GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Stenotrophomonas chelatiphaga DSM 21508

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_057508148.1 ABB28_RS08100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_001431535.1:WP_057508148.1
          Length = 362

 Score =  290 bits (742), Expect = 4e-83
 Identities = 163/369 (44%), Positives = 228/369 (61%), Gaps = 17/369 (4%)

Query: 1   MGQIQLTDLTKRFGD-TVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59
           M ++QL  + K + +  VAV D + ++ D E +VLVGPSGCGKST LRM+AGLE  + G 
Sbjct: 1   MAKVQLQGVRKVYDNGQVAVKDATFEVADGELMVLVGPSGCGKSTLLRMIAGLEEISGGT 60

Query: 60  IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119
           + IG   +N   P++RDIAMVFQ YALYPHMTV +N+ FGL+   G+  A  D+R+ E A
Sbjct: 61  LTIGERVVNDVAPKDRDIAMVFQSYALYPHMTVAENLAFGLKLR-GHDKATIDKRISEAA 119

Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179
           +TLG+ D++D+ P  +SGGQ+QRVALGRA+VR+P VFL+DEPLSNLDAKLR  +RTE+  
Sbjct: 120 QTLGLTDMMDKLPKAMSGGQRQRVALGRALVREPAVFLLDEPLSNLDAKLRHSVRTEIAQ 179

Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239
           L  +L  T +YVTH+Q EAMT+  RI V+ DG +QQ+ +P E Y  P NLFVA F+G P 
Sbjct: 180 LHRKLGTTMIYVTHDQVEAMTLGQRIVVLKDGVIQQIDTPMELYDRPANLFVAGFLGSPA 239

Query: 240 INLVRGTRSES----TFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA 295
           +N++RGT   S          +  PL    ++         +GVRPE ++ ADA      
Sbjct: 240 MNVLRGTLQASASGVVVSDGDWKAPLGHATIDPRWLDKPIAVGVRPEHLQPADAGA---- 295

Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355
             +   +  +  +EP G++  ++L      S   AL        L   G+ + + + P+ 
Sbjct: 296 --EWTFEARIEGIEPVGNEIFVNL-----VSGQHALTMRVAPRALPAVGETLKLAVQPNA 348

Query: 356 IHLFDAETG 364
           +H FDAETG
Sbjct: 349 LHFFDAETG 357


Lambda     K      H
   0.317    0.135    0.386 

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: 333
Number of extensions: 16
Number of successful extensions: 4
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: 362
Length adjustment: 30
Effective length of query: 353
Effective length of database: 332
Effective search space:   117196
Effective search space used:   117196
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: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. 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