Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PfGW456L13_1910 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1910 Length = 562 Score = 247 bits (631), Expect = 8e-70 Identities = 172/536 (32%), Positives = 263/536 (49%), Gaps = 43/536 (8%) Query: 52 HQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 + G TYA+L+ ++ A L L GDR+ + N + + + GL++VN Sbjct: 45 NMGVTLTYAELERQSAAFAGYLQAHTDLVAGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104 Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQ-----QPGHLQ-A 164 NP Y E+ + G + LV + F ++E+ P+ Q + G L A Sbjct: 105 TNPLYTAREMRHQFKDSGARALVYLNMFGQK-----VQEVLPDTDIQYLIEAKMGDLMPA 159 Query: 165 AKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFT 224 AK + TVV + P + F + G + +V GL D +Q+T Sbjct: 160 AKGWLVNTVVSKVKKMVPDYSLPQAVSFKSALRMGRGLGIKPLKV--GLD--DIAVLQYT 215 Query: 225 SGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFGMVL 274 GTTG KGA LTH N++ N C+ +D + P+PLYH + Sbjct: 216 GGTTGLAKGAMLTHGNLVANMQQARACLGQFGSDGQPLLREGQEVMIAPLPLYHIYAFT- 274 Query: 275 GNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAE 328 N C H I P D GF ++ +++ R + L G+ T+F+A +DHP F Sbjct: 275 ANCMCMMVTGNHNVLITNPRDIAGF-----IKELKNWRFSALLGLNTLFVALMDHPDFKT 329 Query: 329 FNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVS 388 + S+L+ G+ +R EQ+ IT YG+TETSPV+C + R+ Sbjct: 330 LDFSSLKLTNSGGTALVKATAERW-EQLTGCRITEGYGLTETSPVACTNPYGD--QSRIG 386 Query: 389 TVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448 TVG P +K+++ D G P+G+RGE C KG +M GYW T E +D GW + Sbjct: 387 TVGLPVPGTTLKVINDD-GVEQPLGERGELCIKGPQIMKGYWQKPDATAEVLDAEGWFKS 445 Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508 GD+A +D +G+V IV R KDM+I G N+YP EIE+ + HP V + V+GVPD++ GE Sbjct: 446 GDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPNVANCAVIGVPDERSGEA 505 Query: 509 LCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 + +++A+ E +++A+CK YKVP++I S PMT GKI + ++RD Sbjct: 506 VKLFVVAREAGVSLE-ELKAYCKENFTAYKVPKHIVLRESLPMTPVGKILRRELRD 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: 778 Number of extensions: 44 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