Alignments for a candidate for aacS in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Shewanella loihica PV-4

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 5210149 Shew_2593 acyl-CoA synthetase (RefSeq)

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



>FitnessBrowser__PV4:5210149
          Length = 574

 Score =  643 bits (1658), Expect = 0.0
 Identities = 317/566 (56%), Positives = 400/566 (70%), Gaps = 7/566 (1%)

Query: 6   AATNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTE 65
           A  N  PL  S   G T  PLIEQTIG +   M A  P++ A+V  HQG R++Y + Q+ 
Sbjct: 8   ATENQFPLQLSQFDGDTSTPLIEQTIGDYLDQMAASHPDQLAIVMHHQGIRWSYQEYQSH 67

Query: 66  AHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALN 125
              LA+ LL +G+ PGDRVGIWS NN EW L Q ATA++G ++V INPAYR  E++YALN
Sbjct: 68  IDELAAGLLAIGIKPGDRVGIWSPNNIEWCLTQFATAKIGAIMVCINPAYRPEELQYALN 127

Query: 126 KVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGAD 185
            VGC+ ++   +FK+S YL ML ELAPE +   PG L++A LP L+ V+ + DEA     
Sbjct: 128 NVGCRAIICAEKFKSSHYLSMLYELAPELKQCLPGQLESANLPSLEFVIRMGDEAS---- 183

Query: 186 EPGLLRFTELIARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN 244
            PG+L F  L      +D + L   AA L   D INIQFTSGTTG PKGATL+H NILNN
Sbjct: 184 -PGMLNFNHLKRPLTESDRKALKDTAAQLSPFDAINIQFTSGTTGSPKGATLSHHNILNN 242

Query: 245 GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQD 304
           G  + + M+L   DRLCIPVPLYHCFGMVLGNL+C + GA+ +YP+D FDPLT L+ V+ 
Sbjct: 243 GLLVAKAMRLGLEDRLCIPVPLYHCFGMVLGNLSCISVGASAIYPSDSFDPLTTLEVVEA 302

Query: 305 ERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIA 364
           ERCT LHGVPTMFIA+L+HP F  F+LS+LRTG+MAG+ CP EVM+RV + M ++E+ I 
Sbjct: 303 ERCTALHGVPTMFIAQLEHPEFKRFDLSSLRTGVMAGATCPEEVMRRVQDLMYMKEVLIG 362

Query: 365 YGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYS 424
           YG TE SP++  +   + L KRV+TVG+   H +VKIVD + G V+P+GQ GE C++GY 
Sbjct: 363 YGQTECSPINNMTEIGSSLEKRVTTVGRALAHTQVKIVD-EFGEVLPVGQPGEVCSRGYC 421

Query: 425 VMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEE 484
           VM  YW D  KT   ID  GW+H+GDL  MD+EGYV IVGRIKDM+IRGGENIYPREIEE
Sbjct: 422 VMQFYWNDAEKTAATIDSEGWLHSGDLGEMDSEGYVKIVGRIKDMIIRGGENIYPREIEE 481

Query: 485 FLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIR 544
            LY HP VQD  + GV  +KYGEE+CAWI  +PG   TE++IR F   + A++KVPRYI+
Sbjct: 482 KLYTHPDVQDAAIFGVKSEKYGEEVCAWIKVQPGASVTEEEIRHFLTEKFAYFKVPRYIK 541

Query: 545 FVTSFPMTVTGKIQKFKIRDEMKDQL 570
           FV  +PMTVTGKIQKFK+R+ M  +L
Sbjct: 542 FVEQYPMTVTGKIQKFKMREMMYQEL 567


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: 856
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: 574
Length adjustment: 36
Effective length of query: 542
Effective length of database: 538
Effective search space:   291596
Effective search space used:   291596
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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, or view the source code.

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