GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Sulfurimonas denitrificans DSM 1251

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011373656.1 SUDEN_RS10595 ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000012965.1:WP_011373656.1
          Length = 236

 Score =  134 bits (337), Expect = 2e-36
 Identities = 86/223 (38%), Positives = 125/223 (56%), Gaps = 13/223 (5%)

Query: 1   MIELKNVNKYYG----THHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           +I L  V K YG    T + L+ +NL +K GE + I+GPSGSGKST +  +  L+ +SSG
Sbjct: 9   VISLHKVVKSYGSAEATTYALRGVNLEIKRGEFVAIMGPSGSGKSTAMNIIGCLDTLSSG 68

Query: 57  E-----VVVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKE 111
           +     V +  L L+ +  +   R Y   +FQ FNL    T ++N+ L P+  +    ++
Sbjct: 69  DYLFGGVDIQKLSLDQRTLLR--RNYIGFIFQGFNLLGKTTAIENVEL-PLLYRGFPARQ 125

Query: 112 AEETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETI 171
             E A   L+ VGL   A+  PA LSGGQQQRVAIAR++ T    +L DEPT  LD    
Sbjct: 126 RSEMAMNALRSVGLEQVAHHTPAELSGGQQQRVAIARAIVTDPFILLADEPTGNLDTAKS 185

Query: 172 QEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAI 214
           +E+++++   + +   T+V+VTHE   A   A RII   DG I
Sbjct: 186 REIMELLSSFNKEKGLTIVMVTHENEMA-SYASRIIRFRDGKI 227


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: 111
Number of extensions: 8
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: 236
Length adjustment: 23
Effective length of query: 219
Effective length of database: 213
Effective search space:    46647
Effective search space used:    46647
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