GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Pseudomonas fluorescens GW456-L13

Align FAA hydrolase family protein (characterized, see rationale)
to candidate PfGW456L13_3411 Fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3411
          Length = 294

 Score =  115 bits (289), Expect = 9e-31
 Identities = 93/277 (33%), Positives = 140/277 (50%), Gaps = 15/277 (5%)

Query: 1   MKLLRYGPVGQEKPGVLD-QSGKIRDLSAYIKDVNGAVLDDASLDKIRKLDLESLPAVEG 59
           M+L R    GQ    +LD QS ++R ++A      G  L       I  L  E LP    
Sbjct: 1   MRLARVEVAGQAFWALLDAQSDRLRRINAPFAQWAG--LGAKLAPDILDLADEWLPL--S 56

Query: 60  SPRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSK 119
           + R+ A +    +   +GLNY  H        PA P+ + K  SA+VG +D++     + 
Sbjct: 57  AARLLAPLEPGSRVFGVGLNYLSHLKRLGSDAPAHPLAYMKPESALVGADDEIDYSPLTT 116

Query: 120 KTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREY--QIERGGTWDKGKGCDT 177
           + D+EVEL  V+G+    +DE  A   + GY V ND+S R+   QI R     + K  D 
Sbjct: 117 QLDYEVELVAVVGR--PLLDEPHASDCLLGYTVGNDISARDAGKQIGRLDLLTQ-KAMDR 173

Query: 178 FGPIGPWLVTRDE--VADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQP 235
             P+GPW+VT DE  VA    L M L V+ +  Q  NT  MIF +  +++YL   +SL+P
Sbjct: 174 ATPVGPWIVTVDELGVAGQPALEMRLSVNDELRQQDNTRQMIFSLDELLNYLDARISLRP 233

Query: 236 GDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLG 272
           GD++ TG+  GVG+       +L++G  +   I+G+G
Sbjct: 234 GDLVFTGSTHGVGL---ESGRFLQSGDRVEAQIEGIG 267


Lambda     K      H
   0.316    0.138    0.419 

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: 247
Number of extensions: 15
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: 281
Length of database: 294
Length adjustment: 26
Effective length of query: 255
Effective length of database: 268
Effective search space:    68340
Effective search space used:    68340
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: 42 (22.0 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