Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013259841.1 DEBA_RS15245 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000143965.1:WP_013259841.1 Length = 548 Score = 528 bits (1359), Expect = e-154 Identities = 253/544 (46%), Positives = 366/544 (67%), Gaps = 7/544 (1%) Query: 23 DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGD 82 D +I++T+G A P+ +A+V V +G R TY+Q LA L+ +G+ PG Sbjct: 3 DRHIIDKTLGQILEQTAADYPDHDAVVYVDRGFRLTYSQFDAVVDELAKGLMALGVEPGQ 62 Query: 83 RVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSD 142 +V +W+ N WV +Q ATA++G +L+ +N Y+ AE++Y L + + LV RF+ +D Sbjct: 63 KVAVWASNVPYWVALQFATAKIGAILLTVNTHYQRAELDYLLKQSETENLVVADRFRDND 122 Query: 143 YLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADE-PGLLRFTELIARGNA 201 +L ++ EL PE + Q+ GHL + + P L+ V ++D E +G P +L + +++ Sbjct: 123 FLDIVYELIPELRTQERGHLHSPRFPHLRRVFFLDQEKHRGMYSIPEVLAMSRMVS---- 178 Query: 202 ADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLC 261 D RLA V A + D +N+Q+TSGTTGFPKG LTH++I NG++IG+ L P DR+C Sbjct: 179 -DERLAAVKAAQKPDDVVNMQYTSGTTGFPKGVMLTHKSIGTNGYWIGKHQNLGPDDRVC 237 Query: 262 IPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL 321 +PVPL+HCFG VLG +A HG+ +V + FDP+ V+ V+ ERCT L+GVPTMFIA L Sbjct: 238 LPVPLFHCFGCVLGVMAAVNHGSCMVILEE-FDPVMVMSAVEQERCTALYGVPTMFIAAL 296 Query: 322 DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDT 381 H F +F+ S+LRTGIMAGSPCP + M+ V+E+MN+RE+TI YG+TE SPV Q+ D Sbjct: 297 THRLFDKFDFSSLRTGIMAGSPCPVKTMREVMERMNMREVTICYGLTENSPVMTQTLPDD 356 Query: 382 PLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAID 441 + +R TVG+ P +EVKIVDP++ +P G GE C +GYSVM GY+ T +AID Sbjct: 357 DVRRRTETVGKAMPGIEVKIVDPESHVELPTGTIGEVCCRGYSVMKGYYNMPEATAQAID 416 Query: 442 EGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVP 501 GW+H+GDL +DA+GY+ I GR KDM+IRGGENIYP E+EEF+ P V+DVQVVGVP Sbjct: 417 HDGWLHSGDLGVLDADGYLAITGRYKDMIIRGGENIYPLEVEEFIRHIPGVRDVQVVGVP 476 Query: 502 DQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFK 561 QKYGE++ A+I G T +D+R C+GQI+ YK+P+Y+ V ++P+T +GK+QK+K Sbjct: 477 SQKYGEQVGAFIQLAEGADLTAEDVRDLCRGQISRYKIPKYVAMVEAYPLTASGKVQKYK 536 Query: 562 IRDE 565 + ++ Sbjct: 537 LVEQ 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: 789 Number of extensions: 34 Number of successful extensions: 3 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: 548 Length adjustment: 36 Effective length of query: 542 Effective length of database: 512 Effective search space: 277504 Effective search space used: 277504 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