Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf1N1B4_575 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_575 Length = 505 Score = 207 bits (526), Expect = 1e-57 Identities = 144/475 (30%), Positives = 224/475 (47%), Gaps = 36/475 (7%) Query: 52 HQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 + G TYA+L+ + A L L PGDR+ + N + + + GL++VN Sbjct: 45 NMGVTLTYAELERYSAAFAGYLQAHTDLMPGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104 Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170 NP Y E+ + G + LV + F ++E+ P+ Q +L AK+ L Sbjct: 105 TNPLYTAREMRHQFKDSGARALVYLNVFGQK-----VQEVLPDTDIQ---YLIEAKMGDL 156 Query: 171 KTVV--WIDDEAGQGADE-------PGLLRFTELIARGNAADPRLAQVAAGLQATDPINI 221 W+ + + P + F + G + V GL D + Sbjct: 157 MPTAKGWLVNTLVSKVKKMVPDYSLPQAISFKSALRLGRGLGIKPLNV--GLD--DIAVL 212 Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFG 271 Q+T GTTG KGA LTH N++ N C+ AD + P+PLYH + Sbjct: 213 QYTGGTTGLAKGAMLTHGNLVANMQQARACLGQFGADGQPLLREGLEVMIAPLPLYHIYA 272 Query: 272 MVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNL 331 + G V + D ++ +++ R + L G+ T+F+A +DHP F + Sbjct: 273 FTANCMCMMVTGNHNVLITNPRDIGNFIKELKNWRFSALLGLNTLFVALMDHPDFKTLDF 332 Query: 332 STLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVG 391 S+L+ G+ +R EQ+ IT YG+TETSPV+C + R+ TVG Sbjct: 333 SSLKLTNSGGTALVKATAERW-EQLTGCRITEGYGLTETSPVACTNPYGD--KSRIGTVG 389 Query: 392 QVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDL 451 P +K+++ D G +G+RGE C KG +M GYW T + +D GW +GD+ Sbjct: 390 LPVPGTALKVIN-DEGVEQSLGERGELCIKGPQIMKGYWQKPEATADVLDADGWFKSGDI 448 Query: 452 ATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 A +D +G+V IV R KDM+I G N+YP EIE+ + HP+V + V+GVPD++ G Sbjct: 449 AVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGVPDERSG 503 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: 703 Number of extensions: 37 Number of successful extensions: 5 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: 505 Length adjustment: 35 Effective length of query: 543 Effective length of database: 470 Effective search space: 255210 Effective search space used: 255210 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: 52 (24.6 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