GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Pedobacter sp. GW460-11-11-14-LB5

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase

Query= reanno::WCS417:GFF2715
         (375 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS22715 CA265_RS22715 acyl-CoA
           dehydrogenase
          Length = 379

 Score =  377 bits (969), Expect = e-109
 Identities = 188/372 (50%), Positives = 264/372 (70%)

Query: 4   NEEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           +EEQL I  AAR FAQ+ LKP   E D   +FP E + ++ ELGF GM+V E++ G    
Sbjct: 6   SEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKYNGSGLD 65

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGAFAL 123
            ++Y + +EE++  D + S ++SV+NS+ C  +  +G++ QKE++LKPLA+G  +GAF L
Sbjct: 66  AISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEKIGAFCL 125

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGISAFI 183
           +EP+AGSDA+S +T A  +GD+Y+LNG K +IT+G  A   +V A T P    +GI+AFI
Sbjct: 126 SEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHKGINAFI 185

Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVG 243
           V     G++V   E+KLG   SDT  ++F DVKVP  NR+GE+G G+K A+  LEGGR+G
Sbjct: 186 VEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTLEGGRIG 245

Query: 244 IASQAVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           IA+QA+G+A+ AFE A  YA+ER+SFGKPI EHQA+AF+LADMATQI  AR +V+ AA L
Sbjct: 246 IAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLVYKAAWL 305

Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363
           +D G P     SMAKL+AS++A  V   A+Q  GGYG++ ++ +ER+ RD ++ QIYEGT
Sbjct: 306 KDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDAKITQIYEGT 365

Query: 364 SDIQRMVISRNL 375
           S+IQ+MVISR +
Sbjct: 366 SEIQKMVISREV 377


Lambda     K      H
   0.319    0.134    0.387 

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: 340
Number of extensions: 15
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: 379
Length adjustment: 30
Effective length of query: 345
Effective length of database: 349
Effective search space:   120405
Effective search space used:   120405
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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