Alignments for a candidate for aacS in Acidovorax caeni R-24608

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Acidovorax caeni R-24608

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_139235370.1 BN2503_RS07000 AMP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_001298675.1:WP_139235370.1
          Length = 557

 Score =  933 bits (2412), Expect = 0.0
 Identities = 464/569 (81%), Positives = 493/569 (86%), Gaps = 13/569 (2%)

Query: 10  SAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRL 69
           +APL  S A+G TD PLIEQTIG FF  M ARQ  REALV  HQG RYTYA+L TE  RL
Sbjct: 2   TAPLTLSQAQGRTDTPLIEQTIGQFFDAMAARQGAREALVCRHQGLRYTYAELHTEVRRL 61

Query: 70  ASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGC 129
           ASALLG+GL  GDR+GIWSHNNAEWVLMQ ATAQVGLVLVNINPAYRT+EVEYALNKVGC
Sbjct: 62  ASALLGLGLQKGDRIGIWSHNNAEWVLMQFATAQVGLVLVNINPAYRTSEVEYALNKVGC 121

Query: 130 KLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGL 189
           K LV+MARFKTSDY GML++L              A+LPQL+ + WID   GQG D  G+
Sbjct: 122 KALVTMARFKTSDYAGMLQQLG------------RARLPQLQHIFWIDTP-GQGEDIAGM 168

Query: 190 LRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIG 249
            RF+ L+A G+A D R+  VAA L  TDPINIQFTSGTTGFPKGATLTHRNILNNGFFIG
Sbjct: 169 QRFSALMASGDAQDARIDVVAATLANTDPINIQFTSGTTGFPKGATLTHRNILNNGFFIG 228

Query: 250 ECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTG 309
           ECM+LTP DRLCIPVPLYHCFGMVLGNLAC THGATIVYPNDGFDPL VL+TVQ ERCTG
Sbjct: 229 ECMQLTPEDRLCIPVPLYHCFGMVLGNLACVTHGATIVYPNDGFDPLLVLETVQAERCTG 288

Query: 310 LHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTE 369
           LHGVPTMFIAELDHPRFAEF+LSTLRTGIMAGSPCP EVMKRVV  M+L +ITIAYGMTE
Sbjct: 289 LHGVPTMFIAELDHPRFAEFDLSTLRTGIMAGSPCPIEVMKRVVSDMHLSQITIAYGMTE 348

Query: 370 TSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGY 429
           TSPVSCQSST TPL KRV+TVGQVQPHLEVKIV P+TGAVVP+GQ GE CT+GYSVMHGY
Sbjct: 349 TSPVSCQSSTATPLEKRVATVGQVQPHLEVKIVHPETGAVVPVGQSGELCTRGYSVMHGY 408

Query: 430 WGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH 489
           WGD  KTREAID  GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH
Sbjct: 409 WGDAEKTREAIDAEGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH 468

Query: 490 PQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSF 549
           PQVQDVQVVGVPD +YGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFV  F
Sbjct: 469 PQVQDVQVVGVPDARYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVPGF 528

Query: 550 PMTVTGKIQKFKIRDEMKDQLGLEEQKTA 578
           PMTVTGKIQKFKIRDEMK+ LGL E+KTA
Sbjct: 529 PMTVTGKIQKFKIRDEMKNSLGLTEEKTA 557


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: 1036
Number of extensions: 28
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: 557
Length adjustment: 36
Effective length of query: 542
Effective length of database: 521
Effective search space:   282382
Effective search space used:   282382
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources