GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Burkholderia phytofirmans PsJN

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>FitnessBrowser__BFirm:BPHYT_RS16055
          Length = 335

 Score =  194 bits (493), Expect = 3e-54
 Identities = 115/309 (37%), Positives = 171/309 (55%), Gaps = 23/309 (7%)

Query: 19  YVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGL 78
           ++ LLV+  +++F   +FLS  N+ N+L Q S+  IIA+G+  +I+T G DLS G  + L
Sbjct: 40  FIGLLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMAL 99

Query: 79  AAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITT 138
           A  +AA L+            +A M     + I  A+G   G  NG  +A+  + P I T
Sbjct: 100 AGTLAAGLM------------VAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVT 147

Query: 139 LGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAFV- 197
           L TM I  G+  +Y    G  PI G     S F  G +      L       ++AV +V 
Sbjct: 148 LATMGIARGLALIY---TGGYPIDGLPDWVSFFGSGKI------LGVQAPVVIMAVIYVI 198

Query: 198 -WVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSA 256
            WVL  +  FG+ ++AIGGN +A ++SGV V    L++Y ++G+  AF  ++   R+ S 
Sbjct: 199 AWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSG 258

Query: 257 TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYII 316
             N G  +ELDAIAA V+GG S SGG G++IG + G ++  V+N GL  +GVNPY Q +I
Sbjct: 259 QPNAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVI 318

Query: 317 KGAIIIFAV 325
           KG II+ A+
Sbjct: 319 KGGIILLAI 327


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: 332
Number of extensions: 20
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: 336
Length of database: 335
Length adjustment: 28
Effective length of query: 308
Effective length of database: 307
Effective search space:    94556
Effective search space used:    94556
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