GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Shewanella loihica PV-4

Align Glucose/galactose porter (characterized)
to candidate 5208608 Shew_1119 glucose/galactose transporter (RefSeq)

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__PV4:5208608
          Length = 418

 Score =  191 bits (485), Expect = 3e-53
 Identities = 131/416 (31%), Positives = 215/416 (51%), Gaps = 44/416 (10%)

Query: 31  LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90
           LFF+ GF T LN  L+P+LK + QL   Q+ LI F F+ A    +LP+  +++++ YK G
Sbjct: 7   LFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRKVGYKTG 66

Query: 91  IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150
           + +G+ +  I   LFIPAA  +V+ALFL A  V+ +G T+LQ A NPYV  +G  E+AA+
Sbjct: 67  MAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGPEESAAA 126

Query: 151 RLTLTQAFNSLGTTVAPVFGAVLILSA--------ATDATVNAEADAVRFPYLLLALAFT 202
           R+++    N     +AP+    LIL +         T A ++  A+ + FPYL +A+   
Sbjct: 127 RVSVMGILNKGAGVIAPLVFTALILDSFKDRVGVELTQAQIDEMANGLVFPYLGMAIFIG 186

Query: 203 VLAIIFAILKPPDVQEDEPALSDKKEGS------AWQYRHLVLGAIGIFVYVGAEVSVGS 256
           VLA++      P+++ ++    +++EG+      A  + +L LG + +F YV  EV  G 
Sbjct: 187 VLALLVKKSPLPELENED----EQEEGTKGHTREALSHPNLALGVVALFFYVAVEVIAGD 242

Query: 257 FLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM-RYIDDGKALAFNAFVAII 315
            +  F        L   +     +Y     ++G  +G   + R+I   KAL  +A + ++
Sbjct: 243 TIGTF-----ALSLGVENYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISAILGLM 297

Query: 316 L-LFITVATTGHIAMWSVLAI-----------------GLFNSIMFPTIFSLALHGLGSH 357
           L L I        A+ + L +                 GL N+I++P ++ LAL G+G  
Sbjct: 298 LTLGILFGDNESYAIANALLVPFGGAMLPDTLLMIAFLGLANAIVWPAVWPLALSGMGKL 357

Query: 358 TSQGSGILCLAIVGGAIVPLIQG--ALADAIGIHLAFLMPIICYAYIAFYGLIGSK 411
           TS GS +L + I GGA  PL  G  + A ++G    +++ + CY +I FY + G K
Sbjct: 358 TSTGSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYAVKGYK 413


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: 493
Number of extensions: 28
Number of successful extensions: 4
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: 418
Length adjustment: 31
Effective length of query: 381
Effective length of database: 387
Effective search space:   147447
Effective search space used:   147447
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