GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Pseudomonas litoralis 2SM5

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

Query= uniprot:A0A1N7U8S3
         (276 letters)



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  155 bits (393), Expect = 8e-43
 Identities = 95/233 (40%), Positives = 133/233 (57%), Gaps = 15/233 (6%)

Query: 27  LQVEGIHKRY--GEHEV--LKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGV 82
           ++ + ++K Y  G  ++  L    L    G V  +IG SG+GKST+LR IN LE+P  G 
Sbjct: 2   IEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGR 61

Query: 83  ITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLD 142
           I + G           T A + + L+  R R+ M+FQHFNL S  TV +N+ +  R    
Sbjct: 62  IMVAG---------EDTTALNAEGLRRFRQRVGMIFQHFNLLSSATVADNVALPLRLAGS 112

Query: 143 VSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSA 202
            +  +   R    LD+VGL    A +YPA LSGGQ+QRV IARALA EP I+L DE TSA
Sbjct: 113 ANRQQIAARVASLLDRVGLSDH-ASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSA 171

Query: 203 LDPELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG 254
           LDP   G+VL+++  +  E   T++++THEM   R+V  QV  +  GR+ E G
Sbjct: 172 LDPHTTGQVLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQG 224


Lambda     K      H
   0.319    0.133    0.372 

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: 212
Number of extensions: 9
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: 276
Length of database: 334
Length adjustment: 27
Effective length of query: 249
Effective length of database: 307
Effective search space:    76443
Effective search space used:    76443
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: 48 (23.1 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