GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pseudomonas putida KT2440

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate PP_3725 PP_3725 putative Acyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF2392
         (383 letters)



>FitnessBrowser__Putida:PP_3725
          Length = 386

 Score =  248 bits (633), Expect = 2e-70
 Identities = 149/384 (38%), Positives = 220/384 (57%), Gaps = 13/384 (3%)

Query: 3   DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMG----ELGLLGMVVPE 58
           + +L+++Q M+ +  R F  +E+ PH +A ++A  +   L AQ+       G     +PE
Sbjct: 2   NFQLTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMPE 61

Query: 59  EWGGSYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASG 118
           E GG  +DY++ AL   E+S    A    ++  + +     L      Q +++L     G
Sbjct: 62  EVGGGGLDYLSQALIERELSKVSWALHVFVARPSKI-----LMACKDEQINDYLLPCVQG 116

Query: 119 RAIGCFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDP--E 176
             + CFALTEP AGS+A+ ++TRA      +V+NGSK F S+A  +  AIVFAVTD    
Sbjct: 117 EKVDCFALTEPGAGSDANAIKTRAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDTYEH 176

Query: 177 LGKK--GLSAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLA 234
            G+K   ++A LV   TPG  + R    +  R   T  +   DCR+P + +LGE GKG  
Sbjct: 177 NGRKRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGKGWE 236

Query: 235 IALSNLEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLN 294
           +A + L  GR+ + A  +G A+ A + +L +A +R QFG+ I  +Q ++  LADM TQ+ 
Sbjct: 237 VANAWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMATQIR 296

Query: 295 AARLLILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYY 354
           AA +L LH A     G     EA  AKLFASE+  KV  +AVQI GG G +++ PVER +
Sbjct: 297 AAEMLTLHTAWKMDQGNMTDGEAGMAKLFASEVLGKVADEAVQIFGGMGLMDEGPVERIW 356

Query: 355 RDARITQIYEGSSEIQRLLIAREL 378
           R+ARI +I+EG+SEIQR +IAREL
Sbjct: 357 RNARIERIWEGTSEIQRHIIAREL 380


Lambda     K      H
   0.318    0.133    0.390 

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: 343
Number of extensions: 18
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: 383
Length of database: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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