Alignments for a candidate for aacS in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Halomonas desiderata SP1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_086509632.1 BZY95_RS09125 AMP-binding protein

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



>NCBI__GCF_002151265.1:WP_086509632.1
          Length = 567

 Score =  699 bits (1804), Expect = 0.0
 Identities = 334/559 (59%), Positives = 422/559 (75%), Gaps = 5/559 (0%)

Query: 15  DSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALL 74
           +S+  G +D PL  +TIG  F   VAR P+ EAL+S+HQG RYT+ +LQ   ++ A A+L
Sbjct: 12  NSYVSGISDTPLKGETIGDCFDATVARFPDGEALLSLHQGLRYTWKELQQAVNQAARAML 71

Query: 75  GMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVS 134
            +G+  GDRVGIWS N AEW + Q ATA++G +LVNINP+YRT E+EYAL + G   L+ 
Sbjct: 72  ALGVKKGDRVGIWSPNCAEWSITQFATAKIGAILVNINPSYRTHELEYALKQSGTSTLIL 131

Query: 135 MARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTE 194
             +FKTSDY+  L ELAPE +   P    AAKLP+LK VV +D +        G+  +  
Sbjct: 132 QGKFKTSDYVATLAELAPELREGAPSTFSAAKLPELKRVVCLDADRAL----TGMFSWQS 187

Query: 195 LIARGN-AADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK 253
           ++A  +  ++  LA V A LQ  +PINIQ+TSGTTG PKGATL+H NILNNGFF+   M 
Sbjct: 188 MLAHADEVSEEHLADVQATLQFDEPINIQYTSGTTGAPKGATLSHHNILNNGFFVARTMG 247

Query: 254 LTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGV 313
            +  DRL IPVPLYHCFGMV+GNL C THGAT++YP DGFDP   L+ V DE+ T L+GV
Sbjct: 248 FSEKDRLVIPVPLYHCFGMVMGNLGCVTHGATMIYPGDGFDPEATLKAVSDEKATALYGV 307

Query: 314 PTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPV 373
           PTMFIAEL+HP FA+++LSTLRTGIMAGS CP EVM++V+++M++ ++TI YGMTETSPV
Sbjct: 308 PTMFIAELEHPDFAQYDLSTLRTGIMAGSICPIEVMRKVIDKMHMEDVTICYGMTETSPV 367

Query: 374 SCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDE 433
           S Q+ TD PL KRV+TVG + PHLEVK+V P+TGAVVP G+ GE CT+GYSVM GYW +E
Sbjct: 368 STQTKTDAPLEKRVTTVGTIHPHLEVKLVSPETGAVVPRGETGELCTRGYSVMLGYWNNE 427

Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493
             T ++ID  GWMHTGDLATMD EGY+ IVGRIKDM+IRGGENIYPREIE+FLY HP + 
Sbjct: 428 EATAKSIDSAGWMHTGDLATMDEEGYIAIVGRIKDMIIRGGENIYPREIEDFLYTHPAIS 487

Query: 494 DVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553
           DVQV+GVPD+KYGEE+ AW+    G +   D+++ FCKG+IAHYK+PRY++FV  FPMTV
Sbjct: 488 DVQVIGVPDEKYGEEVMAWVKLAEGQKLNADELKEFCKGKIAHYKIPRYVKFVDEFPMTV 547

Query: 554 TGKIQKFKIRDEMKDQLGL 572
           TGKIQKFK+R+E   +LGL
Sbjct: 548 TGKIQKFKMREEATHELGL 566


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: 879
Number of extensions: 27
Number of successful extensions: 2
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: 567
Length adjustment: 36
Effective length of query: 542
Effective length of database: 531
Effective search space:   287802
Effective search space used:   287802
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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