GapMind for catabolism of small carbon sources

 

Aligments for a candidate for levG 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_RS01725 BWI76_RS01725 PTS mannose/fructose/sorbose family transporter subunit IID

Query= TCDB::P69805
         (286 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS01725 BWI76_RS01725 PTS
           mannose/fructose/sorbose family transporter subunit IID
          Length = 274

 Score =  343 bits (881), Expect = 2e-99
 Identities = 169/272 (62%), Positives = 209/272 (76%), Gaps = 1/272 (0%)

Query: 13  EKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHL 72
           ++K+TQ D+  +FLRSNL Q S+NFER+  LGFC+ M+PAI+RLYP   E +  A++RHL
Sbjct: 3   QRKITQGDLVSMFLRSNLQQASFNFERIHGLGFCYDMIPAIKRLYPLK-EDQVAALKRHL 61

Query: 73  EFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRP 132
            FFNT P V  P++GVT+A+EE RANGA IDDGAINGIKVGLMGPLAGVGDP+ WGT+RP
Sbjct: 62  VFFNTTPAVCGPVIGVTVAMEEARANGAAIDDGAINGIKVGLMGPLAGVGDPLVWGTLRP 121

Query: 133 VFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDMGGGFLQKLT 192
           + AALGA +A+SG+L+GPLLFF +FN VRLA ++YG+  G+ KG++IV +MGG  LQKLT
Sbjct: 122 ITAALGASLALSGNLVGPLLFFFIFNAVRLAMKWYGLQLGFRKGVNIVSEMGGNLLQKLT 181

Query: 193 EGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTF 252
           EGASILGLFVMG LV KWT +N+PLVVS+     G     TVQ ILDQL PGL+ L LT 
Sbjct: 182 EGASILGLFVMGVLVTKWTTINVPLVVSQTPGADGSTVTMTVQNILDQLCPGLLALGLTL 241

Query: 253 ACMWLLRKKVNPLWIIVGFFVIGIAGYACGLL 284
             + LL KKVNP+W+I   F +GI G A G L
Sbjct: 242 LMVRLLNKKVNPVWLIFALFGLGILGNALGFL 273


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: 305
Number of extensions: 9
Number of successful extensions: 2
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: 274
Length adjustment: 26
Effective length of query: 260
Effective length of database: 248
Effective search space:    64480
Effective search space used:    64480
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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