GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Phaeobacter inhibens BS107

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1247 PGA1_c12630 putative high-affinity branched-chain amino acid transport ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Phaeo:GFF1247
          Length = 251

 Score =  171 bits (433), Expect = 1e-47
 Identities = 98/238 (41%), Positives = 143/238 (60%), Gaps = 6/238 (2%)

Query: 7   TGQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTIC--GSPQAR 64
           T    L V  +  YYG    + G+  +V++GEI++L+G NGAGK++ + +I   GSP   
Sbjct: 16  TAPAFLSVWDMHAYYGESYIVQGISFNVHEGEILALLGRNGAGKTSTLRSIARTGSPMVT 75

Query: 65  TGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVE 124
            G +  + + + +M +HE +   +   PE RRI P +TV ENLQ+      +      +E
Sbjct: 76  KGEIWLDHQPLHKMSSHEASAAGLGLVPEDRRIIPGLTVEENLQLAQIAPPV---GWSIE 132

Query: 125 KIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFE 184
           +++ LFPRL ER  Q G TLSGGEQQML+I RAL    K+LLLDEP  GLAP+IV  I +
Sbjct: 133 RLYELFPRLGERRKQEGVTLSGGEQQMLAIARALARDIKVLLLDEPYEGLAPVIVDEIEK 192

Query: 185 AIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
            +  + + +G+T  +VEQNA  AL L+ RA ++  G +   G+  E+L N E+RA YL
Sbjct: 193 TLIHIKQ-QGITTVIVEQNAVRALELADRAVILDTGGIVFDGAAAEVLENEELRAEYL 249


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: 187
Number of extensions: 11
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: 251
Length adjustment: 24
Effective length of query: 223
Effective length of database: 227
Effective search space:    50621
Effective search space used:    50621
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 17 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