GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcU in Stenotrophomonas chelatiphaga DSM 21508

Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease

Query= TCDB::Q97UY9
         (287 letters)



>NCBI__GCF_001431535.1:WP_042615044.1
          Length = 278

 Score =  120 bits (302), Expect = 3e-32
 Identities = 83/269 (30%), Positives = 137/269 (50%), Gaps = 22/269 (8%)

Query: 16  LALAIVSV---IWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLL--SLAKP 70
           L LA+VS+   +W++ V  M         E  + P  + P+ +TF  Y  +     +   
Sbjct: 20  LVLALVSLAPLLWMVSVSVMPAG------EATTFPPPLTPSHVTFANYHELFARTGMGVN 73

Query: 71  LINSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAISDVLFSLISLATFIPQEATL 130
             NSL++ +  +  S  L  M  Y F  L +          D LF ++  A  IP +  +
Sbjct: 74  FANSLLVSVAITLGSLLLNTMAGYAFAKLRF-------VGRDRLFQVLMAALVIPAQVAM 126

Query: 131 LPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISVIPRSLIEAAKMDGTGDLKI 190
           LPL  L+  +GL++S+ G+I   L      G  L+  +   IP  L+EAA+MDG G+++I
Sbjct: 127 LPLFLLMKQLGLVNSFGGVIVPALATVF--GIFLVRQYARSIPDELLEAARMDGAGEMRI 184

Query: 191 FMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMKLTSIAVLSYSGAYGTLYND 250
           F +IV P+  P  ++  IF  + AWN+F  PL+++T        +A+ + S  +  +  +
Sbjct: 185 FFQIVLPMLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREH-IMDVE 243

Query: 251 TFAAGMVASIIP-LAIFVFLGRYFIRGLM 278
              AG V ++IP LA+F+ L RY+I+GLM
Sbjct: 244 MMMAGAVVTVIPVLALFLLLQRYYIQGLM 272


Lambda     K      H
   0.330    0.144    0.417 

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: 233
Number of extensions: 18
Number of successful extensions: 4
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: 287
Length of database: 278
Length adjustment: 26
Effective length of query: 261
Effective length of database: 252
Effective search space:    65772
Effective search space used:    65772
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 (21.8 bits)
S2: 47 (22.7 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