GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manZ in Hafnia paralvei ATCC 29927

Align PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose (characterized)
to candidate WP_008812477.1 M988_RS15855 PTS system mannose/fructose/sorbose family transporter subunit IID

Query= TCDB::P69805
         (286 letters)



>NCBI__GCF_001655005.1:WP_008812477.1
          Length = 297

 Score =  185 bits (469), Expect = 1e-51
 Identities = 99/282 (35%), Positives = 164/282 (58%), Gaps = 12/282 (4%)

Query: 3   EMVDTTQTTTEKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNE 62
           E  D   +T  + LT+ D+  +  RS L Q S+N+ERMQA G+ ++++P +R+++ +N +
Sbjct: 28  EQDDYIDSTPAEALTKQDLNRMAWRSLLLQASFNYERMQAGGWLYTLIPGLRKIH-KNPQ 86

Query: 63  ARKQAIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVG 122
               +++ H+EF N  PF    + G+ LA+E     G++     I  +KV LMGPL G+G
Sbjct: 87  DLANSMKMHMEFINVHPFDVTFLSGLVLAME-----GSKEKVSTIRAVKVALMGPLGGIG 141

Query: 123 DPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKD 182
           D +FW T+ P+ A +GA +A+ GSL GP++F ++FN+V    R+    YGY  G   +  
Sbjct: 142 DALFWLTLLPICAGIGASLALQGSLFGPIVFLLMFNIVHFGLRFGLAHYGYHAGTSALA- 200

Query: 183 MGGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLM 242
           +     +K++  ASI+G+ V+GALV  + H++ PLV+       GK  V   + +LD+LM
Sbjct: 201 LLKTHTKKISHAASIVGMTVIGALVASYVHLSTPLVM-----HAGKASVALQKDVLDKLM 255

Query: 243 PGLVPLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGLL 284
           P L+PL  T    WL+++  +P+ +I    + G+ G   G L
Sbjct: 256 PNLLPLCFTLLVFWLMKRGFSPVKLIGLTVLFGVVGKFVGFL 297


Lambda     K      H
   0.326    0.143    0.436 

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: 203
Number of extensions: 16
Number of successful extensions: 5
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: 286
Length of database: 297
Length adjustment: 26
Effective length of query: 260
Effective length of database: 271
Effective search space:    70460
Effective search space used:    70460
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 (21.6 bits)
S2: 48 (23.1 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