GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Dehalococcoides mccartyi 195

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= TCDB::A1VZQ3
         (250 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  117 bits (294), Expect = 2e-31
 Identities = 61/208 (29%), Positives = 115/208 (55%), Gaps = 21/208 (10%)

Query: 42  DAFINGFIY-------TLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNV 94
           D F++ F Y       T+ V++++  +  I G  G +   S+  I+R     YVE+ + +
Sbjct: 47  DPFLDIFKYVWVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGI 106

Query: 95  PLVIQIFFLFYALPVL--------------GIRLDIFTIGVLGVGAYHGAYVSEVVRSGI 140
           PL++Q+ + ++A PV+                + +   + + G+   +GAY+SE+ R+GI
Sbjct: 107 PLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGI 166

Query: 141 LAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAEL 200
            ++P+GQ EA+ S G ++ Q MRY+I+PQ +R++LPPM N+ + L+K+TS++  V  A++
Sbjct: 167 QSIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADM 226

Query: 201 MHSADSYAADYGNYAPAYIFAAVLYFII 228
           +     + A   N    +    +LY I+
Sbjct: 227 VRLGREFTATNFNPIEVWTMIGLLYLIL 254


Lambda     K      H
   0.328    0.143    0.422 

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: 180
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 250
Length of database: 273
Length adjustment: 25
Effective length of query: 225
Effective length of database: 248
Effective search space:    55800
Effective search space used:    55800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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