GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Shewanella sp. ANA-3

Align Glucose/galactose porter (characterized)
to candidate 7025962 Shewana3_3110 glucose/galactose transporter (RefSeq)

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__ANA3:7025962
          Length = 432

 Score =  195 bits (495), Expect = 2e-54
 Identities = 131/425 (30%), Positives = 216/425 (50%), Gaps = 27/425 (6%)

Query: 14  ETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFI 73
           + S QK+    +  +  LFF+ GF T LN  L+P+LK + QLN  Q+ LI F F+ A   
Sbjct: 4   DKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTF 63

Query: 74  VSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQV 133
            +LP+  +++++ YK G+ +G+ +  +   LFIPAA  +++ LFL A  V+ +G T+LQ 
Sbjct: 64  TALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQT 123

Query: 134 AANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLIL--------SAATDATVNA 185
           A NPYV  LG  E+AA+R+++    N     +AP+  + LIL        +  T   ++ 
Sbjct: 124 AVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDE 183

Query: 186 EADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEG---SAWQYRHLVLGAI 242
            A+++ FPYL +A+   VLA+       P++  ++       +G   +A  + +L  G I
Sbjct: 184 MANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVI 243

Query: 243 GIFVYVGAEV----SVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMR 298
            +FVYV  EV    ++G+F ++   +      S T     + Y  G  ++ RFI      
Sbjct: 244 ALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTAL 303

Query: 299 YIDD------GKALAFNAFVAIILLFITVATTGHIAMWSVLA----IGLFNSIMFPTIFS 348
            I          A+ F    +  +    +   G +A+   L     +GL N+I++P ++ 
Sbjct: 304 MISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWP 363

Query: 349 LALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADA--IGIHLAFLMPIICYAYIAFYG 406
           LAL GLG  TS GS +L + I GGA  PL  G  + A  +G    +++ + CY +I FY 
Sbjct: 364 LALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYA 423

Query: 407 LIGSK 411
           + G K
Sbjct: 424 VKGHK 428


Lambda     K      H
   0.328    0.141    0.420 

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: 515
Number of extensions: 41
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: 412
Length of database: 432
Length adjustment: 32
Effective length of query: 380
Effective length of database: 400
Effective search space:   152000
Effective search space used:   152000
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