GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Phaeacidiphilus oryzae TH49

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  323 bits (828), Expect = 5e-93
 Identities = 189/376 (50%), Positives = 240/376 (63%), Gaps = 15/376 (3%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA +T D  T++Y    GGD  AV+ + L+I DGEFLVLVGPSGCGKST+LRM+AGLE V
Sbjct: 1   MATVTYDKATRIYP---GGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDV 57

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
             G +R+ +R +  +  +DRDIAMVFQ+YALYPH +V  NM F L+ + G+   EIR +V
Sbjct: 58  NNGAIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIA-GVNKAEIRSKV 116

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
           EE   +L +++ LDRKP  LSGGQ+QRVA+GRAIVR+P+VFLMDEPLSNLDAKLR   RT
Sbjct: 117 EEAAKILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRT 176

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           ++  LQ  LG+TTVYVTHDQ EAMTMGDRVAVL DG LQQV TP + Y RP NLFVAGFI
Sbjct: 177 QIAGLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFI 236

Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASG-----LTLGIRPE--DVTVGE 293
           G P+MNL +  +   T  G  F   +   +RD +G A+      +T+G+RPE  D+  G 
Sbjct: 237 GSPAMNLVEVPI---TDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGT 293

Query: 294 RRSGQ-RTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPE 352
              G+ +     V VVE  G +  V+     G E         G+     GD+  V    
Sbjct: 294 EGGGEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRA 353

Query: 353 DAIHLFDGETGDALKN 368
              H+F   TG  L +
Sbjct: 354 GETHVFSTSTGKRLSD 369


Lambda     K      H
   0.316    0.136    0.384 

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: 485
Number of extensions: 28
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: 383
Length of database: 369
Length adjustment: 30
Effective length of query: 353
Effective length of database: 339
Effective search space:   119667
Effective search space used:   119667
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: 42 (22.0 bits)
S2: 50 (23.9 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