Alignments for a candidate for aacS in Desulfovibrio oxyclinae DSM 11498

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Desulfovibrio oxyclinae DSM 11498

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_018124797.1 B149_RS0108700 long-chain fatty acid--CoA ligase

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



>NCBI__GCF_000375485.1:WP_018124797.1
          Length = 567

 Score =  226 bits (575), Expect = 2e-63
 Identities = 154/552 (27%), Positives = 275/552 (49%), Gaps = 23/552 (4%)

Query: 35  FADMVARQ-PEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAE 93
           + D  AR+ P R+A++   Q    TYA+L+  +   A+ L   GL  GDRV +   N  +
Sbjct: 30  YLDRAARKWPNRKAII--FQNWSCTYAKLKQLSGVFAANLKKQGLKRGDRVALMLPNLPQ 87

Query: 94  WVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPE 153
            ++    T + G V+  +NP Y   E+ +  N  G + L+++           L++L P+
Sbjct: 88  TLIAYWGTLRAGGVVTMVNPLYMETEIVHQFNDSGARFLITLDMLWPK-----LQKLLPD 142

Query: 154 WQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNA-ADPRLAQVAAG 212
              ++      A   +         +  +   +P +    + I         R       
Sbjct: 143 LPTEKYFFTSIADSLRFPLNWLYKFKTAREGKKPAIPFDGKKIQPFKPLVSGRKTFTCDD 202

Query: 213 LQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECM----KLTPADRLCIPV-PLY 267
           +   +   +Q+T GTTG  KG  LTH N+   G  + +C     +L+   ++ + V P +
Sbjct: 203 IDPDEMAMLQYTGGTTGIAKGCILTHFNL---GANVQQCSAMLSELSKDPQIFLGVLPYF 259

Query: 268 HCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFA 327
           H +G+        + GAT++ P   + P  VL+ +   R T   G P+++I+ L     A
Sbjct: 260 HIYGLTTCCTWPISIGATLI-PFPRYVPQDVLKGIHKHRPTVFPGAPSVYISLLQQKNVA 318

Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRV 387
           +F+L +++  +   +P P E ++   E M   +I   +G+TE SPV+  +       ++ 
Sbjct: 319 KFDLKSIQYCVSGSAPMPVEYIEGFYE-MTGAKILEGFGLTEASPVTHLNPIRG--ERKN 375

Query: 388 STVGQVQPHLEVKIVDPDT-GAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446
            ++G   P  + KIVD +  G  +P+G+ GE   +G  VM GY+     T + +   GW+
Sbjct: 376 GSIGLPFPDTDAKIVDMEVAGDPLPVGKMGELVIRGPQVMKGYYNRPDATADVL-RNGWL 434

Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506
            TGD+  MD +GY  IV R KD++I GG NIYPRE++E LY HP +++   VG+P  + G
Sbjct: 435 FTGDIGYMDEDGYFFIVDRKKDLIISGGYNIYPREVDEVLYAHPDIREAVTVGIPHPQRG 494

Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEM 566
           E + A+I+ +PG + +  D+ +FC+ ++A+YKVP+ + F    P T+ GK+ +  +R+E 
Sbjct: 495 EIVKAYIVLEPGVKMSRSDVISFCREKLANYKVPKQVEFRKELPKTMVGKVLRRALREEE 554

Query: 567 KDQLGLEEQKTA 578
            ++    ++K +
Sbjct: 555 IEKAEKRKEKNS 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: 711
Number of extensions: 40
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: 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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