GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Paraburkholderia bryophila 376MFSha3.1

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate H281DRAFT_03803 H281DRAFT_03803 alcohol dehydrogenase

Query= SwissProt::P0A9S1
         (382 letters)



>FitnessBrowser__Burk376:H281DRAFT_03803
          Length = 387

 Score =  192 bits (489), Expect = 1e-53
 Identities = 116/356 (32%), Positives = 196/356 (55%), Gaps = 7/356 (1%)

Query: 31  QKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITVVKEGLGVFQNSGADY 90
           ++  +VTD  L + G++      + A G    + D V+ +P   +V E     +++GA+ 
Sbjct: 35  ERLCVVTDGFLHKSGLLDPALADLAAHGWNATVIDDVIADPPEHIVLEATARARSAGAEI 94

Query: 91  LIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTIN 150
           ++ +GGGS  D  K I  ++   +   +  + G++      +P++ +PTTAGT +EVT  
Sbjct: 95  VLGLGGGSSMDVAKLIAALAPQQQ-QQLSEMYGVNKVTVQRLPLVQMPTTAGTGSEVTAV 153

Query: 151 YVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGVDALTHAIEGYITRGAW 210
            ++T  E R+  V V P  I  +A +DA++  G+P A  AATG+DA+ HAIE Y +    
Sbjct: 154 SIVTVGEARKMGV-VAPQLIADLAILDAELTLGLPVAATAATGIDAMVHAIEAYTSAHLK 212

Query: 211 -ALTDALHIKAIEIIAGALRGSV--AGDKDAGEEMALGQYVAGMGFSNVGLGLVHGMAHP 267
             ++D L IKA+E+++  L  +     ++DA E M LG   AG  F+N  +  VH +A+P
Sbjct: 213 NPVSDMLAIKALELLSRNLLPACEDGNNRDAREAMLLGATFAGQAFANSPVAAVHALAYP 272

Query: 268 LGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVEGMSLEEARNAAVEAVF 327
           +G  Y+ PHG++NA++LPHV+R+NAD   + Y ++A V+     G S  +   A +E + 
Sbjct: 273 IGGIYHVPHGLSNALVLPHVLRFNADSAADLYAELADVVVPGTTG-SARDKTQALIENLE 331

Query: 328 ALNRDVGIPPHLRDVGVRKEDIPALA-QAALDDVCTGGNPREATLEDIVELYHTAW 382
            +  +  IP  LRDVG+ +E +  +A  A L       NPR  +  D + +Y+ A+
Sbjct: 332 RMIAETAIPARLRDVGIEREGLGRMASDAMLQTRLLVNNPRPVSEADALAIYNAAF 387


Lambda     K      H
   0.319    0.136    0.404 

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: 389
Number of extensions: 19
Number of successful extensions: 5
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: 382
Length of database: 387
Length adjustment: 30
Effective length of query: 352
Effective length of database: 357
Effective search space:   125664
Effective search space used:   125664
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 (21.7 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