GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pseudomonas stutzeri RCH2

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate GFF1051 Psest_1084 Acyl-CoA dehydrogenases

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>FitnessBrowser__psRCH2:GFF1051
          Length = 387

 Score =  259 bits (662), Expect = 9e-74
 Identities = 136/366 (37%), Positives = 214/366 (58%)

Query: 10  ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69
           + +  + F    + P A   D+E+ FP +   +  E+G  G+ V E++GG   GYLA+ +
Sbjct: 17  LREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGYLAHVV 76

Query: 70  ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129
           A+EEI+ G  + +     H+++    I + GN +QK R+L  L SG  +GA A++EP AG
Sbjct: 77  AMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAMSEPNAG 136

Query: 130 SDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189
           SD  S+K RA   GD YVLNG K +IT+G +A   +++A TD   G  GI+AFIV  D  
Sbjct: 137 SDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFIVERDWK 196

Query: 190 GYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSV 249
           G+      DKLG   S+TC++ F+DV+VP  N LG E  G K+ ++ L+  RV +A    
Sbjct: 197 GFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLDYERVVLAGGPT 256

Query: 250 GMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKP 309
           G+ ++  +    Y  +R+ FG+ I E Q +  ++ADM TQ+  +R  ++  A   D G+ 
Sbjct: 257 GIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQACDRGET 316

Query: 310 ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRM 369
              +A+   L+ +E A ++   A+Q LGG GY+++FP  R+ RD ++ +I  GTS+I+RM
Sbjct: 317 TRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEIGAGTSEIRRM 376

Query: 370 VISRNL 375
           +I R L
Sbjct: 377 LIGREL 382


Lambda     K      H
   0.319    0.134    0.389 

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: 317
Number of extensions: 14
Number of successful extensions: 1
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: 375
Length of database: 387
Length adjustment: 30
Effective length of query: 345
Effective length of database: 357
Effective search space:   123165
Effective search space used:   123165
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: 50 (23.9 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