GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatP in Burkholderia phytofirmans PsJN

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 BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease

Query= TCDB::B8H230
         (332 letters)



>FitnessBrowser__BFirm:BPHYT_RS27190
          Length = 343

 Score =  217 bits (552), Expect = 4e-61
 Identities = 134/339 (39%), Positives = 190/339 (56%), Gaps = 24/339 (7%)

Query: 2   TAPSSPAPLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSI 61
           + P+        + R DL+   +K   +  L++L+  F   +  F +  N + +  +V+ 
Sbjct: 6   SGPNQALDRQVQQRRRDLI---QKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTS 62

Query: 62  YGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLA 121
              + V  T VI+ GGID++VGS+LA A +AAA +V A V   P    +A+L   L+G A
Sbjct: 63  IAYLGVAATCVIITGGIDLSVGSVLALAGVAAALLVKAGV---PIP--VAMLGGMLVGAA 117

Query: 122 GGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFL-- 179
            G+V G  VT + +P FI TLG M V RG  L +    P+SG  DA+   G+G +  +  
Sbjct: 118 CGWVNGICVTRMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISH 177

Query: 180 --------------PVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDF 225
                         P PVVI  ++ AA  + L  T  GR +YAVG NAEAARLSGVNV  
Sbjct: 178 IGADGFPDTVFPGIPYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQG 237

Query: 226 ITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGT 285
           +    Y + G LAG +G +L +RL +A+   G  YEL  IAS VIGG SL GG G + GT
Sbjct: 238 VKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGT 297

Query: 286 VLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324
            +GA +IGVL NGL M  V+S++QQ++IG++I+  V  D
Sbjct: 298 AIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWID 336


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: 264
Number of extensions: 19
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 (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