Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4309 PS417_22070 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__WCS417:GFF4309 Length = 562 Score = 249 bits (635), Expect = 3e-70 Identities = 173/540 (32%), Positives = 261/540 (48%), Gaps = 51/540 (9%) Query: 52 HQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 + G TYA+L+ ++ A L L PGDR+ + N + + + GL++VN Sbjct: 45 NMGITLTYAELERQSAAFAGYLQQHTDLKPGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104 Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTS----------DYLGMLRELAPEWQGQQPG 160 NP Y E+ + G + LV + F + DYL + ++ G Sbjct: 105 TNPLYTPREMRHQFKDAGVRALVYLNLFGSRVQEVCSDTEIDYL--IEARMGDFMPTAKG 162 Query: 161 HLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPIN 220 L + ++K +V P + F + G L + D Sbjct: 163 WLVNTLVDKVKKMV-------PAYSLPRAVAFKRALHMGAG----LGVTRHPVTLDDIAV 211 Query: 221 IQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCF 270 +Q+T GTTG KGA LTH N++ N + CM T D + P+PLYH + Sbjct: 212 LQYTGGTTGLAKGAMLTHGNLVANMQQVRACMSQTGDDGHPLIKEGQEVMIAPLPLYHIY 271 Query: 271 GMVLGNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHP 324 N C H I P D GF ++ ++ R TGL G+ T+F+A +DHP Sbjct: 272 AFT-ANCMCMMVSGNHNVLITNPRDIGGF-----IKELKKWRFTGLLGLNTLFVALMDHP 325 Query: 325 RFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS 384 F + S L+ G+ +R +Q+ I YG+TETSPV+ S+ Sbjct: 326 DFKSLDFSHLKLTNSGGTALIKATAERW-QQITGCAIGEGYGLTETSPVA--STNPYGNK 382 Query: 385 KRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGG 444 R+ TVG P +K++D D G +P+G+RGE C KG VM GYW T EA+D G Sbjct: 383 SRLGTVGIPVPATAMKVID-DHGVELPLGERGELCIKGPQVMKGYWQQPEATAEALDAEG 441 Query: 445 WMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQK 504 W+ TGD+A +D EG+V+IV R KD++I G N+YP EIE+ + HP V + V+GVPD++ Sbjct: 442 WLKTGDIAVIDEEGFVSIVDRKKDLIIVSGFNVYPNEIEDVVMAHPAVANCAVIGVPDER 501 Query: 505 YGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 GE + +++A+ E +++A+CK YKVP++I S PMT GKI + ++RD Sbjct: 502 TGEAVKLFVVARAEGVSLE-ELKAYCKTNFTGYKVPKHIVLRDSLPMTPVGKILRRELRD 560 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: 797 Number of extensions: 36 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: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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