GapMind for catabolism of small carbon sources

 

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

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family

Query= TCDB::Q9WXW7
         (317 letters)



>FitnessBrowser__Burk376:H281DRAFT_02714
          Length = 331

 Score =  231 bits (589), Expect = 2e-65
 Identities = 127/304 (41%), Positives = 190/304 (62%), Gaps = 3/304 (0%)

Query: 11  RELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLS 70
           REL  L  L+ + +  ++ +P FLT  NL  + R  ++  L++IG   VII+GG  IDLS
Sbjct: 26  RELNVLSVLLLVGLLISVFSPYFLTTNNLMGVFRSFSLIALMSIGMMLVIITGG--IDLS 83

Query: 71  PGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLT 130
            GS++ L+ ++ A +  HG     ++   L   I  GA++G  +T +++P FI TLGTL+
Sbjct: 84  VGSVMGLSSLVTALVFQHGYNAPAAIGAGLAVGIAVGAFNGFMITWIQLPPFIATLGTLS 143

Query: 131 IARGMAAVITKGWPII-GLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKH 189
           I RG+  +ITKG P+   +P SF  IGQG    +P PV ILLA+  V    +R+T +G++
Sbjct: 144 IGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMTAVFSVVMRQTRFGRY 203

Query: 190 LRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAI 249
           + A+GGNEVAAR SGV   RV+   +++SG +A + G+I  +R    +P  G   EL  I
Sbjct: 204 VYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFVSAEPASGFGAELDVI 263

Query: 250 ASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDI 309
           A+  IGG SL+GG GSV GAI+GA++  ++ N +VLLN+ TY    + G VI++AV++DI
Sbjct: 264 AAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQAITGCVILIAVSIDI 323

Query: 310 LRRR 313
            R R
Sbjct: 324 WRVR 327


Lambda     K      H
   0.328    0.143    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: 352
Number of extensions: 25
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: 317
Length of database: 331
Length adjustment: 28
Effective length of query: 289
Effective length of database: 303
Effective search space:    87567
Effective search space used:    87567
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 (21.7 bits)
S2: 48 (23.1 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