GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Bb in Cronobacter condimenti 1330

Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate WP_007665545.1 BN137_RS16135 carbohydrate ABC transporter permease

Query= uniprot:Q6MNM1
         (272 letters)



>NCBI__GCF_000319285.1:WP_007665545.1
          Length = 281

 Score =  158 bits (400), Expect = 1e-43
 Identities = 87/271 (32%), Positives = 151/271 (55%), Gaps = 4/271 (1%)

Query: 4   KTFSWISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTDFL 63
           K   +I  L+  LF ++P  Y +  SLR      T +    G +  + N+V         
Sbjct: 13  KAVIFIGALMACLFCVFPFYYAIISSLREGQELFTPAYFPTGWH--WDNYVVALVDNGIA 70

Query: 64  IWMRNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYI 123
             + NS++V+A T  L + ++ T+A+ALAR  FRGR ++LF++L   MFP   ++   + 
Sbjct: 71  RSLLNSVLVAAVTVGLCLFVSVTAAFALARVPFRGRRVLLFTILCVSMFPQVAVLTGMFE 130

Query: 124 ILSKLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKII 183
           ++  L L DS   L + Y++ +LPF +W +  +  +IP ELEEAA++DG     I  +I 
Sbjct: 131 LVRFLGLYDSLGALVISYTTFSLPFTVWVLTTFMKSIPVELEEAAIVDGAKTGTIIRRIF 190

Query: 184 LPVSSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQ--ASLATQWGLYAA 241
            PV +PA+V T L +F+ +W+E++ A   +      T+P+ +  F   +S    WG   A
Sbjct: 191 APVLAPAMVTTGLLAFIGAWNEFMFALTFIISGDKRTVPVAISLFSGASSYELPWGSIMA 250

Query: 242 GALIVSVPVLILFISISRYLVSGLTMGSVKG 272
            +++V++P+++L +   + +VSGLT G++KG
Sbjct: 251 ASVVVTLPIIVLVLIFQKRIVSGLTSGAIKG 281


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: 233
Number of extensions: 13
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: 281
Length adjustment: 25
Effective length of query: 247
Effective length of database: 256
Effective search space:    63232
Effective search space used:    63232
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