GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Desulfovibrio vulgaris Hildenborough

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>MicrobesOnline__882:209225
          Length = 354

 Score =  161 bits (407), Expect = 3e-44
 Identities = 96/239 (40%), Positives = 133/239 (55%), Gaps = 16/239 (6%)

Query: 6   LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65
           +E + +T  G+    + D NL     E    VGPSG GKTT LR IAGL+   EG + + 
Sbjct: 5   VEGLGRTLAGRE--VLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRV- 61

Query: 66  DRRVNDVPPKDRD--IAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKIL 123
                  PP+     + +VFQ+Y L+PH++V++N+AFG + R V  A +  RV    +  
Sbjct: 62  ------TPPQGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAF 115

Query: 124 -----DIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEI 178
                D+AH+  R P  LS GQRQRVAL RA+V +P V L+DEP +NLD  LR +M A +
Sbjct: 116 RLDTDDLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFV 175

Query: 179 RKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIG 237
           R + +R     + VTHD  EA  +GDR+ VM  G + Q   P  VY  P +   A F+G
Sbjct: 176 RDVVRRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG 234


Lambda     K      H
   0.321    0.138    0.395 

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: 365
Number of extensions: 24
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: 384
Length of database: 354
Length adjustment: 30
Effective length of query: 354
Effective length of database: 324
Effective search space:   114696
Effective search space used:   114696
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 17 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