GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Tatumella morbirosei LMG 23360

Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_038022659.1 HA49_RS07350 galactose/glucose ABC transporter substrate-binding protein MglB

Query= TCDB::P0AEE5
         (332 letters)



>NCBI__GCF_000757425.2:WP_038022659.1
          Length = 331

 Score =  520 bits (1339), Expect = e-152
 Identities = 259/331 (78%), Positives = 291/331 (87%)

Query: 1   MNKKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLL 60
           M  +VL L+ +MA M+   A+HAAD RIGVTIYKYDDNFMS+VRK IE++AKA   VQLL
Sbjct: 1   MKTRVLALTVLMAGMMASFASHAADARIGVTIYKYDDNFMSMVRKDIEKEAKAVGGVQLL 60

Query: 61  MNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRK 120
           MNDSQNDQSKQNDQIDVL+AKGVK LA+NLVDPAAA TVI+KAR  +VPVVFFNKEP+ K
Sbjct: 61  MNDSQNDQSKQNDQIDVLMAKGVKVLAVNLVDPAAAPTVIDKARSNDVPVVFFNKEPTAK 120

Query: 121 ALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEA 180
           AL SYDKAYYVGTDSKESG+IQG LI KHW AN GWDLNKDG +Q+VLLKGEPGHPDAEA
Sbjct: 121 ALASYDKAYYVGTDSKESGVIQGQLIEKHWKANPGWDLNKDGVLQYVLLKGEPGHPDAEA 180

Query: 181 RTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMG 240
           RT YVI+ LN  GIKT+QL LDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMG
Sbjct: 181 RTRYVIETLNKDGIKTQQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMG 240

Query: 241 AVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKG 300
           AVEALKAHNK+S+PVFGVDALPEALALVKSG +AGTVLNDA NQAKA  D++KNLA+GK 
Sbjct: 241 AVEALKAHNKASVPVFGVDALPEALALVKSGQMAGTVLNDAENQAKAVVDMSKNLAEGKP 300

Query: 301 AADGTNWKIDNKVVRVPYVGVDKDNLAEFSK 331
           A +GT + + +K+VRVPYV VD+DNL++F K
Sbjct: 301 ATEGTAFTLKDKIVRVPYVPVDRDNLSKFVK 331


Lambda     K      H
   0.313    0.129    0.363 

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: 453
Number of extensions: 11
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: 332
Length of database: 331
Length adjustment: 28
Effective length of query: 304
Effective length of database: 303
Effective search space:    92112
Effective search space used:    92112
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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