GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Burkholderia phytofirmans PsJN

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate BPHYT_RS20780 BPHYT_RS20780 acyl-CoA dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_26355
         (375 letters)



>FitnessBrowser__BFirm:BPHYT_RS20780
          Length = 381

 Score =  296 bits (757), Expect = 8e-85
 Identities = 159/372 (42%), Positives = 228/372 (61%), Gaps = 1/372 (0%)

Query: 4   TEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTG 63
           ++   QIR+  R+FAQE ++P   E DR+ RFP E   +M ELG FG+ VPE +GG    
Sbjct: 4   SDTHQQIRETTRRFAQEVIRPITEELDRDERFPAEIYTQMGELGLFGITVPEAFGGAGLD 63

Query: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123
             AYA+ +EE++ G  + +    +   VG + +   G D Q+AK++ PL    +  A+ +
Sbjct: 64  VTAYALVMEELSRGYASVADQCGLLELVGTL-LSVHGTDSQRAKYMQPLLRAKLRPAYCI 122

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TE  AG+D S ++T A    D + L+G K +I +   A V  V A TDP+AG+RG+S FI
Sbjct: 123 TEADAGTDVSGIRTTAMRTPDGWELSGAKLWIHNAPVADVAFVLARTDPAAGRRGMSIFI 182

Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVG 243
           V     G S    E K+GQ AS   ++ F+ VK+P    LG+EG G+ I ++ L+ GRVG
Sbjct: 183 VDCALAGVSKGAKEHKMGQRASQVGELHFDRVKLPQDALLGQEGRGFHIMMSVLDKGRVG 242

Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           IAA AVG+A+A  EAA DYA+ R  FG  I E Q + + LADMAT I  AR +VH AA  
Sbjct: 243 IAALAVGIAQAGLEAALDYAQTRKQFGSHIAEFQGIQWMLADMATDIQAARLLVHDAAER 302

Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363
            ++G+ A +  SMAK FA + A K  + A+Q  GG GY+  + +ER+YRD ++ QIYEGT
Sbjct: 303 LEAGERASIACSMAKCFAGDTAVKHSANAVQIFGGSGYIRGYEVERLYRDAKITQIYEGT 362

Query: 364 SDIQRMVISRNL 375
           + IQR +++R+L
Sbjct: 363 NQIQRTIVARDL 374


Lambda     K      H
   0.320    0.134    0.388 

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: 358
Number of extensions: 17
Number of successful extensions: 2
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: 381
Length adjustment: 30
Effective length of query: 345
Effective length of database: 351
Effective search space:   121095
Effective search space used:   121095
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