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_RS01725 BWI76_RS01725 PTS mannose/fructose/sorbose family transporter subunit IID

Query= SwissProt::P69805
         (283 letters)



>FitnessBrowser__Koxy:BWI76_RS01725
          Length = 274

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

Query: 10  EKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHL 69
           ++K+TQ D+  +FLRSNL Q S+NFER+  LGFC+ M+PAI+RLYP   E +  A++RHL
Sbjct: 3   QRKITQGDLVSMFLRSNLQQASFNFERIHGLGFCYDMIPAIKRLYPLK-EDQVAALKRHL 61

Query: 70  EFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRP 129
            FFNT P V  P++GVT+A+EE RANGA IDDGAINGIKVGLMGPLAGVGDP+ WGT+RP
Sbjct: 62  VFFNTTPAVCGPVIGVTVAMEEARANGAAIDDGAINGIKVGLMGPLAGVGDPLVWGTLRP 121

Query: 130 VFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDMGGGFLQKLT 189
           + AALGA +A+SG+L+GPLLFF +FN VRLA ++YG+  G+ KG++IV +MGG  LQKLT
Sbjct: 122 ITAALGASLALSGNLVGPLLFFFIFNAVRLAMKWYGLQLGFRKGVNIVSEMGGNLLQKLT 181

Query: 190 EGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTF 249
           EGASILGLFVMG LV KWT +N+PLVVS+     G     TVQ ILDQL PGL+ L LT 
Sbjct: 182 EGASILGLFVMGVLVTKWTTINVPLVVSQTPGADGSTVTMTVQNILDQLCPGLLALGLTL 241

Query: 250 ACMWLLRKKVNPLWIIVGFFVIGIAGYACGLL 281
             + LL KKVNP+W+I   F +GI G A G L
Sbjct: 242 LMVRLLNKKVNPVWLIFALFGLGILGNALGFL 273


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: 304
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: 283
Length of database: 274
Length adjustment: 25
Effective length of query: 258
Effective length of database: 249
Effective search space:    64242
Effective search space used:    64242
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