GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Pseudomonas litoralis 2SM5

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  159 bits (403), Expect = 5e-44
 Identities = 96/243 (39%), Positives = 142/243 (58%), Gaps = 8/243 (3%)

Query: 1   MIELKNVNKYY--GTHHV--LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           MIE + VNK Y  G   +  L   +L+++ G+   IIG SG+GKST +R +N LEE S+G
Sbjct: 1   MIEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNG 60

Query: 57  EVVV---NNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
            ++V   +   LN +  +   R+   M+FQHFNL    TV  N+ L        ++++  
Sbjct: 61  RIMVAGEDTTALNAEG-LRRFRQRVGMIFQHFNLLSSATVADNVALPLRLAGSANRQQIA 119

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
                 L  VGL D A+ YPA LSGGQ+QRV IAR+L T+   +L DE TSALDP T  +
Sbjct: 120 ARVASLLDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQ 179

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERAR 233
           VL ++ EI+ + N T+V++THEM   + V D++  M+ G IVE+   ++ F +P+    R
Sbjct: 180 VLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTR 239

Query: 234 LFL 236
            F+
Sbjct: 240 SFV 242


Lambda     K      H
   0.317    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: 157
Number of extensions: 8
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: 242
Length of database: 334
Length adjustment: 26
Effective length of query: 216
Effective length of database: 308
Effective search space:    66528
Effective search space used:    66528
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 (21.7 bits)
S2: 47 (22.7 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