GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Bb in Stenotrophomonas chelatiphaga DSM 21508

Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease

Query= uniprot:Q6MNM1
         (272 letters)



>NCBI__GCF_001431535.1:WP_042615044.1
          Length = 278

 Score =  176 bits (446), Expect = 5e-49
 Identities = 96/267 (35%), Positives = 161/267 (60%), Gaps = 4/267 (1%)

Query: 8   WIS--ILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTDFLIW 65
           WI+  +L+ +L S+ P+L+++SVS+ P     T    +   + +F N+ +LFA T   + 
Sbjct: 14  WINGGLLVLALVSLAPLLWMVSVSVMPAGEATTFPPPLTPSHVTFANYHELFARTGMGVN 73

Query: 66  MRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYIIL 125
             NSL+VS A TL  + L + + YA A+ RF GR+ +   L+   + PA + MLP ++++
Sbjct: 74  FANSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLM 133

Query: 126 SKLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIILP 185
            +L L++SF G+  I  + A  F I+ ++ Y  +IP EL EAA +DG  +  IF++I+LP
Sbjct: 134 KQLGLVNSFGGV--IVPALATVFGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVLP 191

Query: 186 VSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQASLATQWGLYAAGALI 245
           +  P LV  ++F+FM +W++++   +VL D + YTLP+ L +          +  AGA++
Sbjct: 192 MLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREHIMDVEMMMAGAVV 251

Query: 246 VSVPVLILFISISRYLVSGLTMGSVKG 272
             +PVL LF+ + RY + GL +GSVKG
Sbjct: 252 TVIPVLALFLLLQRYYIQGLMLGSVKG 278


Lambda     K      H
   0.329    0.139    0.421 

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: 211
Number of extensions: 11
Number of successful extensions: 2
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: 272
Length of database: 278
Length adjustment: 25
Effective length of query: 247
Effective length of database: 253
Effective search space:    62491
Effective search space used:    62491
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