GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Streptacidiphilus oryzae TH49

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_037575735.1 BS73_RS23895 acyl-CoA dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1146
         (375 letters)



>NCBI__GCF_000744815.1:WP_037575735.1
          Length = 385

 Score =  305 bits (780), Expect = 2e-87
 Identities = 162/373 (43%), Positives = 236/373 (63%), Gaps = 2/373 (0%)

Query: 4   TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63
           +EE   +RD  R  AE ++ PFAAE D + RFPREA+D +       + VPE++GG    
Sbjct: 13  SEEHEMLRDTVRSLAEAKIAPFAAEVDEQARFPREALDALVANDLHAVHVPEEYGGAGAD 72

Query: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123
            LA  + +EE++    + S I +V N +G +P++  G +E KAK+L PLA G  + ++ L
Sbjct: 73  ALATVLVIEEVSRVCVSSSLIPAV-NKLGSLPVILSGGEELKAKYLAPLARGEAMFSYCL 131

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           +EP AGSDA+ +KTRA  +GD +VLNG K++IT+   +    V AVTDP    +GISAF+
Sbjct: 132 SEPDAGSDAAGMKTRAVRDGDAWVLNGVKRWITNAGESEYYTVMAVTDPEKRSKGISAFV 191

Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243
           V     G S    E KLG   S T ++ F+++++P    +GEEG G+  A+  L+  R+ 
Sbjct: 192 VEKSDEGVSFGAPEKKLGIKGSPTREVYFDNVRIPADRMIGEEGTGFATAMKTLDHTRIT 251

Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           IAAQA+G+A+ A + A+ Y +ER  FGKPI + Q V F LADMA +I  ARQ+ + AAA 
Sbjct: 252 IAAQALGVAQGALDYAKGYVQERKQFGKPIGDFQGVQFMLADMAMKIEAARQLTYAAAAK 311

Query: 304 RDSGQPALV-EASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEG 362
            +     L    + AK +AS++A  V + A+Q LGGYGY  D+PLER+ RD ++ QIYEG
Sbjct: 312 SERVDSDLTFFGAAAKCYASDVAMAVTTDAVQLLGGYGYTRDYPLERMMRDAKITQIYEG 371

Query: 363 TSDIQRMVISRNL 375
           T+ +QR+V++RNL
Sbjct: 372 TNQVQRIVMARNL 384


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: 341
Number of extensions: 20
Number of successful extensions: 3
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: 385
Length adjustment: 30
Effective length of query: 345
Effective length of database: 355
Effective search space:   122475
Effective search space used:   122475
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 24 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