GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Pseudomonas litoralis 2SM5

Align ABC transporter related (characterized, see rationale)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

Query= uniprot:B2TBJ9
         (263 letters)



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  152 bits (384), Expect = 9e-42
 Identities = 91/237 (38%), Positives = 134/237 (56%), Gaps = 13/237 (5%)

Query: 20  DHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEELKMKRRGD 79
           D   L    L    G V  I+G SG+GKST LR +N LE P +G + +AGE+        
Sbjct: 17  DIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGRIMVAGEDTTAL---- 72

Query: 80  GKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQ-KRSRAESVEEAEAL 138
                 +   + R R ++GM+FQ+FNL S  TV +N +  P+R+    +R +      +L
Sbjct: 73  ------NAEGLRRFRQRVGMIFQHFNLLSSATVADN-VALPLRLAGSANRQQIAARVASL 125

Query: 139 LAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGEVLRVMR 198
           L +VGL++    YPA LSGGQ+QRV IARALA  P ++L DE TSALDP   G+VL+++ 
Sbjct: 126 LDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQVLQLLS 185

Query: 199 SLAEE-GRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQFV 254
            +  E   T++++THEM   R V ++V  +  G++   GT  +VF+  +    R FV
Sbjct: 186 EINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTRSFV 242


Lambda     K      H
   0.318    0.133    0.377 

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: 202
Number of extensions: 10
Number of successful extensions: 3
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: 263
Length of database: 334
Length adjustment: 26
Effective length of query: 237
Effective length of database: 308
Effective search space:    72996
Effective search space used:    72996
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 (21.7 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