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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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:

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:

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:

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:

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