GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Acidovorax sp. GW101-3H11

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= TCDB::P23200
         (336 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2880
          Length = 350

 Score =  134 bits (338), Expect = 3e-36
 Identities = 96/308 (31%), Positives = 161/308 (52%), Gaps = 16/308 (5%)

Query: 20  VVLLVLLAII-IFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGL 78
           V+ LVLL I     +  F +  N+ N+LT+++   IIA+G+  +I++ G DLS G    +
Sbjct: 44  VIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVG---SM 100

Query: 79  AAVVAATLLQSMDNANKVFPEMATMPIALVI--LIVCAIGAVIGLINGLIIAYLNVTPFI 136
           AA++A +++  M   N + P + +   A+V+  L+   +GAV GL++GL+I    + PFI
Sbjct: 101 AALIAGSVILFM---NAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFI 157

Query: 137 TTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAF 196
            TLGT+    GI   Y  +         ++  S             +    +  L+    
Sbjct: 158 VTLGTL----GIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIV 213

Query: 197 VWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSA 256
             V+ N+T +G+ + AIG N + A+ + V+V    ++ Y L GV      +L   R+GSA
Sbjct: 214 GGVILNRTAYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSA 273

Query: 257 TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVIN--YGLTYIGVNPYWQY 314
           +   G ++EL+AIAA +VGG    GG G++ G V G I+ +VI+    LT I ++ Y   
Sbjct: 274 SPTTGLLWELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSI-ISVYLNA 332

Query: 315 IIKGAIII 322
            ++G +II
Sbjct: 333 AVQGFVII 340


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: 306
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 336
Length of database: 350
Length adjustment: 29
Effective length of query: 307
Effective length of database: 321
Effective search space:    98547
Effective search space used:    98547
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