GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Rhizobium freirei PRF 81

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_004129777.1 RHSP_RS32465 ribose ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>NCBI__GCF_000359745.1:WP_004129777.1
          Length = 320

 Score =  217 bits (553), Expect = 3e-61
 Identities = 123/304 (40%), Positives = 185/304 (60%), Gaps = 4/304 (1%)

Query: 11  RELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLS 70
           R+   ++    +  F A  N  F+T  N   L RQ +I G+LAIG TFVI++ G  IDLS
Sbjct: 19  RQFSIVLVFFLIVAFFAFANQYFMTWLNWLNLVRQSSINGILAIGVTFVILTKG--IDLS 76

Query: 71  PGSMVALTGVMVAWLMTHGVPVWI--SVILILLFSIGAGAWHGLFVTKLRVPAFIITLGT 128
            GS++AL G++ A L+T     ++   +   L    G G  +G+ V  ++VP F++TLG 
Sbjct: 77  VGSVMALAGMIAASLVTETNEQFVLFGIFAGLAAGAGLGLVNGVLVAAVKVPPFVVTLGM 136

Query: 129 LTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGK 188
           L++ARG+  + ++G PI  L   F  IG G+ + IP+P+ IL  V L+    L  T +G+
Sbjct: 137 LSVARGLTLIFSEGRPIPNLSDPFKWIGSGQIMYIPVPIVILFVVFLIGWTVLNYTTFGR 196

Query: 189 HLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYA 248
           ++ A GGNE AAR SG++   +    +++SG LAG+ G+++ AR +   P  G  YEL A
Sbjct: 197 YVYAVGGNEKAARTSGISTKVIVGATYVISGLLAGLAGLVLTARTTAALPQAGIGYELDA 256

Query: 249 IASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLD 308
           IA+ VIGGTSL GG GS+LG ++GA II  + N + L+ VS+Y+  V+ G +IVVAV  D
Sbjct: 257 IAAVVIGGTSLAGGRGSLLGTLIGALIIGTINNGMDLMGVSSYYQQVLKGTIIVVAVIAD 316

Query: 309 ILRR 312
            +R+
Sbjct: 317 QIRK 320


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: 316
Number of extensions: 17
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: 320
Length adjustment: 27
Effective length of query: 290
Effective length of database: 293
Effective search space:    84970
Effective search space used:    84970
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 24 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