GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Caldicellulosiruptor hydrothermalis 108

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000166355.1:WP_013403450.1
          Length = 343

 Score =  191 bits (484), Expect = 2e-53
 Identities = 101/242 (41%), Positives = 157/242 (64%), Gaps = 7/242 (2%)

Query: 1   MIELKNVNKYYGTHHV----LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           MI +KN+ K Y ++ +    L N+NL++++G+   IIGPSG+GKST IRC+N LE+ + G
Sbjct: 1   MIRIKNLTKIYHSNGIDIKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHG 60

Query: 57  EVVVNNLVLNHKNKIEI--CRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEE 114
            + ++ + +   +  E+   RK   ++FQHFNL    TV  N+   P+++    KK  + 
Sbjct: 61  SIEIDGVEMTKLSPTELKEMRKKVGIIFQHFNLLSSRTVKGNVAF-PLEIAGLDKKTIDN 119

Query: 115 TAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEV 174
              + L++VGL +K + YP+ LSGGQ+QRV IAR+L      +L DE TSALDPET   +
Sbjct: 120 RVKELLELVGLTNKTDSYPSQLSGGQKQRVGIARALANNPKVLLCDEATSALDPETTLSI 179

Query: 175 LDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARL 234
           L+++KEI+ +   T+VVVTHEM   K++ +++  ME G IVE+ + +E F+NPKT+ A+ 
Sbjct: 180 LNLLKEINREFGITIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQN 239

Query: 235 FL 236
           FL
Sbjct: 240 FL 241


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: 206
Number of extensions: 11
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: 343
Length adjustment: 26
Effective length of query: 216
Effective length of database: 317
Effective search space:    68472
Effective search space used:    68472
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