Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 7025225 Shewana3_2386 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__ANA3:7025225 Length = 557 Score = 221 bits (562), Expect = 8e-62 Identities = 162/545 (29%), Positives = 262/545 (48%), Gaps = 30/545 (5%) Query: 35 FADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAE 93 F VA+ ++ A +++ G TY +L+ + A+ L + L GDRV + N + Sbjct: 29 FETAVAKYADQPAFINM--GATLTYRKLEERSRAFAAYLQNELKLQKGDRVALMMPNLLQ 86 Query: 94 WVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPE 153 + + + G+V+VN+NP Y E+++ L G K +V ++ F + L E+ + Sbjct: 87 YPIALFGILRAGMVVVNVNPLYTPRELKHQLVDSGAKAIVVVSNFART-----LEEVVDQ 141 Query: 154 WQGQQP------GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLA 207 + L A K + VV + D P L E ++RG R+ Sbjct: 142 TPVKSVIITGLGDLLSAPKRTLVNFVVKYIKKLVPKYDLPHALSMRETLSRGR----RMQ 197 Query: 208 QVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR-----LCI 262 V + D +Q+T GTTG KGA LTH+N++ N +PA R + Sbjct: 198 YVKPVITGDDLAFLQYTGGTTGVSKGAMLTHKNVVANVLQANGAY--SPALRDGNEFVVT 255 Query: 263 PVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322 +PLYH F + + L G+ + + D + ++ T L GV T+F A ++ Sbjct: 256 ALPLYHIFALTVNCLLFLHKGSQNLLITNPRDIPGFVAELKKYPFTALTGVNTLFNALVN 315 Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382 FAE + S L+ I G V + + + + YG+TE SP+ + Sbjct: 316 SSDFAELDFSRLKLSIGGGMAVQKAVADKW-QSITKTRLLEGYGLTEASPLL--TCCPYN 372 Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442 L ++G P +++ D D G V+P G+ GE KG +M GYW +T + ID+ Sbjct: 373 LDGYNGSIGFPAPSTLIQVRD-DAGNVLPQGETGELFGKGPQIMKGYWQRPEETAKVIDK 431 Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502 GW+ TGD+ MD +G+ IV R KDM++ G N++P E+EE + HP+V +V VGVP+ Sbjct: 432 DGWLATGDIGYMDEQGFFYIVDRKKDMILVSGFNVFPNEVEEVVALHPKVIEVAAVGVPN 491 Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562 GE + +++AK + T DDI C+ + YKVP+ + F P T GKI + ++ Sbjct: 492 DASGELVKVFVVAKDKSL-TADDIIKHCRAHLTGYKVPKLVEFRDELPKTNVGKILRREL 550 Query: 563 RDEMK 567 RDE+K Sbjct: 551 RDEVK 555 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: 722 Number of extensions: 42 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: 557 Length adjustment: 36 Effective length of query: 542 Effective length of database: 521 Effective search space: 282382 Effective search space used: 282382 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