Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate CCNA_01017 CCNA_01017 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Caulo:CCNA_01017 Length = 530 Score = 236 bits (602), Expect = 2e-66 Identities = 165/525 (31%), Positives = 253/525 (48%), Gaps = 39/525 (7%) Query: 46 EALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVG 105 +A+ +GR T+AQL +++A+ALL GL+ GDR+ N+ + + L A+ G Sbjct: 26 DAVAFSFEGRETTFAQLDRHTNQVANALLAAGLSTGDRIAYVGKNSDHYFELLLGAAKAG 85 Query: 106 LVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAA 165 +V I E+ Y + KL+ ++G REL GH+ A Sbjct: 86 VVTTPIGWRLAAPEIAYIVGDSEAKLV----------FVG--RELI--------GHVDAV 125 Query: 166 KLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTS 225 V I EA D + + + + P +Q +D +TS Sbjct: 126 AAELTHRPVVIAMEAEGAGDYQTFEGWRDAASDVDPHKP--------IQISDIAIQLYTS 177 Query: 226 GTTGFPKGATLTHRNILNNGFFIG----ECMKLTPADRLCIPVPLYHCFGMVLGNLACFT 281 GTTG PKGA LTH N+L E + P+D + +P+ H G G L Sbjct: 178 GTTGRPKGAMLTHHNLLGMRREAAKNPLEWNQWGPSDVSLVAMPVAHIGGTGWG-LVGLI 236 Query: 282 HGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAG 341 +GA V + FDP VL ++ +R + + VP + PR E + S L + Sbjct: 237 NGAKGVVARE-FDPTKVLDFIEKDRISKMFMVPAALQIVVRLPRAREVDYSRLTHILYGA 295 Query: 342 SPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQ---SSTDTPLSKRVSTVGQVQPHLE 398 +P P ++++ +E + YGMTET+ D +KR+ G P +E Sbjct: 296 APIPLDLLRECMEVFGCGFVQ-QYGMTETTGTVVYLPPEDHDPAGNKRMRAAGLPMPGVE 354 Query: 399 VKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEG 458 +KI+D + G +P GE + + M GYW + T + +D GW+ TGD +D +G Sbjct: 355 LKIID-EAGKSLPPNTVGEVAVRSSANMAGYWKLDEATAKTMDADGWLRTGDAGYLDEDG 413 Query: 459 YVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPG 518 Y+ I R+KDM+I GGENIYP E+E +Y HP V +V V+GVPD K+GE + A + KPG Sbjct: 414 YLFIHDRVKDMIISGGENIYPAEVESAVYGHPHVAEVAVIGVPDDKWGEAVKAVVAPKPG 473 Query: 519 TQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 P DDI AF + +IAH+K P+ + F+ + P +GKI + ++R Sbjct: 474 VTPDADDIIAFARTRIAHFKAPKSVDFIPALPRNASGKILRRELR 518 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: 709 Number of extensions: 30 Number of successful extensions: 5 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: 530 Length adjustment: 36 Effective length of query: 542 Effective length of database: 494 Effective search space: 267748 Effective search space used: 267748 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