GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Klebsiella michiganensis M5al

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS19635 BWI76_RS19635 galactoside ABC transporter permease MglC

Query= TCDB::P23200
         (336 letters)



>FitnessBrowser__Koxy:BWI76_RS19635
          Length = 336

 Score =  625 bits (1613), Expect = 0.0
 Identities = 322/336 (95%), Positives = 330/336 (98%)

Query: 1   MSALNKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVA 60
           MSALNKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVA
Sbjct: 1   MSALNKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVA 60

Query: 61  GLIVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIG 120
           GLIVTQGTDLSAGRQVGLAAV+AAT+LQ++DNANKVFPEMATMPI LVIL+VCAIGAVIG
Sbjct: 61  GLIVTQGTDLSAGRQVGLAAVIAATMLQAVDNANKVFPEMATMPIPLVILLVCAIGAVIG 120

Query: 121 LINGLIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGS 180
           LING+IIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDS FS FAQGFVALGS
Sbjct: 121 LINGIIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSHFSQFAQGFVALGS 180

Query: 181 FRLSYITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGV 240
           FRLSYITFYALIAV FVW+LWNKTRFGKNIFAIGGNPEAAKVSGVNV LNLLMIYALSGV
Sbjct: 181 FRLSYITFYALIAVFFVWILWNKTRFGKNIFAIGGNPEAAKVSGVNVALNLLMIYALSGV 240

Query: 241 FYAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVIN 300
           FYAFGG+LEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTV GVVTGVIIFTVIN
Sbjct: 241 FYAFGGLLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVFGVVTGVIIFTVIN 300

Query: 301 YGLTYIGVNPYWQYIIKGAIIIFAVALDSLKYARKK 336
           YGLTYIGVNPYWQYIIKGAIIIFAVALDSLKYARKK
Sbjct: 301 YGLTYIGVNPYWQYIIKGAIIIFAVALDSLKYARKK 336


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: 520
Number of extensions: 19
Number of successful extensions: 1
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: 336
Length adjustment: 28
Effective length of query: 308
Effective length of database: 308
Effective search space:    94864
Effective search space used:    94864
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