GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Dechlorosoma suillum PS

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Dsui_2069 Dsui_2069 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II

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



>FitnessBrowser__PS:Dsui_2069
          Length = 529

 Score =  194 bits (494), Expect = 6e-54
 Identities = 168/537 (31%), Positives = 243/537 (45%), Gaps = 45/537 (8%)

Query: 43  PEREALVSVHQG--------RRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEW 94
           P++ AL++   G        R +TYAQL  E +R A ALL +G+  GD V  + +N   +
Sbjct: 19  PDKPALIAWEGGDHDTPAQRRVWTYAQLNAEVNRHAHALLALGVQKGDVVAAFLYNTPAF 78

Query: 95  VLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEW 154
           V   LA A+VG V   IN  YR A  E A              F   D  G  + L  E 
Sbjct: 79  VFSLLAAARVGAVFNPIN--YRLAAQELA--------------FILED--GQAKVLLFEK 120

Query: 155 QGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQ 214
           +G +   ++ A+   + T  WI  ++   A      R  +L+    A  P +      ++
Sbjct: 121 EGCEV--VEKAREHGVPTAHWIYADS-DAAPAFATARLDQLVRHQPATLPPVI-----VE 172

Query: 215 ATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVL 274
             D   + +TSGTTG PKG   THR+ L +   + + M L+  D      PL H   +  
Sbjct: 173 ENDNCILMYTSGTTGRPKGVLHTHRSKLAHNAMMHQAMTLSREDVGLAVAPLNHTAELHT 232

Query: 275 GNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTL 334
             L     GAT V     FD     +  + E+ T     PTM    L HP  A  +LS+L
Sbjct: 233 SFLPRLQLGATQVLLRR-FDAGEAWRLTEVEKVTHFFAAPTMVTLLLHHPDVASRDLSSL 291

Query: 335 RTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVST-VGQV 393
           R     G+     +++   +++    + I YG TE  P          LS   S  +  +
Sbjct: 292 RLVEYGGASMAPHLIREWDKKVGAGLVQI-YGTTEMGPCMSVLYPHEQLSHAGSAGLPSL 350

Query: 394 QPHLEVKIVDPDTGAVVPIG-----QRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448
              L V  V  D     P       + GE   +G  +M GY         A+   GW HT
Sbjct: 351 NHDLLVARVKADGSPSDPADLAAPDEVGEILVRGPCMMGGYLNRPEANARAL-AFGWYHT 409

Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508
           GDL ++D EGY+ I  RI  M+  G EN+YPRE+E+ L  HP V +V VVG PD  +G+ 
Sbjct: 410 GDLGSLDKEGYLWIRDRIDHMINSGAENVYPREVEDALVEHPGVLEVAVVGEPDDTWGQV 469

Query: 509 LCAWIIAKPGTQPTEDDIRAFC--KGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563
           + A ++AKPG   T++ +  F     ++AHYK PR   F+ + P T +GKIQK  +R
Sbjct: 470 VAAHVVAKPGATLTQEALDHFLLEGDRLAHYKRPRRYHFIEALPKTTSGKIQKHLLR 526


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: 702
Number of extensions: 34
Number of successful extensions: 5
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: 529
Length adjustment: 36
Effective length of query: 542
Effective length of database: 493
Effective search space:   267206
Effective search space used:   267206
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