GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Thiothrix lacustris DSM 21227

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  280 bits (716), Expect = 4e-80
 Identities = 169/360 (46%), Positives = 214/360 (59%), Gaps = 28/360 (7%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA L L +V K Y     G + A++++SL+I  GEF+V VGPSGCGKST LRM+AGLE +
Sbjct: 1   MAFLELKNVDKYY-----GKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
             G+L L+ R +  V    RD+AMVFQSYALYPH +V  NMSF L  +   P   I+++V
Sbjct: 56  NGGQLILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAI-IQEKV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
           +   D L ++  L R P  LSGGQ+QRVA+GR+IVR P+VFL DEPLSNLDA LR   R 
Sbjct: 115 KMAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRV 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+  L  ELG TTVYVTHDQ EAMT+ DRV VL DG ++QVGTPL+ Y +P N FVA FI
Sbjct: 175 EIASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFI 234

Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300
           G P MN+   SL G         +P           A    +GIRPE + +     G   
Sbjct: 235 GMPQMNVAPASLFG--------QFP-----------AQVAEVGIRPEHLQMVSPEDG--L 273

Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDA-IHLFD 359
              +VV+VE  GNE  VH+R               G++ V  GDR  + + +   IH FD
Sbjct: 274 LAGKVVLVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFD 333


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: 393
Number of extensions: 14
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: 348
Length adjustment: 30
Effective length of query: 353
Effective length of database: 318
Effective search space:   112254
Effective search space used:   112254
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: 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