GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Phaeobacter inhibens BS107

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC

Query= TCDB::Q9WXW7
         (317 letters)



>FitnessBrowser__Phaeo:GFF2276
          Length = 324

 Score =  162 bits (409), Expect = 1e-44
 Identities = 106/315 (33%), Positives = 172/315 (54%), Gaps = 13/315 (4%)

Query: 9   TFRELGPLVA----LVSLAVFT---AILNPRFLTAFNLQALGRQIAIFGLLAIGETFVII 61
           T +++G L+A    L++ A+F     I NP+FLT  N + + R  AI G++A+G TFV+I
Sbjct: 5   TKQDIGKLLAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVI 64

Query: 62  SGGGAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPA 121
           SG   +DLS GSM++ + ++V  L     P  +++  +   ++  GA  G  V  L++ +
Sbjct: 65  SGN--LDLSVGSMMSFSTIVVLDLHDKLGPT-LAIPAMFAMTLCLGALIGFLVGYLKLNS 121

Query: 122 FIITLGTLTIARGMAAVIT--KGWPIIGLPSSFLKI-GQGEFLKIPIPVWILLAVALVAD 178
            I+TLG L+   G+    +  K   I     ++  I GQG  L I  P+ I +A+A +  
Sbjct: 122 LIVTLGMLSAIHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALLG 181

Query: 179 FFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQP 238
             L KT +G+ + A GGN  AA FSG+   RV  + +++S       G+I A+R    Q 
Sbjct: 182 IILAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQN 241

Query: 239 GVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIG 298
            VG   EL  +A+ ++GG SL GG G++   ++G  I+  + N L+L+ +      VV  
Sbjct: 242 TVGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTW 301

Query: 299 IVIVVAVTLDILRRR 313
           I+I++AV LDI  +R
Sbjct: 302 IIIILAVWLDIAAKR 316


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: 295
Number of extensions: 21
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: 324
Length adjustment: 28
Effective length of query: 289
Effective length of database: 296
Effective search space:    85544
Effective search space used:    85544
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