Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_4550 PP_4550 long-chain-fatty-acid/CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Putida:PP_4550 Length = 562 Score = 243 bits (621), Expect = 1e-68 Identities = 166/534 (31%), Positives = 258/534 (48%), Gaps = 43/534 (8%) Query: 54 GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112 G +YA+L+ + A+ L L PG+R+ + N ++ + + GL++VN N Sbjct: 47 GVTLSYAELERHSAAFAAWLQQHTDLKPGERIAVQMPNVLQYPIAVFGAMRAGLIVVNTN 106 Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEW------QGQQPGHLQAAK 166 P Y E+ + G + LV + F ++E+ P+ + + L AAK Sbjct: 107 PLYTEREMRHQFKDSGARALVYLNMFGKR-----VQEVLPDTGIEYLIEAKMGDLLPAAK 161 Query: 167 LPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSG 226 + TVV + P + F +++ G P+ L D +Q+T G Sbjct: 162 GWLVNTVVDKLKKMVPAYRLPQAVPFKQVLREGRGLSPK----PVSLNLDDIAVLQYTGG 217 Query: 227 TTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFGMVLGN 276 TTG KGA LTH N++ N + C D + P+PLYH + N Sbjct: 218 TTGLAKGAMLTHGNLVANMLQVLACFSQHGPDGQKLLKDGQEVMIAPLPLYHIYAFT-AN 276 Query: 277 LACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFN 330 C H I P D GF ++ + R + L G+ T+F+A +DHP F + + Sbjct: 277 CMCMMVTGNHNVLITNPRDIPGF-----IKELGKWRFSALLGLNTLFVALMDHPGFRQLD 331 Query: 331 LSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTV 390 S L+ G+ +R + R I YG+TETSPV+ S+ R+ TV Sbjct: 332 FSALKVTNSGGTALVKATAERWEDLTGCR-IVEGYGLTETSPVA--STNPYGQLARLGTV 388 Query: 391 GQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGD 450 G K++D D G +P+G+RGE C KG VM GYW T +A+D GW TGD Sbjct: 389 GIPVAGTAFKVIDDD-GNELPLGERGELCIKGPQVMKGYWQQPEATAQALDAEGWFKTGD 447 Query: 451 LATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELC 510 +A +D +G+ IV R KDM+I G N+YP EIE+ + HP+V + +GVPD++ GE + Sbjct: 448 IAVIDPDGFTRIVDRKKDMIIVSGFNVYPNEIEDVVMGHPKVANCAAIGVPDERSGEAVK 507 Query: 511 AWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 +++ + G + D+++A+CK YKVP++I S PMT GKI + ++RD Sbjct: 508 LFVVPREGGL-SVDELKAYCKANFTGYKVPKHIVLRESLPMTPVGKILRRELRD 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: 787 Number of extensions: 46 Number of successful extensions: 6 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: 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