GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Phaeacidiphilus oryzae TH49

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

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  311 bits (797), Expect = 2e-89
 Identities = 173/339 (51%), Positives = 225/339 (66%), Gaps = 28/339 (8%)

Query: 1   MAGIKIDKINKFY--GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58
           MA +  DK  + Y  G   A+  ++L+I DGEF+V VGPSGCGKST LR LAGLE V++G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 59  RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118
            I IG RDVT + P DRD+AMVFQ+YALYPHMTV +NM F +K+ G      + ++ EAA
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178
           ++L L ++LDRKP  LSGGQRQRVA+GRAIV+ P VFL DEPLSNLDAKLRV  R ++ G
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238
           L ++LG T +YVTHDQVEAMTM D++ VL  G ++QV +P ++Y +P + FVA FIGSPA
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 239 MNVFS---SDVGLQ------DISLDA---------SAAFVGCRPEHIEIVPDGDG----- 275
           MN+     +D G++       +S DA             VG RPEH++IV   +G     
Sbjct: 241 MNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDK 300

Query: 276 HIAATVHVKERLGGESLLYLGLKGGGQ---IVARVGGDD 311
            +A TV+V E LG +  +Y   K G +   +V RVGG D
Sbjct: 301 GLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRD 339


Lambda     K      H
   0.320    0.139    0.396 

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: 391
Number of extensions: 18
Number of successful extensions: 2
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: 338
Length of database: 369
Length adjustment: 29
Effective length of query: 309
Effective length of database: 340
Effective search space:   105060
Effective search space used:   105060
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