GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF1247 PGA1_c12630 putative
           high-affinity branched-chain amino acid transport
           ATP-binding protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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