Alignments for a candidate for aacS in Thermophagus xiamenensis HS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Thermophagus xiamenensis HS1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_010527149.1 GQW_RS0106210 AMP-binding protein

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



>NCBI__GCF_000220155.1:WP_010527149.1
          Length = 549

 Score =  513 bits (1321), Expect = e-150
 Identities = 256/539 (47%), Positives = 355/539 (65%), Gaps = 7/539 (1%)

Query: 27  IEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGI 86
           IE T+G        + P+ + +V   +G R++Y++       LA  L+ +G+  GD+VGI
Sbjct: 8   IEDTLGQLLEQWADKLPDHDFMVYPDRGLRFSYSEFNQRVDNLAKGLMAIGVQKGDKVGI 67

Query: 87  WSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGM 146
           W++N  +W  +  ATA++G VLV IN  Y+ AE+E+ +       L  +  ++ SDY+ M
Sbjct: 68  WANNVPDWTTLMFATAKIGAVLVTINTNYKLAELEFLIKNADLNTLCLIDGYRDSDYVDM 127

Query: 147 LRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADP-R 205
           + +L PE +    G L++ K PQL+ VV++  +  +G     +    EL+  G   D   
Sbjct: 128 IFQLVPELKTAPRGKLKSKKFPQLRNVVFLGPQKHRG-----MYNTPELLLLGTQVDDME 182

Query: 206 LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVP 265
           L +  + +   D +N+Q+TSGTTGFPKG  LTH NI+NNG  IG+ M+ TP DRL + VP
Sbjct: 183 LLKRKSEVSCHDVVNMQYTSGTTGFPKGVMLTHFNIVNNGKGIGDNMQYTPDDRLLLCVP 242

Query: 266 LYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPR 325
           L+HCFG VLG  A  THG ++V   D FDPL VL  VQ E+CT ++GVPTMFIAE++HP 
Sbjct: 243 LFHCFGCVLGVCAVITHGVSMVITED-FDPLRVLAAVQKEKCTSIYGVPTMFIAEMNHPM 301

Query: 326 FAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK 385
           F  F+LS+LRTGIMAGS CP E MK+V+ +MN R+I I YG+TE SP    +  D     
Sbjct: 302 FDMFDLSSLRTGIMAGSLCPIETMKQVMTKMNCRDIIIVYGLTEASPGMTTTHIDDSPEI 361

Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445
           R +TVG+  P +EVKI DPDTG  +   Q+GE C +GY+VM GY+ D   TREAIDE GW
Sbjct: 362 RATTVGKELPGVEVKIFDPDTGEELGPNQQGEICCRGYNVMKGYYNDPQATREAIDEDGW 421

Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505
           +H+GDLA    +GY  I GRIKDM+IRGGENIYPREIE FLY  P+++ V+VVG+PD+KY
Sbjct: 422 LHSGDLAVKTEDGYYKITGRIKDMIIRGGENIYPREIENFLYNMPEIEMVEVVGLPDEKY 481

Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           GE + A+I  K G   TE+++R FC+G+IA YK+P+++ FV  FP T +GKIQK+K+R+
Sbjct: 482 GEIVGAFIKLKEGAFLTEEEVRDFCRGKIARYKIPKHVFFVDDFPKTASGKIQKYKLRE 540


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: 787
Number of extensions: 38
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: 549
Length adjustment: 36
Effective length of query: 542
Effective length of database: 513
Effective search space:   278046
Effective search space used:   278046
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