GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas fluorescens GW456-L13

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate PfGW456L13_2433 Phenylacetate degradation enoyl-CoA hydratase PaaB (EC 4.2.1.17)

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2433
          Length = 263

 Score =  146 bits (368), Expect = 5e-40
 Identities = 87/263 (33%), Positives = 141/263 (53%), Gaps = 5/263 (1%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60
           M +E+IL      V L++LNRP  LN+ N  +  E+  AL++   +  +  +++TG  + 
Sbjct: 1   MNFEHILFSIEAGVALLSLNRPDQLNSFNTQMHGEVKEALKQVRQNPDVRVLLLTGEGRG 60

Query: 61  FAAGADIGMMSTYTYMDVYK-GDYITRNWETV----RSIRKPIIAAVAGFALGGGCELAM 115
           F AG D+   +      V   G+ I + +  +    R +  P+I AV G A G G  + +
Sbjct: 61  FCAGQDLSDRNVAPGSAVPDLGESIEKFYNPLIRQLRDLPMPVICAVNGVAAGAGANIPL 120

Query: 116 MCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAG 175
            CD++ AA +A F Q   K+G++P +GGT  LPR V  A+A  L L    + A +AE+ G
Sbjct: 121 ACDLVLAARSASFIQAFCKIGLIPDSGGTWTLPRLVGMARAKALALLGNRLSAEQAEQWG 180

Query: 176 LVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLF 235
           L+ + +  A L DEA+  A  +A  P+  + ++K S+N +   +  E +  E+ L     
Sbjct: 181 LIYQCVEDAELRDEALKLARHLATQPTYGLALIKRSLNASMSNSFDEQLELEKDLQRLAG 240

Query: 236 ATEDQKEGMAAFVEKRKPVFKHR 258
            +ED +EG+ AF+EKR P FK R
Sbjct: 241 RSEDYREGVGAFMEKRTPSFKGR 263


Lambda     K      H
   0.321    0.134    0.380 

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: 139
Number of extensions: 5
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: 258
Length of database: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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 (21.9 bits)
S2: 47 (22.7 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