Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 7026089 Shewana3_3231 AMP-dependent synthetase and ligase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__ANA3:7026089 Length = 534 Score = 218 bits (555), Expect = 5e-61 Identities = 162/525 (30%), Positives = 258/525 (49%), Gaps = 38/525 (7%) Query: 54 GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112 G+ ++ ++ ++ A+ L L PGDR+ I N ++V+ + GL+LVN N Sbjct: 38 GKTSSFNDIERDSRYFAAYLQNNTNLKPGDRIAIQLPNITQFVIAAYGALRAGLILVNTN 97 Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKT 172 P Y E+ + N G K LV + SD L L ++ P L + P Sbjct: 98 PLYTERELIHQFNDSGAKALVVL-----SDLLPTLAKVV----ATTPIELVISTHP---- 144 Query: 173 VVWIDDEAGQGADEPGL--LRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGF 230 +D Q + GL + F +++ +G A P V A A D +Q+T GTTG Sbjct: 145 ---LDLIDPQVQPKTGLKNVEFCQVLKQG-AELPFSRFVPA---ANDLAALQYTGGTTGL 197 Query: 231 PKGATLTHRNILNNGFFIGECMK--LTPADRLCI-PVPLYHCFGMVLGNLACFTHGATIV 287 KGA LTH N+L N + + +T + + + P+P+YH + ++ + F G V Sbjct: 198 SKGAMLTHGNMLANAAQVKSRIGSVITEGEDIFVAPLPIYHIYAFMVNLVLYFECGGCSV 257 Query: 288 YPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTE 347 + D +++T+ TG G+ T+F+A P F + S L+ I G+ T Sbjct: 258 LIPNPRDISGLIKTLAKYPFTGFAGLNTLFVALCHQPEFKALDFSHLKITISGGTAL-TA 316 Query: 348 VMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTG 407 + +Q I+ YG++ETSPV S + P +++ T+G+ EVK++D + G Sbjct: 317 AAANIWQQTTGNTISEGYGLSETSPVI---SLNAPGYQKIGTIGKPVLGTEVKLLD-ENG 372 Query: 408 AVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIK 467 V G+ GE +G VM GYW + +T + G+ TGD+A ++ EG+ IV R K Sbjct: 373 NEVAQGEAGELAARGPQVMLGYWNNPQETANVMTADGFFKTGDIAILNEEGFHQIVDRKK 432 Query: 468 DMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTED--- 524 DM+I G N+YP E+E L HP + + VVGV D+ GE + A+++ K +Q E Sbjct: 433 DMIIVSGFNVYPNEVENVLASHPNIIECAVVGVKDEHSGEAVKAFVVLKDDSQDHEQMKT 492 Query: 525 DIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQ 569 I FC+ Q+ YK+P+ I F+ P + GKI +R E+K Q Sbjct: 493 AILNFCREQLTAYKLPKLIEFMPQLPKSTVGKI----LRRELKHQ 533 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: 714 Number of extensions: 33 Number of successful extensions: 6 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: 534 Length adjustment: 36 Effective length of query: 542 Effective length of database: 498 Effective search space: 269916 Effective search space used: 269916 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