GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Dinoroseobacter shibae DFL-12

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 3609616 Dshi_2999 AMP-dependent synthetase and ligase (RefSeq)

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



>FitnessBrowser__Dino:3609616
          Length = 506

 Score =  231 bits (590), Expect = 4e-65
 Identities = 165/518 (31%), Positives = 247/518 (47%), Gaps = 46/518 (8%)

Query: 54  GRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINP 113
           G   T+      A R A+ L G+GL PGDR+ +    + E + +     Q G+V + +N 
Sbjct: 26  GDTLTHGGFVELAARYAATLTGLGLAPGDRLALQVEKSPEALAVYAGCVQAGIVFLPLNT 85

Query: 114 AYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTV 173
           AY  AE+ Y +   G KL++   R +                G  P   +A    QL T+
Sbjct: 86  AYTPAEISYFVGNSGAKLVLCDPRAEA---------------GLTPVAAEAGA--QLLTL 128

Query: 174 VWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKG 233
                     AD  G   F +  A   A    +A+    L A       +TSGTTG  KG
Sbjct: 129 A---------ADGTG--SFPDAAATAPATFETVARTEDDLAA-----FLYTSGTTGRSKG 172

Query: 234 ATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLG-NLACFTHGATIVYPNDG 292
           A L+ RN+L+N   + +  + T  D L   +P++H  G+ +G N+     G+ I  P   
Sbjct: 173 AMLSQRNLLSNAEVLVDYWRFTDKDVLLHALPIFHTHGLFVGTNITLLAGGSMIFLPK-- 230

Query: 293 FDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRV 352
           FD   VL  +   R T + GVPT +   L   RF    ++ +R  +   +P   E   R 
Sbjct: 231 FDAEAVLANLP--RATTMMGVPTFYTRLLAEDRFDRDLVAHMRLFVSGSAPLLAET-HRE 287

Query: 353 VEQMNLREITIAYGMTETSPVSCQSSTDTPL--SKRVSTVGQVQPHLEVKIVDPDTGAVV 410
            E      I   YGMTET+      +T  P   ++R  TVG   P +E+K+ DPDTGA +
Sbjct: 288 FEARTGHRILERYGMTETN-----MNTSNPYDGARRAGTVGFPLPGVELKVCDPDTGAEL 342

Query: 411 PIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMV 470
           P G+ G+   +G +V  GYW    KT   +   G+  TGDL  +D +GYV IVGR KD++
Sbjct: 343 PQGEIGQIEVRGPNVFQGYWQMPEKTAAELRADGFFITGDLGLIDDQGYVQIVGRGKDLI 402

Query: 471 IRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFC 530
           I GG NIYP+E+E  L   P V +  V+G P   +GE +   ++ +PG +   + + A  
Sbjct: 403 ISGGYNIYPKEVELALDEAPGVLESAVIGAPHPDFGESVVGILVPQPGARIDTEAVAARL 462

Query: 531 KGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568
            GQ+A +K PR +  + + P    GK+QK  +R++  D
Sbjct: 463 AGQLARFKQPRKLVVMDALPRNTMGKVQKNVLREQFAD 500


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: 696
Number of extensions: 30
Number of successful extensions: 3
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: 506
Length adjustment: 35
Effective length of query: 543
Effective length of database: 471
Effective search space:   255753
Effective search space used:   255753
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: 52 (24.6 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