GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas fluorescens GW456-L13

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate PfGW456L13_4639 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4639
          Length = 254

 Score =  265 bits (677), Expect = 7e-76
 Identities = 139/247 (56%), Positives = 182/247 (73%), Gaps = 8/247 (3%)

Query: 9   ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68
           ++ + L K++G  +VL+GV+ +    DVIS+IG SG GKSTFLRC+N LE  + G + + 
Sbjct: 4   LTIEGLHKSYGDHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSLD 63

Query: 69  GVDLSGAK-------IDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMA 121
           G ++   K        D   L+++R R+ MVFQHFNL+ H+TVL+N+ +APR+VL     
Sbjct: 64  GQNIRMIKDRHGMHVADANELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGCDRK 123

Query: 122 EAKDRALTYLDKVGLGTK-ADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPE 180
           EA+DRA  YLDKVGL  + AD YP  LSGGQ+QRVAIAR L M+PE++LFDEPTSALDPE
Sbjct: 124 EAEDRARRYLDKVGLAPRVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPE 183

Query: 181 LVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSD 240
           LVGEVL V++ LAEEG TM +VTHEM FAR+VS++V F +QG++EEEG P EV  NPKS+
Sbjct: 184 LVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEEGAPEEVLGNPKSE 243

Query: 241 RLRAFLS 247
           RL+ FLS
Sbjct: 244 RLKQFLS 250


Lambda     K      H
   0.321    0.139    0.397 

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: 213
Number of extensions: 7
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: 252
Length of database: 254
Length adjustment: 24
Effective length of query: 228
Effective length of database: 230
Effective search space:    52440
Effective search space used:    52440
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 (21.9 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