GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Dinoroseobacter shibae DFL-12

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3606947 Dshi_0375 ABC transporter related (RefSeq)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Dino:3606947
          Length = 273

 Score =  202 bits (513), Expect = 9e-57
 Identities = 106/259 (40%), Positives = 163/259 (62%), Gaps = 9/259 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           L+++ ++++KFGG+ AI D SF+ + G+I A+IGPNGAGK+++ N I+GFY P  G + F
Sbjct: 21  LMEMRNITLKFGGVTAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGQVMF 80

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
                      ++  +++ ++  +ARTFQNI LF G++VL+N++     +L       + 
Sbjct: 81  RGAPRP-----KMKPYQVARQG-IARTFQNIALFEGMSVLDNIMTG---RLTHMKSNMLD 131

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
             I  G  ++E  E  E     ++  ++ +    P G LPYG ++R+E+ARA+   P+LL
Sbjct: 132 QAIWWGKAQKEETENREKVEKIIDFLEIQNIRKTPVGRLPYGLKKRVELARALAAEPKLL 191

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEP AG+N  E   ++  +     E GT+I LIEHDM VVM++SD VVV++YG+KI D
Sbjct: 192 LLDEPMAGMNVEEKEDMSRYILDTNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGD 251

Query: 254 GTPDHVKNDPRVIAAYLGV 272
           GTPD V+N+  VI AYLGV
Sbjct: 252 GTPDEVRNNQDVIDAYLGV 270


Lambda     K      H
   0.318    0.136    0.386 

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: 202
Number of extensions: 10
Number of successful extensions: 3
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: 292
Length of database: 273
Length adjustment: 26
Effective length of query: 266
Effective length of database: 247
Effective search space:    65702
Effective search space used:    65702
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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