GapMind for catabolism of small carbon sources

 

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

Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate H281DRAFT_03877 H281DRAFT_03877 xylose-binding protein

Query= CharProtDB::CH_003787
         (330 letters)



>FitnessBrowser__Burk376:H281DRAFT_03877
          Length = 342

 Score =  383 bits (983), Expect = e-111
 Identities = 193/320 (60%), Positives = 248/320 (77%), Gaps = 3/320 (0%)

Query: 13  SLLLTNVAAHAKE--VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQ 70
           SL L    AHA +   +IG  IDDLR+ERW +DRD FV  AE LGAKV VQSA+ +E  Q
Sbjct: 21  SLSLAAPLAHASKDHPEIGFCIDDLRVERWSRDRDYFVAAAEKLGAKVSVQSADASEARQ 80

Query: 71  MSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNE 130
           +SQIEN+I+RGVDV+VI+P+N + L NVV EA++ GIKV++YDR+I DAD+D YISFDNE
Sbjct: 81  ISQIENLISRGVDVIVIVPFNSKTLGNVVAEARKAGIKVVSYDRLILDADVDAYISFDNE 140

Query: 131 KVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVD 190
           KVGELQA+ +    P+GNYFL+GG+P DNNAK+ R GQ+KVLKP +D G IK+VG QWV 
Sbjct: 141 KVGELQAEGVYKAQPKGNYFLLGGAPTDNNAKMLREGQLKVLKPAIDKGDIKLVGQQWVP 200

Query: 191 GWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAG 250
            W    AL+I+E+ALTANNNKIDA+VASND TAGGAIQAL+AQ ++GKV +SGQDADLA 
Sbjct: 201 EWSASTALRIVEDALTANNNKIDAIVASNDGTAGGAIQALAAQHMAGKVPVSGQDADLAA 260

Query: 251 IKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDV 310
           +KR+ AGTQTMTVYKP+ L+A  AA+++V L  G++P  +   +NG K V + LL P  +
Sbjct: 261 VKRLIAGTQTMTVYKPLKLIAGEAAKLSVALAKGEKPAFNAQYDNGKKKVDTVLLQPTLL 320

Query: 311 NKNNIKDTVIKDGFHKESEL 330
            K+N+ D VIKDGF+ +++L
Sbjct: 321 TKSNV-DVVIKDGFYTQAQL 339


Lambda     K      H
   0.314    0.132    0.366 

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: 359
Number of extensions: 14
Number of successful extensions: 2
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: 330
Length of database: 342
Length adjustment: 28
Effective length of query: 302
Effective length of database: 314
Effective search space:    94828
Effective search space used:    94828
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: 42 (22.0 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