GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manZ in Klebsiella michiganensis M5al

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 BWI76_RS03970 BWI76_RS03970 PTS mannose/fructose/sorbose family transporter subunit IID

Query= TCDB::P69805
         (286 letters)



>FitnessBrowser__Koxy:BWI76_RS03970
          Length = 283

 Score =  209 bits (531), Expect = 7e-59
 Identities = 108/284 (38%), Positives = 168/284 (59%), Gaps = 8/284 (2%)

Query: 1   MSEMVDTTQTTTEKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPEN 60
           +SE     Q   E ++T  D+R VF RS   + SWN+ER   L F ++++P +++LYP  
Sbjct: 6   ISEETLRPQEQEETRITPRDLRRVFWRSFQMEFSWNYERQMNLAFVYALIPVLKKLYPRK 65

Query: 61  NEARKQAIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAG 120
            E    A++RHL FFNT P +   +LG+T A+EE+ +    +D  AI+ +K  LMGPLAG
Sbjct: 66  EELAA-ALKRHLVFFNTTPHIVTLLLGITTAMEEKNSQQKNMDANAIDNVKASLMGPLAG 124

Query: 121 VGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIV 180
           +GD  FWGT+R +   +G  +A+ G++LGP+LF ++FN+  +  R++   +GY  G  ++
Sbjct: 125 LGDSFFWGTLRLIATGIGTSLALKGNILGPILFLLVFNVPHILVRWFFTRWGYVLGTGVL 184

Query: 181 KDM-GGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILD 239
           + +   G ++ LT GASI+GL V+GA+      + IP+           E  T VQ I++
Sbjct: 185 QRIQKSGMMESLTYGASIIGLMVVGAMTASMIDITIPVSFG------AGEAKTQVQDIIN 238

Query: 240 QLMPGLVPLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGL 283
            ++P ++PLL      WLL +KV PL II G  ++GI G   GL
Sbjct: 239 DILPCMLPLLSFGIVYWLLGRKVKPLSIIGGMALVGILGSWIGL 282


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: 245
Number of extensions: 16
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: 283
Length adjustment: 26
Effective length of query: 260
Effective length of database: 257
Effective search space:    66820
Effective search space used:    66820
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 17 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