Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_1879 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1879 Length = 511 Score = 244 bits (623), Expect = 6e-69 Identities = 171/545 (31%), Positives = 266/545 (48%), Gaps = 35/545 (6%) Query: 27 IEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGI 86 +E +IG + AR + A++ +G+ +++ + ++ RLA++L MG+ D V I Sbjct: 1 MEHSIGNWVGRSAARFGNKPAII--FEGKYWSFLDIDVQSSRLAASLESMGVKREDVVSI 58 Query: 87 WSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGM 146 +S N+ EW++ A ++G ++ +N E +A+ G ++A F TSD L Sbjct: 59 YSPNSPEWIITYYAILKIGAIVNPLNTMLTAREAAFAIKNCG-----AVAVFSTSDKLLA 113 Query: 147 LRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRL 206 L+E H+ ++ L + G G+ F L+ A Sbjct: 114 LQE-----------HIGPTEVISLISF--------DGITVAGMRHFNLLVDANVAVRE-- 152 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266 G+Q D I +TSGTTG PKGA L+HR IL N T +D +PL Sbjct: 153 -YPVTGIQKDDISTIGYTSGTTGQPKGAVLSHRCILTNVSMTATMHLRTASDIAVSALPL 211 Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326 H +G V+ N A +G T+V + FD +L ++Q T L GVPTM+I L+ P Sbjct: 212 SHVYGNVVMNSA-IAYGMTLVL-HKTFDAEAILSSIQIYGATLLEGVPTMYIYLLNCPNL 269 Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386 +++S+L + G P M+ V + R + + +GMTE + S +R Sbjct: 270 GAYDVSSLTRCTVGGQMMPYTAMENVERALGCRLLEL-WGMTELGGLGTTHSLYG--ERR 326 Query: 387 VSTVGQVQPHLEVKIVDPDT-GAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445 + ++G PHLE +I + G +P+G+ GE +G VM Y G T E + GW Sbjct: 327 LGSIGVALPHLEARIAQLELDGDALPLGEIGELQIRGPVVMKHYLGRPDATAETKTDEGW 386 Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505 + TGDLA MD+EG++ IV R+KDM I G NIYP E+E + HP V V V V D+ Sbjct: 387 LRTGDLARMDSEGFIYIVDRLKDMFITAGFNIYPAELERVIAEHPSVAMVAVGSVLDEIK 446 Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565 GE A+I+ K G + I C+ ++A YKVPR + V P T +GK+ + +R Sbjct: 447 GELAKAYIVPKTGYEIDIQQIERHCRDRLAAYKVPRLFQIVEDLPKTSSGKVMRRMLRQI 506 Query: 566 MKDQL 570 + +L Sbjct: 507 FESKL 511 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: 581 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 511 Length adjustment: 35 Effective length of query: 543 Effective length of database: 476 Effective search space: 258468 Effective search space used: 258468 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