GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Alicycliphilus denitrificans K601

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  207 bits (527), Expect = 4e-58
 Identities = 122/294 (41%), Positives = 176/294 (59%), Gaps = 7/294 (2%)

Query: 20  LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79
           L  +DL +  GE +  LGPSGCGK+T+LR+IAGLE  + G++   G  ++ LPA ER+  
Sbjct: 35  LRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDISWLPASERDYG 94

Query: 80  MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139
           +VFQ+YAL+P++++ +N+A+GL   K   AEI  RV E+ A+  L     + P  +SGGQ
Sbjct: 95  IVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGLPTAGGKYPSQLSGGQ 154

Query: 140 QQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAM 199
           QQR A+ARA+   P + L DEPLS LDA +R +LR +I+RL +++  TT+ VTHDQ EA+
Sbjct: 155 QQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQVGITTIMVTHDQEEAL 214

Query: 200 TLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETA 259
           +++DR+++M  G I Q G+P E+Y  P + F A F+G   +N L G  Q   G+ F    
Sbjct: 215 SMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVLRG--QALGGKRFRVGK 270

Query: 260 HQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILG 313
            +      E   RL     V L +RP+  R+A   E        V V  VE LG
Sbjct: 271 MEIECEASEGSFRL--GEDVSLYLRPED-RVAEHLEAGTPYRLGVLVNKVEFLG 321


Lambda     K      H
   0.321    0.137    0.403 

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: 342
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: 406
Length of database: 377
Length adjustment: 31
Effective length of query: 375
Effective length of database: 346
Effective search space:   129750
Effective search space used:   129750
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: 50 (23.9 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