GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pseudomonas stutzeri RCH2

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF2427 Psest_2475 Acyl-CoA dehydrogenases

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



>FitnessBrowser__psRCH2:GFF2427
          Length = 392

 Score =  256 bits (655), Expect = 6e-73
 Identities = 138/372 (37%), Positives = 213/372 (57%), Gaps = 1/372 (0%)

Query: 5   EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64
           ++QT  +D  R+F ++ + P   +W+ +H+ PR     + E G  G+ +PEQ GGC  G 
Sbjct: 16  DDQTLFQDSVRRFLQQEVAPHYEQWEADHQLPRALWHRLGEAGLLGVDLPEQLGGCAAGV 75

Query: 65  LAYAMTLEEIAA-GDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123
               M  EEI+  G G  ++  ++H ++    I   GN  Q+A +L  +A+G +LGA A+
Sbjct: 76  ETCLMICEEISRQGFGGLASGYNIHANIVMPYIHHLGNPAQQACWLPRMAAGEVLGAIAM 135

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TEP AGSD ++++  A+     + LNG K FIT+G  A +VIV A TDP+A  RG+S F+
Sbjct: 136 TEPGAGSDLAAMRASAQKVPGGWKLNGSKVFITNGLLADMVIVCAKTDPNARARGVSLFL 195

Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243
           V T  PG+S  +   K+GQHASDT ++ F+DL VP    LG+ G+G+   +  L   R+G
Sbjct: 196 VDTTLPGFSRGKAIRKIGQHASDTAELFFDDLIVPEDALLGDAGKGFAYLMQELPRERLG 255

Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           +AAQA+G    A +   DY ++R +FG+ I + Q   F LA++   + + R         
Sbjct: 256 VAAQAIGAIDGALQLTLDYVQQRRAFGQRIADFQNTRFTLAEVRAHLEMGRAYFEKCLQR 315

Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363
              G+ +  +A+  KL  SEM  +     LQ  GGYGY  ++P+ R Y D R+  IY GT
Sbjct: 316 YARGEMSSTDAAALKLMLSEMQCRCVDQCLQLFGGYGYTLEYPISRFYVDARIQTIYAGT 375

Query: 364 SDIQRMVISRNL 375
           S+I + VI+R++
Sbjct: 376 SEIMKEVIARDM 387


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: 337
Number of extensions: 14
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: 392
Length adjustment: 30
Effective length of query: 345
Effective length of database: 362
Effective search space:   124890
Effective search space used:   124890
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