GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Rhodobacter johrii JA192

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_003046325.1:WP_108223269.1
          Length = 363

 Score =  152 bits (383), Expect = 2e-41
 Identities = 97/318 (30%), Positives = 160/318 (50%), Gaps = 20/318 (6%)

Query: 20  VVLLVLLAII-IFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGL 78
           +VL+V ++I        F S   L+ IL Q ++  I+      +++T G DLS G  + L
Sbjct: 49  IVLVVSVSIFGALLGQKFFSAFTLTLILQQVAIVGIVGAAQTLVVLTAGIDLSVGAIMVL 108

Query: 79  AAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITT 138
           ++V+              F     +P  L +L   A GA IG +NG ++A + + PFI T
Sbjct: 109 SSVIMGQ-----------FTFRYGIPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFIVT 157

Query: 139 LGTMIIVYGINSLY--------YDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYA 190
           LG   IV   N LY         D    +PI  F              G    +Y     
Sbjct: 158 LGMWQIVLAANFLYSANETIRSQDISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAVLL 217

Query: 191 LIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEA 250
           ++ V  +  +  +T +G++++A+G +P+AA+++GV     L+ +Y LSG+  A  G +  
Sbjct: 218 ILLVLVIAYVLRQTAWGRHVYAVGDDPDAAELAGVQTRNVLVTVYTLSGLICALAGWVMI 277

Query: 251 GRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNP 310
           GR+GS +   G    +++I A V+GG+S  GG G+V+G++ G +I  V + GL  +G +P
Sbjct: 278 GRLGSVSPTAGQFANIESITAVVIGGISLFGGRGSVLGMLFGALIVGVFSLGLKLMGTDP 337

Query: 311 YWQYIIKGAIIIFAVALD 328
            W Y++ G +II AVA+D
Sbjct: 338 QWTYLLIGMLIIAAVAVD 355


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: 283
Number of extensions: 10
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: 336
Length of database: 363
Length adjustment: 29
Effective length of query: 307
Effective length of database: 334
Effective search space:   102538
Effective search space used:   102538
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 24 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