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF1060 HP15_1039 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Marino:GFF1060 Length = 542 Score = 213 bits (542), Expect = 2e-59 Identities = 176/568 (30%), Positives = 265/568 (46%), Gaps = 52/568 (9%) Query: 14 VDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASAL 73 VD++ + V IE+T + PE A++ H RY +AQ RLASAL Sbjct: 12 VDANYAVQSPVDFIERTATVY--------PEYPAVI--HGAIRYNWAQTYERCRRLASAL 61 Query: 74 LGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLV 133 G G+ GD V + N V +G VL +N + + L+ K+++ Sbjct: 62 KGRGIGRGDTVAVMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVI 121 Query: 134 SMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDD-EAGQGADEPGLLRF 192 + F ++R+ ++L V+ +DD E G+G L + Sbjct: 122 ADREFGE-----VIRDAV-------------SRLDTKPLVIDVDDPEYGEGVQVSDL-DY 162 Query: 193 TELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECM 252 + G DP Q + D I++ +TSGTTG PKG HR N Sbjct: 163 EAFLQEG---DPTF-QWSFPENEWDAISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVW 218 Query: 253 KLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHG 312 + +P++HC G G + DP +LQ ++D + T + G Sbjct: 219 SMDMHPVYLWTLPMFHCNGWCFPWTITAMAGTHVCLRR--VDPEKILQLIRDHQVTHMCG 276 Query: 313 VPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTET-S 371 P + A L+ P A+ + + AG+ P +V+ +E+M + ++T YG+TE Sbjct: 277 APIVLNALLNVPESAKAGIDHDVKSMTAGAAPPAQVIG-AIEEMGI-QVTHVYGLTEVYG 334 Query: 372 PVSC---QSSTDT-PLSKRVSTVGQ--VQPHL--EVKIVDPDTGAVVPIGQR--GEFCTK 421 PV+ +S D PL R + V+ H + DP+T VP + GE + Sbjct: 335 PVTVCAWKSEWDALPLHDRARKKARQGVRYHTLAGTMVGDPNTMEPVPKDGKTIGEIFLR 394 Query: 422 GYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPRE 481 G +VM GY + T EA GGW HTGDLA +GY+ I R+KD++I GGENI E Sbjct: 395 GNTVMKGYLKNPKATEEAF-RGGWFHTGDLAVWHEDGYMEIKDRLKDIIISGGENISTIE 453 Query: 482 IEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP-GTQPTEDDIRAFCKGQIAHYKVP 540 +E+ LYRHP V + VV PD+K+GE CA++ KP +E+DI FC+ +A +KVP Sbjct: 454 VEDTLYRHPAVLEAAVVARPDEKWGETPCAFVTLKPEAGDVSEEDIINFCREHLARFKVP 513 Query: 541 RYIRFVTSFPMTVTGKIQKFKIRDEMKD 568 + I F + P T TGKIQKF +RD+ K+ Sbjct: 514 KTIVF-SELPKTSTGKIQKFVLRDQAKE 540 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: 703 Number of extensions: 46 Number of successful extensions: 7 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: 542 Length adjustment: 36 Effective length of query: 542 Effective length of database: 506 Effective search space: 274252 Effective search space used: 274252 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