Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013257333.1 DEBA_RS02530 AMP-dependent synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000143965.1:WP_013257333.1 Length = 503 Score = 234 bits (598), Expect = 5e-66 Identities = 170/537 (31%), Positives = 255/537 (47%), Gaps = 39/537 (7%) Query: 27 IEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGI 86 +E IGA ++ P+RE + +G RY++AQ+ + ++LA+ L G G+ GDRV + Sbjct: 1 MELNIGALISERARLSPDREGFIG--EGYRYSFAQVNSRVNQLAAYLAGRGIGFGDRVAV 58 Query: 87 WSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGM 146 NN + A A++G + V +N + E+EY L G L+ D+L + Sbjct: 59 LCKNNEHIGVALFAAAKLGAIAVMLNWRLQGPELEYILGDCGATTLLYDV-----DFLPV 113 Query: 147 LRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRL 206 + L AK+P + GQG D + + +A A+P L Sbjct: 114 VDGLR-------------AKIPVKNYI----RRGGQGPDAD----YEQALASQPDAEPTL 152 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266 D I +TSGTTG PKGA LTH N+L I ++ R + PL Sbjct: 153 RG-----GGDDGAVIMYTSGTTGRPKGAVLTHHNLLWQTMAISHTVRWYYDHRFLVVAPL 207 Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326 +H G L + H + Y FDP+ V + + +E+ T + VP M A + Sbjct: 208 FHIGG--LAPVVTNVHEGSTSYFMPEFDPVKVWKVIAEEKITTMMSVPLMVQALYMVAQK 265 Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386 + S+L I G+ + + + M +R + YG TE S S T +R Sbjct: 266 MPVDSSSL-LNITCGAAAVPKSLIQAFLAMGVR-VQQVYGATEVSG-SATFWTHEMDPER 322 Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446 + G+ H +++I DP +G +P GQ GE KG V YWG T EA + GW Sbjct: 323 CDSQGKADFHTQIRIADPASGQTLPTGQVGEIWVKGPIVFKEYWGKPQATAEA-KQDGWY 381 Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 TGD+ MD +GYV +V R+KDM+I GGENIYP E+E + HP V +V VVG D+K+G Sbjct: 382 RTGDMGRMDDKGYVFVVDRLKDMIISGGENIYPAELEAVIASHPAVAEVAVVGRHDEKWG 441 Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 E A++ KP + +I C+ +A +K + +RFV + P GKI K +R Sbjct: 442 EIPVAYLALKPEAKLEAKEIFDLCRKNLAAFKCVKEVRFVEALPRNPVGKILKTTLR 498 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: 630 Number of extensions: 31 Number of successful extensions: 5 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: 503 Length adjustment: 35 Effective length of query: 543 Effective length of database: 468 Effective search space: 254124 Effective search space used: 254124 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 24 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