GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Escherichia coli BW25113

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate 15814 b1695 putative oxidoreductase (VIMSS)

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



>FitnessBrowser__Keio:15814
          Length = 383

 Score =  167 bits (424), Expect = 3e-46
 Identities = 116/350 (33%), Positives = 184/350 (52%), Gaps = 10/350 (2%)

Query: 30  DREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMALEEIAAGDGACSTIMSVHN 89
           D+   +P+E +  +A+ G   + VPE++GG    Y+   +AL E++     C     +  
Sbjct: 33  DQNGTYPREFMRALADNGISMLGVPEEFGGIPADYVTQMLALMEVSK----CGAPAFLIT 88

Query: 90  SVGCVPILK-FGNDDQKERFLKP-LASGAMLGAFALTEPQAGSDASSLKTR-ARLNGDHY 146
           +  C+  ++ FG+ +Q  +  +  L +G    A ALTEP AGSD +S  T   R NG  Y
Sbjct: 89  NGQCIHSMRRFGSAEQLRKTAESTLETGDPAYALALTEPGAGSDNNSATTTYTRKNGKVY 148

Query: 147 VLNGCKQFITSGQNAGVVIVFAVT-DPSAGKRGISAFIVPTDSPGYKVARVEDKLGQHAS 205
           + NG K FIT  +    ++V A    P   K+  + + V +  PG K+  +  K+G H  
Sbjct: 149 I-NGQKTFITGAKEYPYMLVLARDPQPKDPKKAFTLWWVDSSKPGIKINPLH-KIGWHML 206

Query: 206 DTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSVGMARAAFEAARDYARE 265
            TC++  ++V+V  ++ +GEEG G+   + N E  R+  A++S G A  AFE A  YA +
Sbjct: 207 STCEVYLDNVEVEESDMVGEEGMGFLNVMYNFEMERLINAARSTGFAECAFEDAARYANQ 266

Query: 266 RESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPALVEASMAKLFASEMA 325
           R +FGKPI  +Q +  +LA MA +I   R MV   A   D  +     A++AKL+ +  A
Sbjct: 267 RIAFGKPIGHNQMIQEKLALMAIKIDNMRNMVLKVAWQADQHQSLRTSAALAKLYCARTA 326

Query: 326 EKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVISRNL 375
            +V   A+Q +GG GY  +  + R +RDVR  +I  GT +I   V  R +
Sbjct: 327 MEVIDDAIQIMGGLGYTDEARVSRFWRDVRCERIGGGTDEIMIYVAGRQI 376


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: 296
Number of extensions: 11
Number of successful extensions: 4
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: 383
Length adjustment: 30
Effective length of query: 345
Effective length of database: 353
Effective search space:   121785
Effective search space used:   121785
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