GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  199 bits (506), Expect = 9e-56
 Identities = 104/263 (39%), Positives = 161/263 (61%), Gaps = 8/263 (3%)

Query: 22  IDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPRARNISMVF 81
           I+LEV++ E+  ++GP+G GK+  L  IAG+     G I    R +  L P  R +  V+
Sbjct: 19  INLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVGFVY 78

Query: 82  QSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPSQLSGGQRQR 141
           Q YAL+PH+TV EN+ F  +I   P + IK+++ E  A+L + HLL R PS LSGG++QR
Sbjct: 79  QDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGEQQR 138

Query: 142 VAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTLS 201
            A+ RA++  P++ L DEPLS LD + +   + E+KK+H  ++ T ++VTHD  EAM L+
Sbjct: 139 TALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAMYLA 198

Query: 202 DRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLTDGKLAFASGATLPL 261
           D+I +M  G I QVGTP+++F +P   FVA F+G    N+ E  + D K++ A    +  
Sbjct: 199 DKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFEGQVNDDKVSLAPDVDI-- 254

Query: 262 PPRFRSLVREGQKVTFGLRPDDV 284
              F +  ++G KV   + P+D+
Sbjct: 255 ---FVNTGKQG-KVKVAVPPEDI 273


Lambda     K      H
   0.320    0.137    0.397 

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: 294
Number of extensions: 14
Number of successful extensions: 1
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: 365
Length of database: 344
Length adjustment: 29
Effective length of query: 336
Effective length of database: 315
Effective search space:   105840
Effective search space used:   105840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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