GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Pantoea rwandensis LMG 26275

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_084935579.1 HA51_RS15825 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_002095475.1:WP_084935579.1
          Length = 249

 Score =  258 bits (658), Expect = 1e-73
 Identities = 137/236 (58%), Positives = 173/236 (73%), Gaps = 1/236 (0%)

Query: 9   QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68
           + +L    V+ +YG ++AL  V + VN+GE V+LIGANGAGKSTL+M+I G P+  +G +
Sbjct: 3   ESMLSFEQVDVFYGPVQALKQVSLTVNQGETVALIGANGAGKSTLLMSIFGQPRIASGDI 62

Query: 69  VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFT 128
              G  I    TH IA   IAQ+PEGRRIFP MTV ENL MG      +H  ED E+++ 
Sbjct: 63  RLRGESIGHRSTHFIAASGIAQAPEGRRIFPDMTVEENLLMGTIAVGERHVKEDKERMYQ 122

Query: 129 LFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRK 188
           LFPRL ER  QR  TLSGGEQQML+I RALM+RPKLLLLDEPSLGLAP++VK IF  +R+
Sbjct: 123 LFPRLLERRKQRAMTLSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFNILRE 182

Query: 189 LNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244
           L + +G+T+FLVEQNA  AL+L+ R YVMVNG++ +SG G+ELL N EVR+AYL G
Sbjct: 183 LTQ-QGMTLFLVEQNARHALQLADRGYVMVNGEIKLSGRGEELLNNDEVRSAYLGG 237


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: 215
Number of extensions: 8
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: 247
Length of database: 249
Length adjustment: 24
Effective length of query: 223
Effective length of database: 225
Effective search space:    50175
Effective search space used:    50175
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 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