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_004095992.1 M988_RS13035 PTS system mannose/fructose/sorbose family transporter subunit IID

Query= TCDB::P69805
         (286 letters)



>NCBI__GCF_001655005.1:WP_004095992.1
          Length = 288

 Score =  183 bits (464), Expect = 4e-51
 Identities = 108/254 (42%), Positives = 151/254 (59%), Gaps = 9/254 (3%)

Query: 34  SWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHLEFFNTQPFVAAPILGVTLALE 93
           S ++ER+Q+L FC SM P I++LYPE  E R +A++RHL FFNT+    A I GV +A+E
Sbjct: 42  SSSYERLQSLIFCASMTPIIKKLYPEKEE-RAEALKRHLNFFNTEQTFGAVIQGVAIAME 100

Query: 94  EQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLF 153
           EQ+  G  I D +I GIK GLMGPLAG+GD + W  V P+  A+    A  GS  G +L 
Sbjct: 101 EQKTRGEPISDASITGIKTGLMGPLAGIGDSVIWAAVMPLLIAIFIPFAAKGSAFGGILP 160

Query: 154 FILFNLVRLATRYYGVAYGYSKGID-IVKDMGGGFLQKLTEGASILGLFVMGALVNKWTH 212
            IL+  + LA  Y  V  GY+ G D I+  + GG +++L  GA++LGL +MGAL   +  
Sbjct: 161 LILYTGITLAVSYGLVHKGYTLGRDSIITLLQGGRIKELIYGANVLGLIMMGALSASYVK 220

Query: 213 VNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTFACMWLLRKKVNPLWIIVGFF 272
           +  PL +S +    G E V  VQ ILD + PGL+PL   F+  + L KK  P +  +   
Sbjct: 221 ITSPLKISAL---EGSEIV--VQQILDSIAPGLLPLAAVFSIYFYLTKK-GPRYTTILLS 274

Query: 273 VIGIAGYACGLLGL 286
           V+ +    C LLG+
Sbjct: 275 VV-VISVVCSLLGV 287


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: 227
Number of extensions: 19
Number of successful extensions: 4
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: 288
Length adjustment: 26
Effective length of query: 260
Effective length of database: 262
Effective search space:    68120
Effective search space used:    68120
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: 47 (22.7 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