GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Paraburkholderia bryophila 376MFSha3.1

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate H281DRAFT_06133 H281DRAFT_06133 hypothetical protein

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



>FitnessBrowser__Burk376:H281DRAFT_06133
          Length = 377

 Score =  479 bits (1233), Expect = e-140
 Identities = 239/373 (64%), Positives = 295/373 (79%)

Query: 1   MLPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60
           M+ T E   I ++ R FA ERL P A++WD+ H FP  A+ E+ ELG  GM+V E+WGG 
Sbjct: 1   MILTQEHEMIRESIRTFAAERLAPHASDWDKNHTFPAAALKELGELGALGMVVEEKWGGA 60

Query: 61  DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGA 120
              Y++  +ALEEIAAGDGA STI+SV NS+ C    K+G++ QKE++L+PLA G  LG 
Sbjct: 61  GLDYMSLVLALEEIAAGDGATSTIVSVQNSLACGITSKYGSEKQKEQWLRPLAQGQKLGC 120

Query: 121 FALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180
           F LTEP  GSDAS+L+T AR +GD +VLNG KQFIT+G+ A V IVFAVTD SA K+GIS
Sbjct: 121 FCLTEPHTGSDASALRTTARRDGDEWVLNGVKQFITTGKYADVAIVFAVTDKSADKKGIS 180

Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGG 240
            F++PT +PGY VAR+E+K+GQHASDT QI+FED +V ++  +G+EG+GY+IAL+NLE G
Sbjct: 181 CFLIPTATPGYVVARLEEKMGQHASDTAQIIFEDCRVHLSAMMGQEGDGYRIALSNLEAG 240

Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300
           R+GIA+Q+VGMARAAFEAA  YA+ERE+FGK +IEHQAV FRLADMATQI  AR MV  A
Sbjct: 241 RIGIAAQAVGMARAAFEAAVKYAKERETFGKLLIEHQAVTFRLADMATQIEAARMMVWRA 300

Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360
           A L+D+GK  L EASMAK+FASEMAEKVCS A+Q  GG GY+SDFP+ERIYRDVRVCQIY
Sbjct: 301 ATLKDAGKACLTEASMAKMFASEMAEKVCSDAIQIHGGCGYVSDFPVERIYRDVRVCQIY 360

Query: 361 EGTSDIQRMVISR 373
           EG +DIQRMVI R
Sbjct: 361 EGANDIQRMVIGR 373


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: 419
Number of extensions: 13
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: 377
Length adjustment: 30
Effective length of query: 345
Effective length of database: 347
Effective search space:   119715
Effective search space used:   119715
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