GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Alkalihalobacterium alkalinitrilicum DSM 22532

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_078430749.1 BK574_RS01735 ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  157 bits (397), Expect = 3e-43
 Identities = 91/301 (30%), Positives = 162/301 (53%), Gaps = 4/301 (1%)

Query: 7   KRTFRELGPLVALVSLAVFTAILNPRFLTAF-NLQALGRQIAIFGLLAIGETFVIISGGG 65
           K      G ++A + + +  +IL+P    +F N   + RQI+   ++A+G T V+     
Sbjct: 13  KSLISSYGTIIAGLGIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVK-- 70

Query: 66  AIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIIT 125
             DLS G+M +L GV+ A L   G P+   +++ ++     G ++G  VTK +V +F+ T
Sbjct: 71  EFDLSIGAMASLGGVLSALLAASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTT 130

Query: 126 LGTLTIARGMAAVITKGWPII-GLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKT 184
           L   T+  G+   +T G  +   +P  F  +GQ +   +P    I+  + ++  + + +T
Sbjct: 131 LAMGTVIGGVTFWLTGGATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQT 190

Query: 185 VYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMY 244
             G+ L A GGNE A+  SG+N+ R + IAF + G LA   G ++A+RL    P  G  +
Sbjct: 191 SLGRRLYAIGGNEKASEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGF 250

Query: 245 ELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVA 304
            L A A+  +G T +  G  ++LG + GA+II ++ N L +L V ++  N++ G +I++A
Sbjct: 251 FLNAYAAVFLGMTIVKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIA 310

Query: 305 V 305
           +
Sbjct: 311 L 311


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: 27
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: 321
Length adjustment: 28
Effective length of query: 289
Effective length of database: 293
Effective search space:    84677
Effective search space used:    84677
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 Apr 09 2024. 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