GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Collimonas pratensis Ter91

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_061945961.1 CPter91_RS07485 ribose ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_001584185.1:WP_061945961.1
          Length = 328

 Score =  196 bits (498), Expect = 7e-55
 Identities = 124/317 (39%), Positives = 181/317 (57%), Gaps = 20/317 (6%)

Query: 13  LKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSA 72
           L+  G+  VLL+L+         F ++ NLS I  Q+SV I++A G+  +I+T G DLS 
Sbjct: 22  LRTVGMLPVLLLLVLGFALMSENFFTVQNLSIITQQASVNIVLAAGMTFVILTAGIDLSV 81

Query: 73  GRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNV 132
           G  +  AAVVA  +L S+       P+   + IA  I      G ++GL NG +IA++ +
Sbjct: 82  GAILAAAAVVA--MLASLS------PQFGMLGIAAGI----GFGLLLGLANGALIAFMRL 129

Query: 133 TPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALI 192
            PFI TLG +  + G+  L  D      +   D  F+ F      LG   + ++   AL+
Sbjct: 130 PPFIVTLGALTAMRGLARLLAD---DKTVFNPDLPFA-FIGNDSLLG---VPWLVIIALV 182

Query: 193 AVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGR 252
            VA  W +  +T  G  I+A+GGN EAA++SG+ V   LL +YA+SG+    G ++ A R
Sbjct: 183 VVALSWFILRRTVIGVQIYAVGGNHEAARLSGIKVWKVLLFVYAVSGLLAGLGAVMTASR 242

Query: 253 IGSATN-NLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPY 311
           + +A    LG  YELDAIAA ++GG SF+GGVG++ G + G +I  V+  GL  +GV+  
Sbjct: 243 LSAANGLQLGQSYELDAIAAVILGGTSFTGGVGSIGGTLIGALIIAVLTNGLVLLGVSDI 302

Query: 312 WQYIIKGAIIIFAVALD 328
           WQYIIKG +II AVALD
Sbjct: 303 WQYIIKGIVIIGAVALD 319


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: 303
Number of extensions: 14
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: 328
Length adjustment: 28
Effective length of query: 308
Effective length of database: 300
Effective search space:    92400
Effective search space used:    92400
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.

Links

Downloads

Related tools

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