GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Alicycliphilus denitrificans K601

Align TreV, component of Trehalose porter (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  206 bits (524), Expect = 7e-58
 Identities = 113/264 (42%), Positives = 163/264 (61%), Gaps = 2/264 (0%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           +E+  I K +     +  I   +  GE    LGPSG GK+TLL+I+AG+E    G I+  
Sbjct: 20  LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G DI+  P  +R+  +VFQ+YAL+PN+++ +N+A+ L    M+K EI  RV +   + G+
Sbjct: 80  GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGL 139

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
                K  +Q+SGGQQQRVALARA+  NP   LLDEPLS LDA VR   R E++R+QK++
Sbjct: 140 PTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQV 199

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
             T I VTHDQ+EALS++DRI +++ G  EQV  P  +YE P + +VA FVG+  +N L 
Sbjct: 200 GITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--VNVLR 257

Query: 243 GELMKEKAQEIGFRPEWVEVGKGN 266
           G+ +  K   +G      E  +G+
Sbjct: 258 GQALGGKRFRVGKMEIECEASEGS 281


Lambda     K      H
   0.318    0.137    0.385 

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: 260
Number of extensions: 9
Number of successful extensions: 1
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: 324
Length of database: 377
Length adjustment: 29
Effective length of query: 295
Effective length of database: 348
Effective search space:   102660
Effective search space used:   102660
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: 49 (23.5 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