GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Phaeacidiphilus oryzae TH49

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  326 bits (835), Expect = 7e-94
 Identities = 185/375 (49%), Positives = 237/375 (63%), Gaps = 18/375 (4%)

Query: 1   MAPVTLKKLVKRY--GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58
           MA VT  K  + Y  G    V  +DLE+ D EF+ LVGPSGCGKST+LRM+AGLE+V+ G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 59  AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118
           AI IG R V  LPP+ R+I+MVFQ+YALYPHMTVA+NMGF+LKIAG    EI+++V EAA
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178
            ILDL   L+R+P  LSGGQRQRVAMGRAIVR+P VFL DEPLSNLDAKLR   RT+I  
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238
           L  R+  T +YVTHDQVEAMT+ DR+ +++DG ++QV TP +++ RPA  FVAGFIGSP 
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 239 MNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQK-VTFGLRPDDVYPSGHGLHAGDAD 297
           MN+ E  +TDG + F                  G K VT G+RP+ +   G G   G  D
Sbjct: 241 MNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVG-GTEGGGED 299

Query: 298 AVHEIELPVTITEPLGNETLVFTQFN-GRDWVSRMLNPRPLRPGEAVPMSFDLAR----- 351
               + + V + E LG +  V+     G + +  ++       G  +PM  D  R     
Sbjct: 300 --KGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRV----GGRDIPMKGDQLRVVPRA 353

Query: 352 --AHLFDGETGRALA 364
              H+F   TG+ L+
Sbjct: 354 GETHVFSTSTGKRLS 368


Lambda     K      H
   0.320    0.137    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: 413
Number of extensions: 18
Number of successful extensions: 1
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: 365
Length of database: 369
Length adjustment: 30
Effective length of query: 335
Effective length of database: 339
Effective search space:   113565
Effective search space used:   113565
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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