GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Desulfacinum infernum DSM 9756

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  254 bits (648), Expect = 4e-72
 Identities = 153/361 (42%), Positives = 211/361 (58%), Gaps = 22/361 (6%)

Query: 3   RLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTE 62
           ++ + DV K Y     G + AV  +S  +++G+ LV++GPSGCGK+T LR++AGLE VT 
Sbjct: 2   QIEIRDVRKDY-----GRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTS 56

Query: 63  GELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEE 122
           G + +    +  +    R+I+MVFQSYAL+PH +VR N+ FGL+    +P DEI +R++ 
Sbjct: 57  GTIHIAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRK-VPADEIERRLKR 115

Query: 123 TTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTEL 182
             D+LG+S  LD KPG+LSGG QQRVALGRAI+ +  V LMDEPLSNLDAKLR  MR E+
Sbjct: 116 VVDLLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREI 175

Query: 183 QRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGE 242
             LQ  LG+T +YVTHDQ EAMTM DR+ ++ DG++ Q  +P + Y RP N FVA FIG 
Sbjct: 176 CSLQRRLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGT 235

Query: 243 PSMNLFD-GSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTF 301
           P MN+       G      G      G   D+         GIRPE++ + E  SGQ   
Sbjct: 236 PPMNIVPLCPTQGGAALEPGGRLLFPGMDPDR------YLFGIRPENLRLAE--SGQ--- 284

Query: 302 DAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGE 361
            A V   E  G++  V         G +    T G+  +  G    +++    ++LFD  
Sbjct: 285 PAMVTGREYLGSDTFVSCEI----HGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDAR 340

Query: 362 T 362
           T
Sbjct: 341 T 341


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: 402
Number of extensions: 26
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: 365
Length adjustment: 30
Effective length of query: 353
Effective length of database: 335
Effective search space:   118255
Effective search space used:   118255
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.

Links

Downloads

Related tools

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