GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas fluorescens FW300-N2E3

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AO353_07245 AO353_07245 alcohol dehydrogenase

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07245
          Length = 382

 Score =  241 bits (616), Expect = 2e-68
 Identities = 143/384 (37%), Positives = 217/384 (56%), Gaps = 5/384 (1%)

Query: 1   MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60
           M+ S+F I    + GA ++      +        LIVTD  L K   +G V+ AL +   
Sbjct: 1   MSISSFKIAHKLLTGAGAIEQLAAELTRLDVDNPLIVTDAALVK---SGTVELALAQLGG 57

Query: 61  FSV-IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRD 119
            +  I+D   P+P    V   +++ +E   D +I LGGGS  D AK +A  A   G + D
Sbjct: 58  RTYEIFDRVLPDPEIAIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALED 117

Query: 120 YEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSL 179
             G+D+  +   P+IAI TTAGT SE+T   I++D    +K  I+  ++ P +++    +
Sbjct: 118 LFGIDQVPRKGPPLIAIPTTAGTGSEVTNVAILSDRVAQLKKGIISDYLLPDVALVSPQM 177

Query: 180 MIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKA 239
            +  P+S+TAA+G+DAL HA+E+Y+S+ A+PITDA A+ A+ +I + LP A  + SN +A
Sbjct: 178 TLTCPRSVTAASGVDALVHAVESYLSLNASPITDALAIGAIKLIIKALPKAYTNPSNLQA 237

Query: 240 REAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAAR 299
           RE MA A  +AGMAF NA +G VHA+A+ LGG +N+ HGV NA+LLP+V  +N      R
Sbjct: 238 REDMATASLMAGMAFGNAGVGAVHALAYPLGGRFNVTHGVSNALLLPYVMAWNKMACIER 297

Query: 300 LRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK 359
           ++D A A+GV     +  E A+  + A+  L   V+IP GL  L + E+    +A  A  
Sbjct: 298 MQDIAEALGVKTAQLSAEEAADKAVEAMARLCAAVEIPQGLHSLGIPEDAIPAMAVEAAG 357

Query: 360 -DACGFTNPIQATHEEIVAIYRAA 382
            +     NP + +  +I  IYRAA
Sbjct: 358 IERLMRNNPRKLSTADIEKIYRAA 381


Lambda     K      H
   0.318    0.131    0.373 

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: 357
Number of extensions: 15
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: 383
Length of database: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
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 (21.8 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