GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  207 bits (528), Expect = 3e-58
 Identities = 110/259 (42%), Positives = 164/259 (63%), Gaps = 12/259 (4%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           M+ +  D+VTK Y         AV++++L+I +GE + L+GPSGCGK+TTLRM+AG E  
Sbjct: 1   MSFIQFDNVTKYYNRAA---TPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQP 57

Query: 61  TEGELRLEDRVL----NGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEI 116
           T G++R+ D V+      +  + R I MVFQ YAL+PH ++  N++FGL       + + 
Sbjct: 58  TTGKIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNR---WKNRDK 114

Query: 117 RQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176
           ++R +E  +++G+ +   R P +LSGGQQQRVAL RA+   P+V LMDEP SNLDA LR 
Sbjct: 115 KKRAQEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLRE 174

Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFV 236
           +MR ++  +  +   T + VTHDQ +A  + DRV V+++G +QQ+  P + Y  P N FV
Sbjct: 175 KMRYDVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFV 234

Query: 237 AGFIGEPSMNLFDGSLSGD 255
           A F+G+   NL  G+L  D
Sbjct: 235 AQFVGK--TNLISGTLCPD 251


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: 337
Number of extensions: 15
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: 351
Length adjustment: 30
Effective length of query: 353
Effective length of database: 321
Effective search space:   113313
Effective search space used:   113313
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