GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Paucidesulfovibrio gracilis DSM 16080

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  228 bits (581), Expect = 2e-64
 Identities = 114/231 (49%), Positives = 163/231 (70%), Gaps = 3/231 (1%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78
           G  VAV+E  L I+ GE + L+GPSGCGK+T LRM+AGLET T+G++ ++ R +N     
Sbjct: 55  GKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRINDTPIH 114

Query: 79  DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138
            R++ M+FQ+YAL+PHK++  N++FGL+    +  +E+R++V +  +M+ +  +  R   
Sbjct: 115 KRNLGMIFQNYALFPHKTIFENVAFGLKYRN-VSREEMREKVAQALEMVRLPGVEKRYAS 173

Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198
           QLSGGQQQR+AL RAIV +P+V LMDEPLS LD KLR EMR E+  +Q +L +TT++VTH
Sbjct: 174 QLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNLTTLFVTH 233

Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFD 249
           DQ EA++M +++ V+ DG  QQ GTP D Y  P+N FVA F+G    N FD
Sbjct: 234 DQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFD 282


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: 400
Number of extensions: 14
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: 383
Length of database: 406
Length adjustment: 31
Effective length of query: 352
Effective length of database: 375
Effective search space:   132000
Effective search space used:   132000
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