GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Crocosphaera subtropica ATCC 51142

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_000017845.1:WP_009545830.1
          Length = 238

 Score =  117 bits (294), Expect = 2e-31
 Identities = 76/236 (32%), Positives = 127/236 (53%), Gaps = 7/236 (2%)

Query: 12  LQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFE 71
           L +  +   YG    +  V++ V  GEIV L+G NGAGK+T      G  +   G V   
Sbjct: 3   LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62

Query: 72  GRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFP 131
            +++TR+P ++ ARL I    +   IF  ++V EN+Q+     N+  F +  +++ TL  
Sbjct: 63  QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVALEQTNVP-FRQRPQRLHTLLK 121

Query: 132 --RLKERHAQRGGTLSGGEQQMLSIGRAL---MARPKLLLLDEPSLGLAPLIVKGIFEAI 186
             RL++    +G  +SGGE++   + R+L      P  LLLDEP  G+ P+ V  I   I
Sbjct: 122 EFRLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFAGVDPIAVSEIQTMI 181

Query: 187 RKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
            +L + + + + + + N  A L +++RAY+M +G++  +GS +E+  NP VR  YL
Sbjct: 182 AQLCDRQ-MGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYNNPLVRQYYL 236


Lambda     K      H
   0.320    0.137    0.387 

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: 137
Number of extensions: 7
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: 247
Length of database: 238
Length adjustment: 23
Effective length of query: 224
Effective length of database: 215
Effective search space:    48160
Effective search space used:    48160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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