GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Caldicellulosiruptor hydrothermalis 108

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000166355.1:WP_013403450.1
          Length = 343

 Score =  140 bits (352), Expect = 6e-38
 Identities = 75/226 (33%), Positives = 124/226 (54%), Gaps = 5/226 (2%)

Query: 16  LEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDPS-- 73
           ++ +  V+L+I+ G+    +GPSG GKSTL+R I  LE+ + G + ID V M  + P+  
Sbjct: 18  IKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHGSIEIDGVEMTKLSPTEL 77

Query: 74  ---KRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRK 130
              ++ + ++FQ + L    TV+ N+ F L  AG+ +  I+ RV E   ++ L    D  
Sbjct: 78  KEMRKKVGIIFQHFNLLSSRTVKGNVAFPLEIAGLDKKTIDNRVKELLELVGLTNKTDSY 137

Query: 131 PKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYV 190
           P QLSGGQ+QRV I RA+  +PK+ L DE  S LD E  + +   +  ++++   TIV V
Sbjct: 138 PSQLSGGQKQRVGIARALANNPKVLLCDEATSALDPETTLSILNLLKEINREFGITIVVV 197

Query: 191 THDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGS 236
           TH+      + +K+ VM  G + + G   +++ +P       F+ S
Sbjct: 198 THEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQNFLRS 243


Lambda     K      H
   0.321    0.139    0.396 

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: 267
Number of extensions: 13
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: 358
Length of database: 343
Length adjustment: 29
Effective length of query: 329
Effective length of database: 314
Effective search space:   103306
Effective search space used:   103306
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 (21.8 bits)
S2: 49 (23.5 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