Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AZOBR_RS09405 AZOBR_RS09405 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__azobra:AZOBR_RS09405 Length = 544 Score = 221 bits (562), Expect = 8e-62 Identities = 177/575 (30%), Positives = 260/575 (45%), Gaps = 53/575 (9%) Query: 10 SAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRL 69 + P + R A VPL T F P++ A+V + R ++ +++ A L Sbjct: 4 TTPSAELSRRTANHVPL---TPLDFLRRSAMVYPDKTAVV--YGPLRRSWLEVEHRARAL 58 Query: 70 ASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGC 129 ASA+ G+ PG+ V + + N + G VL IN V + L Sbjct: 59 ASAVSRAGVRPGEVVSVLAFNTPAMLEAHFGVPGAGAVLNAINTRLDPPAVAFILEHAES 118 Query: 130 KLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGL 189 +L + + R AP VVWIDD A Q AD G Sbjct: 119 RLFLVDRGLSAVARAALERMTAPP------------------RVVWIDDPAAQDADPVGD 160 Query: 190 LRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHR----NILNNG 245 L + + + G+ P + I + +TSGTTG PKG HR N L N Sbjct: 161 LEYEDFLKTGDPEAPWRRPE----DEWESIALNYTSGTTGNPKGVLYHHRGAHLNALGNV 216 Query: 246 FFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDE 305 G L P +P++HC G A GAT V DP + + + +E Sbjct: 217 ITFG----LRPDSVYLWTLPMFHCNGWTYP-WAVTAVGATHVCLR-AVDPAAIFRLIAEE 270 Query: 306 RCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAY 365 + T L G P + + P + + G P + +E+M R +T Y Sbjct: 271 KVTHLCGAPVVLTMLIHAPDAVKRAFDHGPVQVATGGAAPPSAVIAGMERMGFR-LTHLY 329 Query: 366 GMTETSPVSC-----QSSTDTPLSKR-VSTVGQVQPHL---EVKIVDPDTGAVVPIGQR- 415 GMTE S ++ + PL +R V Q P++ E ++DPDTG VP Sbjct: 330 GMTECYGPSTGCAWQEAWAELPLEERAVKMARQGVPNVTMSEQTVLDPDTGREVPADGET 389 Query: 416 -GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGG 474 GE +G +VM GY + A T EA+ +G W+HTGDLA + + YV I R KD++I GG Sbjct: 390 LGELALRGNTVMKGYLKNPAATDEALRDG-WLHTGDLAVLHPDRYVEIKDRAKDIIISGG 448 Query: 475 ENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQ--PTEDDIRAFCKG 532 ENI E+EE LY+HP V + VV PD K+GE CA++ KPG++ +E ++ +C+ Sbjct: 449 ENIASLEVEEVLYKHPHVMEAAVVARPDAKWGETPCAFVTLKPGSEGRVSEAEVIGWCRD 508 Query: 533 QIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 +AH+K PR + F + P T TGKIQKF +R++ + Sbjct: 509 HLAHFKTPRTVVF-GALPKTSTGKIQKFVLREQAR 542 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: 716 Number of extensions: 41 Number of successful extensions: 9 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