GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Jannaschia aquimarina GSW-M26

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_043919730.1 jaqu_RS14580 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000877395.1:WP_043919730.1
          Length = 269

 Score =  201 bits (511), Expect = 1e-56
 Identities = 111/265 (41%), Positives = 168/265 (63%), Gaps = 11/265 (4%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           DT+L + +++++FGG+ AI D SF+ + G+I A+IGPNGAGK+++ N I+GFY P  G +
Sbjct: 15  DTVLDLRNITLRFGGVEAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEV 74

Query: 72  TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131
            F      Q     +  +++ ++  +ARTFQNI LF G++VL+N++  + N  MKA+ + 
Sbjct: 75  WFRGAPRPQ-----MKPYQVARQG-IARTFQNIALFEGMSVLDNVMTGRLNA-MKANIFQ 127

Query: 132 ILGLIGVGPYKREA-AEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190
                G    + EA  E++E    +LE   +      P G LPYG ++R+E+ARA+   P
Sbjct: 128 QAFWWGKASKEEEANRESVERVIDFLEIQHI---RKTPVGRLPYGLKKRVELARALAAEP 184

Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250
            LL LDEP AG+N  E   ++  +  +  E GT+I LIEHDM VVM++SD VVV++YG+K
Sbjct: 185 SLLLLDEPMAGMNVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGRK 244

Query: 251 ISDGTPDHVKNDPRVIAAYLGVEDE 275
           I DGTP  V+++  VI AYLGV  +
Sbjct: 245 IGDGTPAEVRSNQDVIDAYLGVSHD 269


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: 204
Number of extensions: 8
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: 269
Length adjustment: 26
Effective length of query: 266
Effective length of database: 243
Effective search space:    64638
Effective search space used:    64638
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 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