Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013418553.1 RVAN_RS04370 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000166055.1:WP_013418553.1 Length = 583 Score = 240 bits (613), Expect = 1e-67 Identities = 183/588 (31%), Positives = 284/588 (48%), Gaps = 55/588 (9%) Query: 2 TSSAAATNSAPLVDSHARGATDVPLIE-QTIGAFFADMVARQPEREALVSVHQGRRYTYA 60 T + A + P + S+ G + E + + + VAR P++ A S G+ TYA Sbjct: 21 TQAGTAATTYPWLRSYPAGVDWFQVFEPKALPVALEETVARFPDKPA--SWFFGKTMTYA 78 Query: 61 QLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEV 120 +L R AL G+G+ G RVG+ N +V+ AT + G +V++NP Y E+ Sbjct: 79 ELGAAVDRATKALQGLGVREGTRVGLLFPNCPAFVIFYYATLKAGGTVVSLNPLYTVPEL 138 Query: 121 EYALNKVGCKLLVS------MARFKTSDYLGML--------RELAPEWQGQQPGHLQAAK 166 Y + G K++V+ + + K G L +++ P +G G + Sbjct: 139 AYQVKDAGAKIVVTADLAATLPKAKALVDNGTLDTVIVTPFKKMLPGLKGFLFGLFKGKD 198 Query: 167 LPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSG 226 L W GLL EL+ D V A +Q+T G Sbjct: 199 L-----ATWTPGR--------GLLSAEELLDNDGHYDRSAIDVNAVAA------LQYTGG 239 Query: 227 TTGFPKGATLTHRNILNN-----GFFIGECMKLTPADRLCIPVPLYHCFGMV-LGNLACF 280 TTG PKGA LTH N+ N +F G + + +R +P +H F M L N A Sbjct: 240 TTGTPKGAMLTHSNLSINVQQAAAWFPG--LAIPGEERFFCVIPFFHSFAMTGLMNFAIL 297 Query: 281 THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMA 340 I+ P F+ L+T+ + T + GVPT+F A P + +LS+L+ I Sbjct: 298 KGAQMIMLPR--FELKLALKTIDQTKPTIMAGVPTLFNAMAKVPDIKKHDLSSLKFCISG 355 Query: 341 GSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEV- 399 G+ P EV +R E ++ + YG++ETSPV+ + P K+ ++G P E+ Sbjct: 356 GAALPLEV-RRDFESVSGCGLVEGYGLSETSPVTHINPLTGP--KKECSIGLPVPGTEMS 412 Query: 400 --KIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAE 457 K+ DP VP+G++GE C +G VM GYW +T + G + TGD+A MD + Sbjct: 413 LRKLGDPQEE--VPLGEKGEICIRGPQVMKGYWNKPKETADTF-VGEFFRTGDVAYMDED 469 Query: 458 GYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP 517 G+ IV RIKD++I G N+YPR IEE +Y HP V +V V+GVPD+ GE A++ + Sbjct: 470 GFTYIVDRIKDLIICSGFNVYPRRIEEAIYEHPAVDEVTVIGVPDKYRGEAPKAFVKLRE 529 Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565 G Q T++++ F K +I+ ++P I F P T+ GK+ K +++ E Sbjct: 530 GQQVTKEEMLDFLKERISKIELPADIEFRAELPKTLIGKLSKKELKAE 577 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: 767 Number of extensions: 40 Number of successful extensions: 6 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: 583 Length adjustment: 36 Effective length of query: 542 Effective length of database: 547 Effective search space: 296474 Effective search space used: 296474 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