GapMind for catabolism of small carbon sources

 

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

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate PfGW456L13_3453 Short-chain dehydrogenase/reductase SDR

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3453
          Length = 272

 Score =  136 bits (343), Expect = 4e-37
 Identities = 86/259 (33%), Positives = 130/259 (50%), Gaps = 19/259 (7%)

Query: 17  ERLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIK 76
           +RL  KV ++TGA  GIG A    FA + A +V++D+  E  + VAA   E G + + ++
Sbjct: 6   KRLDGKVCVITGAGSGIGRASALRFAREGATVVVTDLFAESAQAVAA---EIGVNALVLQ 62

Query: 77  ADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDP--------LQMTEEDWHRCFAI 128
            DV ++  L  M    +   GRIDVL N A   V+R+P        +    E +H C  +
Sbjct: 63  VDVGQEDALREMVEQTVRTFGRIDVLFNNA---VYRNPATTRDIDFINFNTELFHNCMRV 119

Query: 129 DLDGAWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEY 188
           ++ G    CK  LP M+ QG GSI+  +ST S       F Y  +K  L    + +   +
Sbjct: 120 NVLGGVLACKYALPHMLAQGSGSILFTSSTSSIAGEISQFSYGASKAALNWYVQTIAATF 179

Query: 189 APKGIRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLA 248
             +GIR N I PG I T     + N      A +    DL    ++G+P ++A  A FLA
Sbjct: 180 GKRGIRCNGILPGVIRTPAMESWAN-----EAMKSAFLDLQNVPQLGEPEDIAAMAAFLA 234

Query: 249 SDEAPFINASCITIDGGRS 267
           SD+A ++N + + +DGG S
Sbjct: 235 SDDAAYVNGTLMRVDGGMS 253


Lambda     K      H
   0.321    0.138    0.424 

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: 139
Number of extensions: 9
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: 272
Length of database: 272
Length adjustment: 25
Effective length of query: 247
Effective length of database: 247
Effective search space:    61009
Effective search space used:    61009
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 (21.9 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