GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pseudomonas simiae WCS417

Align Glucose transporter, OEOE_0819. Does not transport fructose (characterized)
to candidate GFF971 PS417_04925 MFS transporter

Query= TCDB::Q04FN1
         (395 letters)



>FitnessBrowser__WCS417:GFF971
          Length = 421

 Score =  127 bits (319), Expect = 6e-34
 Identities = 105/362 (29%), Positives = 170/362 (46%), Gaps = 25/362 (6%)

Query: 14  IFLIAGNLRLTIIVIPPISSYIMQSFDLDQTKIGLLTSIPLICFGLLSVLAPLVIRKLGS 73
           + L+A NLR  +  + P+ S +  S  L   + GLLT++P++C GL + LAP++ R+ G+
Sbjct: 42  LVLVALNLRPALSSLSPLLSEVSSSLGLSAARAGLLTTLPVLCLGLFAPLAPILARRFGA 101

Query: 74  YRTMITALGILIIANFFRVLSAPW----LFVGSFFTGAAITILNILTPTVIVERAPKHAN 129
            R +   LGIL++     VL + +    LFVGS   GA+I I+ +L P ++     K A 
Sbjct: 102 ERVV---LGILLMLAGGIVLRSAFGEVGLFVGSLIAGASIGIIGVLLPGIVKRDFAKQAG 158

Query: 130 VLNGLYTATLNLWAAGIGYLVAPLAKQIG--WQAVVQLTSILPIITLAGWFLIKNKTSNN 187
            + G+YT  L L AA       PL+   G  W   +    +  ++    W          
Sbjct: 159 TMTGVYTMALCLGAALAAGASVPLSDYFGHRWSIGLGFWMLPALLAALCWL--------P 210

Query: 188 DLEKNTVSNQQNIKLIEIINHPKIWLLAIFMGLQSFIYYGLIAWLPSILNHLKLSLLATG 247
            +     +++   ++  ++  P  W + ++MGLQS + Y +  W+PSIL  +   L AT 
Sbjct: 211 QIGHKHGAHRVAYRVKGLLRDPLAWQVTLYMGLQSSLAYIVFGWVPSIL--IDRGLSATD 268

Query: 248 SLFALFQFIGIPISYIIPRISAGKNAFKWVLGGLFVGYVSGLSLLNLKS---PTLPVITI 304
           +  AL    G  I  ++  ++A   A +     L +  V  L+L  L       L  +  
Sbjct: 269 AGLAL---SGSIIVQLLSALTAPWLATRGKDQRLAIVVVMLLTLGGLMGCLYAPLDGLWG 325

Query: 305 AIIALGLTTAAIFSLALGLITTLSDSAREISVIGGVVQSLGYLLACISPTLLGKLNSSFG 364
             I LGL     FSLAL LI   S  A   + + G+ Q +GY LA + P  +G ++   G
Sbjct: 326 WAILLGLGQGGTFSLALTLIVLRSRDAHVAANLSGMAQGIGYTLASLGPLAVGLIHDWTG 385

Query: 365 NW 366
            W
Sbjct: 386 GW 387


Lambda     K      H
   0.327    0.143    0.429 

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: 533
Number of extensions: 42
Number of successful extensions: 5
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: 395
Length of database: 421
Length adjustment: 31
Effective length of query: 364
Effective length of database: 390
Effective search space:   141960
Effective search space used:   141960
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 (21.7 bits)
S2: 50 (23.9 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