GapMind for catabolism of small carbon sources

 

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

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 3606823 Dshi_0253 AMP-dependent synthetase and ligase (RefSeq)

Query= metacyc::MONOMER-20125
         (556 letters)



>FitnessBrowser__Dino:3606823
          Length = 519

 Score =  163 bits (412), Expect = 2e-44
 Identities = 141/515 (27%), Positives = 225/515 (43%), Gaps = 53/515 (10%)

Query: 41  TWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDA 100
           T +Q   R    A  + + GI  G VV+++APN+P           AGA +  +N     
Sbjct: 45  TGAQLEGRIRACAGGLRARGIGPGDVVAIMAPNMPDYATAFHGAAFAGATVTTLNPTYTT 104

Query: 101 RTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEF 160
              +  L  S ++++       DL  EA+    +   V   V M         +  G   
Sbjct: 105 EEAAHQLRDSGAQMLVTVPAFADLAAEAV----QGTGVTETVMMGTTGPGSLEALFGPPL 160

Query: 161 FCSYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW 220
                  + R              D ++L Y+SGTT  PKGV+  HR + +    +    
Sbjct: 161 AAQVAVDLAR--------------DIVVLPYSSGTTGLPKGVMLSHRNLVVNVDQTAEII 206

Query: 221 GVPKQPVYLWTLPMFHANGWSYPWGM-AAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGA 279
           G+  Q V +  LP FH  G +       + G   + + +FD E    + + H    +  A
Sbjct: 207 GITVQDVTVGFLPFFHIYGMTVLMNCYLSRGAAVVTMPRFDLEQFLSLCQTHRPRQLYIA 266

Query: 280 PVVLNMLSNAPGSEPLKTT-VQIMTAGAPPPSAVLFRT--ESLGFAVSHGYGLTETAGLV 336
           P V   L+  P  +    + V+ + +GA P    +       LG  +  GYG+TE + + 
Sbjct: 267 PPVALALAKHPMVDDYDLSGVEFILSGAAPLGGDVAEAVGRRLGVEMVQGYGMTEMSPV- 325

Query: 337 VSCAWKKEWNHLPATERARLKSRQGVG-TVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRG 395
               +     ++P +          VG T    +  +VDP TG     + +  GEV +RG
Sbjct: 326 --SHFTPPGQNVPGS----------VGPTAPSAESRIVDPETG-----EDAAEGEVWVRG 368

Query: 396 GSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEV 455
             +M GYL  P+ TA+++T DGW  TGD+G     G L I DR K++I   G  ++  E+
Sbjct: 369 PQIMQGYLNRPDATAETVTRDGWLKTGDLGRFDEAGNLFITDRVKELIKVSGFQVAPAEL 428

Query: 456 ESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKP--TEKEIVEYCRSKLPRYM 513
           E++L +HP I +AAV+  PD+  GE P AFV     +   P  +E  ++ +    L  Y 
Sbjct: 429 EAVLLTHPAITDAAVIGVPDDSAGERPMAFV-----VRSDPDLSEGAVIAHAAEHLAHYK 483

Query: 514 VPKTVVFKEELPKTSTGKVQKFILR-----DMARG 543
               V F E +PK+++GK+ + +LR     DMA G
Sbjct: 484 RIARVAFVEAVPKSASGKILRRLLRAKVGEDMATG 518


Lambda     K      H
   0.319    0.135    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: 692
Number of extensions: 37
Number of successful extensions: 4
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: 556
Length of database: 519
Length adjustment: 35
Effective length of query: 521
Effective length of database: 484
Effective search space:   252164
Effective search space used:   252164
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 (21.7 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