Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate BPHYT_RS19375 BPHYT_RS19375 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__BFirm:BPHYT_RS19375 Length = 576 Score = 717 bits (1850), Expect = 0.0 Identities = 353/565 (62%), Positives = 430/565 (76%), Gaps = 9/565 (1%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S+ RG+TD+PL E T+G F D A P+R A+V Q R+T+ + E LA+ LL Sbjct: 19 SYVRGSTDIPLSEATVGRFLRDTAASFPDRPAVVFREQLIRWTWKEFAEEVDILAAGLLT 78 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +G+ GDRVGIWS N EW+L Q ATA++G VLVNINPAYR AE+EYALNKVGCK +++ Sbjct: 79 LGIAKGDRVGIWSPNRVEWLLTQFATARIGAVLVNINPAYRLAELEYALNKVGCKAIIAA 138 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 RFKTS YL ML+ LAPE Q PG L AA+LP+L+ V+ + D + PG+L F+++ Sbjct: 139 ERFKTSMYLEMLQALAPELATQAPGELHAARLPELRYVIRMCD-----TETPGMLTFSDV 193 Query: 196 IARGNAA--DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK 253 I RG +L + A L +PINIQFTSGTTG PKGATLTH N++NN +I M+ Sbjct: 194 IERGRVCLDVAKLDAIGATLSCHEPINIQFTSGTTGNPKGATLTHSNVVNNARYIAMAMR 253 Query: 254 LTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGV 313 L+ D LCIPVPLYHCFGMVL LAC + GA +V+P +GFDP L V +E+CT LHGV Sbjct: 254 LSEQDGLCIPVPLYHCFGMVLAVLACVSVGAKMVFPGEGFDPAATLAAVAEEQCTALHGV 313 Query: 314 PTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPV 373 PTMFIAELDHP FA ++ S LRTGIMAGSPCP E MK+VV +M+L EITIAYGMTETSPV Sbjct: 314 PTMFIAELDHPNFATYDFSRLRTGIMAGSPCPIETMKKVVSRMHLSEITIAYGMTETSPV 373 Query: 374 SCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDE 433 S QSST PL KR +TVG++QPHLEVKIVDP GA+VP+G+ GE CT+GYSVM GYWGDE Sbjct: 374 SFQSSTTDPLDKRTTTVGRIQPHLEVKIVDP-LGAIVPVGETGELCTRGYSVMQGYWGDE 432 Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493 AKTRE+I + GWMHTGDLAT+DAEGY NIVGR+KDM+IRGGENIYPREIEEFL+RHP++Q Sbjct: 433 AKTRESIVD-GWMHTGDLATLDAEGYCNIVGRLKDMLIRGGENIYPREIEEFLFRHPKIQ 491 Query: 494 DVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553 VQV GVPD KYGEE+CAW++ + G Q T ++I+ FC GQIAHYKVP+YIRFV PMTV Sbjct: 492 SVQVFGVPDTKYGEEVCAWVVLRSGEQVTAEEIQQFCHGQIAHYKVPKYIRFVDELPMTV 551 Query: 554 TGKIQKFKIRDEMKDQLGLEEQKTA 578 TGK+QKF +R++M +L L E KTA Sbjct: 552 TGKVQKFIMREQMISELKLREDKTA 576 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: 914 Number of extensions: 34 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: 576 Length adjustment: 36 Effective length of query: 542 Effective length of database: 540 Effective search space: 292680 Effective search space used: 292680 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