Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF3324 PS417_17010 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__WCS417:GFF3324 Length = 544 Score = 608 bits (1569), Expect = e-178 Identities = 303/564 (53%), Positives = 392/564 (69%), Gaps = 28/564 (4%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S++RG+ D L+ TIG F VA+ P+ EALV HQ RRYT+ QL A A L Sbjct: 7 SYSRGSQDKTLLAMTIGQAFDRTVAQFPDGEALVVRHQQRRYTWRQLAETVDLHARAFLA 66 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +G+ GDR+GIW+ N AEW + Q+A+A++G++LVNINPAYR++E+EY L + GC+ LV Sbjct: 67 LGMQTGDRLGIWAPNCAEWCISQIASAKLGVILVNINPAYRSSELEYVLKQSGCQWLVCA 126 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 FKTSDY ML+ L P+ +G ++ +D + PG L + +L Sbjct: 127 GSFKTSDYHAMLQALNPDLRG----------------MISLDP-----SPPPGFLPWAQL 165 Query: 196 IARGNAAD-PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 A G +L L +NIQ+TSGTTGFPKGATL+H NILNNG+ +GE + L Sbjct: 166 AALGTGIPLEQLHSRQTSLHFDQAVNIQYTSGTTGFPKGATLSHHNILNNGYMVGESLGL 225 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 T DRL IPVPLYHCFGMV+GNL C THG T++YPNDGFDPL L V +E TGL+GVP Sbjct: 226 TAQDRLVIPVPLYHCFGMVMGNLGCITHGTTMIYPNDGFDPLLTLTAVAEEHATGLYGVP 285 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMFIA LDHP+ F+LS+LRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGMTETSPVS Sbjct: 286 TMFIAMLDHPQLGGFDLSSLRTGIMAGATCPIEVMRRVISEMHMSEVQIAYGMTETSPVS 345 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 Q+ D L +RV+TVG+ QP LE KI+D D G V G+ GE CT+GYSVM GYW + Sbjct: 346 LQTGADDDLERRVTTVGRTQPQLENKIIDAD-GNTVARGEIGELCTRGYSVMLGYWNNPD 404 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 TREAID+ GWMHTGDLA+MDA GYV I GR KDM+IRGGEN+YPRE+EEF + HP V D Sbjct: 405 ATREAIDDAGWMHTGDLASMDAHGYVCIAGRNKDMIIRGGENVYPRELEEFFFTHPAVAD 464 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554 VQV+G+PD++YGE + AW+ PG E +++ +CKG+IAH+K P++ +FV FPMTVT Sbjct: 465 VQVIGIPDERYGEAIVAWVKFHPGHVANELELQTWCKGRIAHFKTPKHFKFVEEFPMTVT 524 Query: 555 GKIQKFKIRDEMKDQLGLEEQKTA 578 GKIQKF++R ++ ++E K A Sbjct: 525 GKIQKFRMR-----EISIQELKNA 543 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: 887 Number of extensions: 36 Number of successful extensions: 3 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: 544 Length adjustment: 36 Effective length of query: 542 Effective length of database: 508 Effective search space: 275336 Effective search space used: 275336 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