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_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  234 bits (598), Expect = 2e-66
 Identities = 143/358 (39%), Positives = 214/358 (59%), Gaps = 22/358 (6%)

Query: 4   LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63
           + L+ V K +  E       + ++ LDI  GEFL ++GPSGCGK+T LR++AG E+ + G
Sbjct: 8   IRLEHVAKEFDGE-----TVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSG 62

Query: 64  ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123
           E+ L+ R +  V    R +  VFQSYAL+PH SV  N++FGL  S G+P  EI +RV + 
Sbjct: 63  EIILDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMS-GIPKVEIGERVAKA 121

Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183
             M+G++    R+P  LSGGQQQRVA+ RA+V  P V L+DEPLS LD KLR +MRTEL+
Sbjct: 122 LRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELK 181

Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243
           +L+ E+G+T ++VTHDQ EA +M DRV V+++G + QVGTP++ Y +P N+FVA F+GE 
Sbjct: 182 QLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE- 240

Query: 244 SMNLFDGSLSGDTFRG------DGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERR-- 295
             N+F+G ++G +  G      +G    LS     Q G    + + +RPED+ V      
Sbjct: 241 -TNVFEG-VAGQSDGGILQALVEGRTCELSSHRGFQPG--DRIRVLLRPEDLLVEREEPE 296

Query: 296 -SGQRTFDAEVVVVEPQGNENAVHLRFVDGDE--GTQFTATTTGQSRVEAGDRTTVSF 350
              +      ++    +G+   + ++   G E   T+F      +   +AG+R  VS+
Sbjct: 297 DDDKLWLPGRIMETVYKGSTWDMVVQLDSGHEILVTEFFDEDADKMNFQAGERVVVSW 354


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: 464
Number of extensions: 23
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: 370
Length adjustment: 30
Effective length of query: 353
Effective length of database: 340
Effective search space:   120020
Effective search space used:   120020
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