GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudomonas fluorescens FW300-N2E2

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf6N2E2_5970 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= TCDB::P23200
         (336 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5970
          Length = 322

 Score =  166 bits (421), Expect = 6e-46
 Identities = 109/316 (34%), Positives = 164/316 (51%), Gaps = 22/316 (6%)

Query: 19  YVVLLVLLAIIIF---QDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQ 75
           +V+LL  + I +        FLS LN+  +    S   I A  +   + +   DLS G  
Sbjct: 24  WVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSV 83

Query: 76  VGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPF 135
           +  A VVAA +++   + N VF         L I     +G ++GLING++IA L V   
Sbjct: 84  IACAGVVAAVVMR---DTNSVF---------LGISAALVMGLIVGLINGIVIAKLRVNAL 131

Query: 136 ITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVA 195
           ITTL TM IV G   L Y F     +      F  F  G +    F +       ++   
Sbjct: 132 ITTLATMQIVRG---LAYIFANGKAVGVSQESFFVFGNGQM----FGVPVPILITIVCFL 184

Query: 196 FVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGS 255
           F   L N T +G+N  AIGGN EAA ++GVNV    ++I+A+ GV  A  G++ A R+ S
Sbjct: 185 FFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTS 244

Query: 256 ATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYI 315
               +G  +EL  I+ACV+GGVS SGG+G +  V+ GV+I  +I   +    ++ ++QY+
Sbjct: 245 GQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYV 304

Query: 316 IKGAIIIFAVALDSLK 331
           I+G+I++ AV +D LK
Sbjct: 305 IRGSILLLAVVIDRLK 320


Lambda     K      H
   0.327    0.143    0.415 

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: 270
Number of extensions: 15
Number of successful extensions: 6
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: 336
Length of database: 322
Length adjustment: 28
Effective length of query: 308
Effective length of database: 294
Effective search space:    90552
Effective search space used:    90552
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: 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