GapMind for catabolism of small carbon sources

 

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

Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate H281DRAFT_02631 H281DRAFT_02631 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= uniprot:D4GP36
         (317 letters)



>FitnessBrowser__Burk376:H281DRAFT_02631
          Length = 300

 Score =  116 bits (291), Expect = 6e-31
 Identities = 77/245 (31%), Positives = 133/245 (54%), Gaps = 8/245 (3%)

Query: 57  NFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVLLVGFTTICLVLGLFLA 116
           + A+SF +++G+ TP  + + L  Y +   +D F  A +NNL+ LV F  +   LGL  A
Sbjct: 49  SIALSFYNWDGM-TPR-TFIGLANYVELFHADTFYLALKNNLIWLV-FFLLAPPLGLLFA 105

Query: 117 ILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILNLVVTTLGFNPVDWLGN 176
           + L+  I+     ++++  P  LS VV   ++ W ++   G+L L+V     + +  LG+
Sbjct: 106 LYLNQQIKGMRVVKSLFFAPFVLSGVVVGLVFSWFYDPAFGLLKLIVG----HGIPVLGD 161

Query: 177 PSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVDGASITRTYLRIIVPQLKE 236
           P      ++ A +W  + Y MV+YL GL SI  +  EAAR++GA        +I+PQL+ 
Sbjct: 162 PRTVTFGIVFAALWPQTPYCMVLYLTGLTSINPEVVEAARMEGAKGWSLLWHVILPQLRP 221

Query: 237 ASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVRRAFKFGEWAYSAAIATML 296
           A+  A V+ ++ AL++F  +  + G   P + + +LA  M  +A K+    YSA+IA +L
Sbjct: 222 ATFMAVVLTVIGALRSFDLISVMSGG-GPFDSSTVLAYYMYDQAIKYYREGYSASIAVVL 280

Query: 297 LIMAL 301
             + L
Sbjct: 281 FAIML 285


Lambda     K      H
   0.326    0.140    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: 240
Number of extensions: 13
Number of successful extensions: 4
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: 317
Length of database: 300
Length adjustment: 27
Effective length of query: 290
Effective length of database: 273
Effective search space:    79170
Effective search space used:    79170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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