GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Dyella japonica UNC79MFTsu3.2

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_1687 N515DRAFT_1687 ABC-2 type transport system ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1687
          Length = 324

 Score =  122 bits (307), Expect = 1e-32
 Identities = 77/223 (34%), Positives = 122/223 (54%), Gaps = 12/223 (5%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           I+   LTKRFG+  AVD + L++        +GP+G GKSTT+RML GL TP+ G+I   
Sbjct: 12  IRARGLTKRFGNFTAVDHVDLEVPARHVYGFLGPNGSGKSTTIRMLCGLLTPSEGEI--- 68

Query: 64  GDHMNYRVPQNRD-----IAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEV 118
            D +   VP+  +     I  + Q ++L+  + VR+N++F +   +G   A   +R+ E+
Sbjct: 69  -DVLGLSVPREAEALRKRIGYMTQKFSLFDDLGVRENLQF-MAAVQGVPKARTRQRIDEL 126

Query: 119 AETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 178
            E     D   +    +SGGQ+QR+AL  A++ DPE+  +DEP S +D + R +   +L 
Sbjct: 127 IEQYHFGDRQKQLAGTMSGGQKQRLALACAVIHDPELLFLDEPTSAVDPESRRDFWEKLF 186

Query: 179 NLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFE 221
            L D  A TT+ V+ +  +      R+AV+D G L    +P E
Sbjct: 187 ELTD--AGTTMLVSTHLMDEAERCHRLAVLDRGVLVADGTPAE 227


Lambda     K      H
   0.317    0.135    0.386 

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: 311
Number of extensions: 14
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 383
Length of database: 324
Length adjustment: 29
Effective length of query: 354
Effective length of database: 295
Effective search space:   104430
Effective search space used:   104430
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