GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manZ in Klebsiella michiganensis M5al

Align PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component (characterized)
to candidate BWI76_RS17900 BWI76_RS17900 PTS mannose transporter subunit IID

Query= SwissProt::P69805
         (283 letters)



>FitnessBrowser__Koxy:BWI76_RS17900
          Length = 283

 Score =  525 bits (1353), Expect = e-154
 Identities = 261/282 (92%), Positives = 269/282 (95%)

Query: 1   MVDTTQTTTEKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEA 60
           MVD T+ TTEKKLTQSDIRGVF+RSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENN+A
Sbjct: 1   MVDMTKNTTEKKLTQSDIRGVFIRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNDA 60

Query: 61  RKQAIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGD 120
           RKQAI+RHLEFFNT P+VAAP+LGVTLA+EEQRANGAEIDDGAINGIKVGLMGPLAGVGD
Sbjct: 61  RKQAIKRHLEFFNTHPYVAAPVLGVTLAMEEQRANGAEIDDGAINGIKVGLMGPLAGVGD 120

Query: 121 PIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDM 180
           PIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFN VRL TRYYGVAYGY KGIDIVKDM
Sbjct: 121 PIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNAVRLLTRYYGVAYGYRKGIDIVKDM 180

Query: 181 GGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMP 240
           GGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVS IT Q G+  VTTVQTILDQLMP
Sbjct: 181 GGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSTITGQDGQTRVTTVQTILDQLMP 240

Query: 241 GLVPLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGLLG 282
           GLVPLLLTFACMWLLRKKVN LWIIVGFFVIGIAGYA GLLG
Sbjct: 241 GLVPLLLTFACMWLLRKKVNALWIIVGFFVIGIAGYAVGLLG 282


Lambda     K      H
   0.326    0.143    0.439 

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: 404
Number of extensions: 11
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: 283
Length of database: 283
Length adjustment: 26
Effective length of query: 257
Effective length of database: 257
Effective search space:    66049
Effective search space used:    66049
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