GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Sulfurivirga caldicuralii DSM 17737

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_074201578.1 BUQ81_RS06435 phosphate ABC transporter ATP-binding protein PstB

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_900141795.1:WP_074201578.1
          Length = 262

 Score =  107 bits (268), Expect = 2e-28
 Identities = 83/256 (32%), Positives = 130/256 (50%), Gaps = 24/256 (9%)

Query: 1   MIELKNVNKYY--GTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG-- 56
           M+E+K+ +  Y       LK+INL V +     +IGPSG GKST +R MN + ++  G  
Sbjct: 6   MMEVKDFSFTYPNAPKPSLKHINLRVVKNRITALIGPSGCGKSTLLRAMNRIHDLYPGCK 65

Query: 57  -----------EVVVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQ 105
                        V N L    +N +   R+   M+FQ    +P M++  N+    +KLQ
Sbjct: 66  YEGAINLQCVDGSVKNILEWTKENDLIRLRQKVGMIFQKPTPFP-MSIYDNIAYG-LKLQ 123

Query: 106 K-KSKKEAEETAFKYLKVVGLL----DKANVYPATLSGGQQQRVAIARSLCTKKPYILFD 160
             +SK E ++   + L+   L     D+       LSGGQQQR+ IARS+  +   ILFD
Sbjct: 124 GIRSKSELDDRVEEALRDGALWNEVKDRLKDDARGLSGGQQQRLCIARSVALRPDVILFD 183

Query: 161 EPTSALDPETIQEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIP 220
           EPTSALDP +   + +++ E+  Q   T+ +VTH M  A  ++D   FM  G ++E +  
Sbjct: 184 EPTSALDPISTVAIEEMIMELREQ--YTICIVTHNMQQAARISDYTAFMYLGELIEYDET 241

Query: 221 SEFFSNPKTERARLFL 236
              F+NP  ++   ++
Sbjct: 242 DTIFTNPSQKQTEDYI 257


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: 136
Number of extensions: 4
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: 242
Length of database: 262
Length adjustment: 24
Effective length of query: 218
Effective length of database: 238
Effective search space:    51884
Effective search space used:    51884
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: 46 (22.3 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