GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatP in Klebsiella michiganensis M5al

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate BWI76_RS07245 BWI76_RS07245 ABC transporter

Query= TCDB::B8H230
         (332 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07245 BWI76_RS07245 ABC
           transporter
          Length = 343

 Score =  211 bits (537), Expect = 2e-59
 Identities = 133/333 (39%), Positives = 198/333 (59%), Gaps = 29/333 (8%)

Query: 12  TDKPRFDLLAFAR-KHR----TILFLLLLV-------AVFGAANERFLTARNALN-ILSE 58
           T+KP F    F + +HR    T +F+++LV       A +   ++ FL   N L  I+ +
Sbjct: 12  TEKPSF----FGQLRHRLPKDTGIFIVMLVIALTFEIAGWYVRDQSFLLNTNRLILIVLQ 67

Query: 59  VSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPA-------TWLIA 111
           V+I GIIAVG+T VI+  GID++ GS++A A++ AA +        P          +I 
Sbjct: 68  VAIIGIIAVGVTQVIITTGIDLSSGSVIALAAVVAASLAQTSDSLSPMFPSLVNMPAIIP 127

Query: 112 LLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWW 171
           +     +GL  G   G  VT   +P FI TLG M   RG       G PIS  +D++   
Sbjct: 128 IGAGIGVGLLCGLTNGFLVTRTGIPPFIATLGMMVSARGLAQYYTQGNPISFLSDSFTAI 187

Query: 172 GSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVY 231
           G G +     PV+IF +VAA  H+AL++TRYG+ VYA+GGN  +A++SG+NV+     VY
Sbjct: 188 GQGAM-----PVIIFFVVAAVFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLVIVY 242

Query: 232 AIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALL 291
           AI GAL+GL+G +L+AR+ S ++  G  YEL  IA+ VIGG+SL GG G + GT++GA++
Sbjct: 243 AIAGALSGLAGVVLAARVSSGQSSMGMSYELDAIAAAVIGGSSLMGGVGRITGTLIGAMI 302

Query: 292 IGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324
           +G++ +G   + V +YVQ ++ G+IIVAAV  D
Sbjct: 303 LGLIKSGFTFVGVDAYVQDIIKGIIIVAAVTID 335


Lambda     K      H
   0.325    0.140    0.413 

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: 270
Number of extensions: 16
Number of successful extensions: 3
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: 332
Length of database: 343
Length adjustment: 28
Effective length of query: 304
Effective length of database: 315
Effective search space:    95760
Effective search space used:    95760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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