GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Pseudomonas fluorescens FW300-N2C3

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate AO356_19860 AO356_19860 short-chain dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_19860
          Length = 253

 Score =  135 bits (340), Expect = 9e-37
 Identities = 77/245 (31%), Positives = 134/245 (54%), Gaps = 4/245 (1%)

Query: 22  KVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQADVSK 81
           +V ++TG A GIG A   AFA++  ++V++D+     E      R+ G +   ++ +V+ 
Sbjct: 8   QVAVVTGGAAGIGCATAQAFAAEGLKVVVADLDVAGGERTVQSIRDGGGEALFVRCNVTL 67

Query: 82  QQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWYGCKAV 140
           + D+Q +    ++ +GR+D   N AG+ + +  L + T +++     +++ G W   K  
Sbjct: 68  ESDVQHLMDEVIKAYGRLDYAFNNAGIEIEKGKLADGTLDEFDAIMGVNVKGVWLCMKYQ 127

Query: 141 LPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAP 200
           LP ++ QG G+I+N ASV      P    Y  +KH ++GLT++  IEYA K +RVNA+ P
Sbjct: 128 LPLLLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYARKKIRVNAVCP 187

Query: 201 GYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINASCI 260
             I+T +    +   ADP  + + A  +HP  R+G+  E+A   ++L SD A F     +
Sbjct: 188 AVIDTDMFRRAYE--ADP-KKGEFANAMHPVGRIGKVEEIASAVLYLCSDGAAFTTGHSL 244

Query: 261 TIDGG 265
            +DGG
Sbjct: 245 AVDGG 249


Lambda     K      H
   0.321    0.137    0.419 

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: 158
Number of extensions: 8
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: 272
Length of database: 253
Length adjustment: 25
Effective length of query: 247
Effective length of database: 228
Effective search space:    56316
Effective search space used:    56316
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