GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatP in Pseudomonas simiae WCS417

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 GFF3462 PS417_17725 ribose ABC transporter permease

Query= TCDB::B8H230
         (332 letters)



>lcl|FitnessBrowser__WCS417:GFF3462 PS417_17725 ribose ABC
           transporter permease
          Length = 330

 Score =  227 bits (578), Expect = 4e-64
 Identities = 130/290 (44%), Positives = 182/290 (62%), Gaps = 5/290 (1%)

Query: 32  LLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASI 91
           L+++  V   A++ FLTA N  NI  +VSI  IIAVGMT VIL GGID++VG ++A +  
Sbjct: 38  LVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTCVILTGGIDLSVGPVMALSGT 97

Query: 92  AAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGA 151
             A ++ A +  G     +A+    LIG+A G   G  V +LH+P  IVTL  M + RG 
Sbjct: 98  LTAGLMVAGLPPG-----LAIGAGMLIGVAFGIGNGLFVAYLHMPPIIVTLATMGIARGL 152

Query: 152 TLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGG 211
            L+  DG PISG  D + ++G   +  + VP++I  L     +V L++TR GR +YA+GG
Sbjct: 153 GLMYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVAYVLLQHTRIGRYIYAIGG 212

Query: 212 NAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIASVVIG 271
           N EA RLSGV        VY I G  A ++G +L++RL S +  AG  +EL  IA+VV+G
Sbjct: 213 NEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQPNAGVSFELDAIAAVVLG 272

Query: 272 GASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAV 321
           GAS+ GG G + GT+LGA+L+GVL+NGL ML V+ YVQ V+ G II+ A+
Sbjct: 273 GASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVIKGGIILLAI 322


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: 274
Number of extensions: 11
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: 332
Length of database: 330
Length adjustment: 28
Effective length of query: 304
Effective length of database: 302
Effective search space:    91808
Effective search space used:    91808
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