GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Paraburkholderia bryophila 376MFSha3.1

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate H281DRAFT_02384 H281DRAFT_02384 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Burk376:H281DRAFT_02384
          Length = 254

 Score =  203 bits (517), Expect = 2e-57
 Identities = 111/239 (46%), Positives = 152/239 (63%), Gaps = 7/239 (2%)

Query: 10  PLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQAR---TG 66
           P+L VNG+   YG + AL G  + V  G+IVS+IG NGAGKSTL+  I G+        G
Sbjct: 10  PILDVNGLSVRYGKVEALHGAAIKVRAGQIVSVIGPNGAGKSTLLNAIMGALPTTGHAKG 69

Query: 67  SVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNL---KHFAEDV 123
           +VV++G D++ +P  +     +   PE R +F  M+V +NL +GA        ++F + +
Sbjct: 70  AVVYQGEDVSAVPVEKRVARGMCLVPEKRELFASMSVEDNLVLGAYRRKRAGERNFLDQM 129

Query: 124 EKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIF 183
           E +F LFPRLKER  Q  GTLSGGE+QML++GRALM +P LL+LDEPSLGLAPLIVK IF
Sbjct: 130 EPVFQLFPRLKERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGLAPLIVKEIF 189

Query: 184 EAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
             I  L +  G+   L+EQNA AAL++S   YV+  G++ + G+  +L  NP V   YL
Sbjct: 190 HIISALRQT-GVATLLIEQNARAALQISDYGYVLETGELALEGAASDLAQNPRVIETYL 247


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: 190
Number of extensions: 8
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: 254
Length adjustment: 24
Effective length of query: 223
Effective length of database: 230
Effective search space:    51290
Effective search space used:    51290
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