GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Skermanella stibiiresistens SB22

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037448510.1 N825_RS06700 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000576635.1:WP_037448510.1
          Length = 378

 Score =  310 bits (793), Expect = 6e-89
 Identities = 175/364 (48%), Positives = 222/364 (60%), Gaps = 16/364 (4%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA +TL DV K +     G +  +  + LDI D EF V VGPSGCGKST LR++AGLE +
Sbjct: 1   MADVTLRDVRKSF-----GGVEIIHGVDLDIRDNEFTVFVGPSGCGKSTLLRLIAGLEDI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           T GE+ ++   +N +  ++R I+MVFQSYALYPH +V  NM+FGL+ +     D I ++V
Sbjct: 56  TSGEMTIDGVRVNDLPPKERGISMVFQSYALYPHMTVYDNMAFGLKLANS-GKDAINRKV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
            E    L I  LLDRKP  LSGGQ+QRVA+GRAIVR+P+VFL DEPLSNLDA LR +MR 
Sbjct: 115 REAAGTLQIESLLDRKPRDLSGGQRQRVAIGRAIVREPKVFLFDEPLSNLDAALRVQMRI 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           EL +L+ +L  T VYVTHDQ EAMT+ D++ VL  G ++Q G+PL+ YH P NLFVAGFI
Sbjct: 175 ELAKLKDDLNATMVYVTHDQVEAMTLADKIVVLRAGHVEQAGSPLELYHHPRNLFVAGFI 234

Query: 241 GEPSMNLFDGSL-----SGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERR 295
           G P MNL +  +      G T +  G D     A    L   + +TLGIRPE +   E  
Sbjct: 235 GSPRMNLIETKVVSTDRDGATIQIPGGDTMTVPAQAAGLAHGAPVTLGIRPEHLV--EAD 292

Query: 296 SGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAI 355
            G    D  V VVE  G E   H+R  DG         T G++ V  G+   V  P  A 
Sbjct: 293 QGDTILDCTVFVVERLGGETYCHVRIADGQ---TLVLRTDGETTVRPGEPIRVGIPAAAC 349

Query: 356 HLFD 359
           HLFD
Sbjct: 350 HLFD 353


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: 454
Number of extensions: 32
Number of successful extensions: 5
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: 378
Length adjustment: 30
Effective length of query: 353
Effective length of database: 348
Effective search space:   122844
Effective search space used:   122844
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 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