Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_007153301.1 MDG893_RS08275 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000170835.1:WP_007153301.1 Length = 542 Score = 201 bits (511), Expect = 6e-56 Identities = 175/570 (30%), Positives = 258/570 (45%), Gaps = 53/570 (9%) Query: 13 LVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASA 72 L + A AT PL F A + PE A++ H R + Q RLASA Sbjct: 9 LEPTDANNATLTPL------DFLARTASVYPEYPAVI--HGATRRNWQQTYERCRRLASA 60 Query: 73 LLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLL 132 L G+ GD V N + +G VL +N + + L K+L Sbjct: 61 LADRGVGKGDTVAAMLPNIPPMLECHFGIPMLGAVLNALNTRLDAKAIAFMLEHGEAKVL 120 Query: 133 VSMARFKT--SDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGAD-EPGL 189 ++ F ++ +GML P PQ V+ ++D GA + Sbjct: 121 IADREFGDVINEAVGML---------DNP--------PQ---VIDVNDPEFSGAGTQVSD 160 Query: 190 LRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIG 249 L + +A G+ A Q+ A D I++ +TSGTTG PKG HR N Sbjct: 161 LDYDAFVASGDPAFDW--QMPA--DEWDAISLCYTSGTTGNPKGVVYHHRGAYENAMGNQ 216 Query: 250 ECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTG 309 + +P++HC G G + +P +LQ + + + + Sbjct: 217 AVWSMGMHPVYLWTLPMFHCNGWCFPWTITAFAGTHVCLRK--VEPEKILQLISEHKVSH 274 Query: 310 LHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTE 369 + G P + L A+ + S + AG+ P +V++ +E M R +T YG+TE Sbjct: 275 MCGAPIVLNTLLGASEAAKSSFSHTVQAMTAGAAPPAKVIE-AIENMGFR-VTHVYGLTE 332 Query: 370 T-SPVSC----QSSTDTPLSKRVSTVGQ--VQPHL--EVKIVDPDTGAVVPIGQR--GEF 418 PV+ D P+ R + V+ H + + DP+T VP GE Sbjct: 333 VYGPVTVCAWKSEWDDLPVEDRARIKARQGVRYHTLAGMMVGDPETMEAVPKDGNTIGEI 392 Query: 419 CTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIY 478 +G +VM GY + T EA GGW HTGDLA A+GY I R+KD++I GGENI Sbjct: 393 FLRGNTVMKGYLKNPKATEEAF-RGGWFHTGDLAVWHADGYAEIKDRLKDIIISGGENIS 451 Query: 479 PREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP-GTQPTEDDIRAFCKGQIAHY 537 E+E+ LYRHP + + VV PD+K+GE CA++ KP + +EDDI AFC+ ++A + Sbjct: 452 TIEVEDVLYRHPDILEAAVVARPDEKWGETPCAFVTLKPEAGEVSEDDIIAFCRERMAKF 511 Query: 538 KVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 KVP+ I F + P T TGKIQKF +RD+ K Sbjct: 512 KVPKTIVF-SELPKTSTGKIQKFVLRDDAK 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: 728 Number of extensions: 45 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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