GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Paucidesulfovibrio gracilis DSM 16080

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= SwissProt::Q9YGA6
         (372 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  255 bits (651), Expect = 2e-72
 Identities = 135/292 (46%), Positives = 191/292 (65%), Gaps = 12/292 (4%)

Query: 4   VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63
           +RL  V K F   T + ++ L+++ GEF+ +LGPSGCGKTT LR++AG E PS G+I + 
Sbjct: 8   IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67

Query: 64  DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123
            + + D      VPP  R +  VFQSYAL+PHM+V+DN+AF L++  +P+ EI +RV + 
Sbjct: 68  GRSMRD------VPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKA 121

Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183
             ++GL     R+P  LSGGQ+QRVA+ RA+V +P V L+DEPLS LD KLRV+MR ELK
Sbjct: 122 LRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELK 181

Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243
           +L+R++G+T I+VTHDQ EA +M DR+ VMN G + QVG+P EVY++P N FVA F+G  
Sbjct: 182 QLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE- 240

Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGY-VGREVIFGIRPEDL 294
             N  + +    G  D G  +  +     E+    G+  G  +   +RPEDL
Sbjct: 241 -TNVFEGVA---GQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDL 288


Lambda     K      H
   0.323    0.142    0.406 

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: 386
Number of extensions: 24
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: 372
Length of database: 370
Length adjustment: 30
Effective length of query: 342
Effective length of database: 340
Effective search space:   116280
Effective search space used:   116280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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