GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Pseudomonas fluorescens GW456-L13

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PfGW456L13_3453 Short-chain dehydrogenase/reductase SDR

Query= metacyc::MONOMER-16231
         (254 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3453
          Length = 272

 Score =  143 bits (360), Expect = 4e-39
 Identities = 90/254 (35%), Positives = 139/254 (54%), Gaps = 11/254 (4%)

Query: 1   MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60
           +K L+GK  ++TGA +GIGRA+A+  A+ GA V +    ++  AQ+  AEI   G  A+ 
Sbjct: 5   LKRLDGKVCVITGAGSGIGRASALRFAREGATVVVTDLFAES-AQAVAAEI---GVNALV 60

Query: 61  VKGDVADPQTAQDFVAKAVETFGKVDVMVSNA-----GICPFHAFLDMPVDVVERTFKVN 115
           ++ DV      ++ V + V TFG++DV+ +NA            F++   ++     +VN
Sbjct: 61  LQVDVGQEDALREMVEQTVRTFGRIDVLFNNAVYRNPATTRDIDFINFNTELFHNCMRVN 120

Query: 116 LHGAYFMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIAL 175
           + G     + A   M+ QG  GSI+  SS S++ G   Q  Y  +KA ++  +Q+ A   
Sbjct: 121 VLGGVLACKYALPHMLAQG-SGSILFTSSTSSIAGEISQFSYGASKAALNWYVQTIAATF 179

Query: 176 GKHGIRCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMA 235
           GK GIRCN +LPG I T   +    +  K  +++ +  + +LG PED+A    FLASD A
Sbjct: 180 GKRGIRCNGILPGVIRTPAMESWANEAMKSAFLDLQN-VPQLGEPEDIAAMAAFLASDDA 238

Query: 236 AYVTGAALLVDGGM 249
           AYV G  + VDGGM
Sbjct: 239 AYVNGTLMRVDGGM 252


Lambda     K      H
   0.318    0.133    0.379 

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: 135
Number of extensions: 4
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: 254
Length of database: 272
Length adjustment: 25
Effective length of query: 229
Effective length of database: 247
Effective search space:    56563
Effective search space used:    56563
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: 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