Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate SMc02162 SMc02162 long-chain-fatty-acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Smeli:SMc02162 Length = 566 Score = 237 bits (604), Expect = 1e-66 Identities = 170/548 (31%), Positives = 261/548 (47%), Gaps = 22/548 (4%) Query: 25 PLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRV 84 PL ++IG FF VA+ R A + G+ T++ L T + ++ + L +GL GDRV Sbjct: 31 PLTYRSIGEFFDHAVAQYSWRPAFTCM--GKALTFSDLNTHSAKIGAWLQSLGLAKGDRV 88 Query: 85 GIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYL 144 + N + ++ + G +VN+NP Y E+E+ L G K + + F + Sbjct: 89 AVMMPNILQNPVIVYGILRAGFTVVNVNPLYTPRELEHQLVDAGAKAIFVLENFAHTVEQ 148 Query: 145 GMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADP 204 + R G + AK + VV + PG L F ++A+G Sbjct: 149 VLARTEVKHVVVASMGDMLGAKGAIVNLVVRRVKKLVPAWSIPGHLSFKTVLAKGATLGF 208 Query: 205 RLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN----GFFIGECMKLTPADR- 259 + VA G D +Q+T GTTG KGATLTH N+L+N ++ P Sbjct: 209 KRPNVAPG----DVAFLQYTGGTTGVSKGATLTHANLLSNMAQMELWLNTAFLRKPRPES 264 Query: 260 ---LCIPVPLYHCFGMVLGNL-ACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315 +C +PLYH F + + +L T G I+ PN P V + + R G+ T Sbjct: 265 LTFMCA-LPLYHIFALTVNSLMGLATGGNNILIPNPRDIPAFVKELGR-YRTNIFPGLNT 322 Query: 316 MFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSC 375 +F A +++ F + + S+L G V +R +E I YG++ETSPV+ Sbjct: 323 LFNALMNNSEFRKLDFSSLILTFGGGMAVQRPVAERWLELTGC-PIHEGYGLSETSPVAT 381 Query: 376 QSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAK 435 + DT T+G P EV+I D D G +P+G+ GE C +G VM GYW + Sbjct: 382 ANRLDT--DDFTGTIGIPLPSTEVEIRDED-GRTLPVGEIGEICIRGPQVMAGYWQRPEE 438 Query: 436 TREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDV 495 T AI G+ TGD+ M+AEG IV R KDM++ G N++P EIEE HP + + Sbjct: 439 TARAISPDGFFRTGDVGFMNAEGLTKIVDRKKDMILVSGFNVFPNEIEEVAATHPGILEC 498 Query: 496 QVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTG 555 +GV D GE + +++ K TE++++ C + +YK PRY+ F T P + G Sbjct: 499 AAIGVADPHSGEAVKLFVVRK-DPNLTEEEVKRHCAASLTNYKRPRYVEFRTELPKSNVG 557 Query: 556 KIQKFKIR 563 KI + +R Sbjct: 558 KILRKDLR 565 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: 775 Number of extensions: 38 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: 566 Length adjustment: 36 Effective length of query: 542 Effective length of database: 530 Effective search space: 287260 Effective search space used: 287260 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