GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Pseudomonas fluorescens FW300-N1B4

Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate Pf1N1B4_4176 Alcohol dehydrogenase (EC 1.1.1.1)

Query= BRENDA::Q97YM2
         (349 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4176
          Length = 327

 Score = 82.8 bits (203), Expect = 1e-20
 Identities = 91/347 (26%), Positives = 148/347 (42%), Gaps = 28/347 (8%)

Query: 10  KAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILG 69
           +A +L    +PL  E+  IP P   ++LI++   GVCRTDL +  G E  Q   LP + G
Sbjct: 2   RAMVLHAPGQPLQREERAIPIPDAHQLLIKVLACGVCRTDLHLVDG-ELPQAV-LPRVPG 59

Query: 70  HENAGTIVEVG-ELAKVKKGDNV-VVYATWGDLTCRYCREGKFNICKNQIIPGQTTNGGF 127
           HE  G +  VG  +A    G  V V +  W    C +CR G+ N+C      G   +GG+
Sbjct: 60  HEIVGEVTAVGANVAPDWVGKRVGVPWLGWTCGECTFCRSGRENLCDRARFTGCHLDGGY 119

Query: 128 SEYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIGGL 187
           +EY +  +       ++LS  EAAPL  AG     A++ A     K A  + +  G G  
Sbjct: 120 AEYTVADAHFCFPIPDALSAAEAAPLLCAGLIGFRALQMA-----KGARHLGLY-GFGAA 173

Query: 188 AVYTIQILKALMKNITIVGISRSKKHRDFALELGADYV--SEMKDAESLINKLTDG-LGA 244
           A   IQ+ +   + +         + + +A  LGA++   S+      L   L    +GA
Sbjct: 174 AHLAIQVARGRGQQVYAFTRPDDSEGQAYARTLGAEWAGPSDQPPPHPLDASLIFAPVGA 233

Query: 245 SIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSLND 304
            +   L  T            + G +I  G+    +    +   +W ++ + S   +L  
Sbjct: 234 LVPPALEAT-----------VKGGCVICAGIHMSDIPSFPY-RLLWGERSIRS-VANLTR 280

Query: 305 LEDVVRLSE--SGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVITP 349
            +     +E     +   +    LDD N+A  +L  G+V G  V+ P
Sbjct: 281 EDGTAFFAELRHTPVHSDVTCFALDDANQALASLRAGQVKGAIVLIP 327


Lambda     K      H
   0.317    0.136    0.389 

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: 255
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 349
Length of database: 327
Length adjustment: 28
Effective length of query: 321
Effective length of database: 299
Effective search space:    95979
Effective search space used:    95979
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 (21.6 bits)
S2: 49 (23.5 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