GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Mucilaginibacter mallensis MP1X4

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_091380910.1 BLU33_RS22265 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_900105165.1:WP_091380910.1
          Length = 382

 Score =  260 bits (664), Expect = 5e-74
 Identities = 144/392 (36%), Positives = 228/392 (58%), Gaps = 18/392 (4%)

Query: 1   MRRLPTLCLLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLR 60
           M++L  +       L+    +    S Y++L+GTYT G+S+GI VYR     G +     
Sbjct: 1   MKKLLLIVSFLFPVLSYAQSKKPVPSTYDVLIGTYTNGTSKGIYVYRLYEETGKLSYLNE 60

Query: 61  VAHT-----SNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQV 115
             +      +NPSYL  + + + ++ VNEN +GG        T+  F+  +G+++ I+  
Sbjct: 61  FTNVDDTAFTNPSYLCVSDNNKFVYAVNENKKGG-------VTALTFNANTGKMKFINSQ 113

Query: 116 QTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQV-ESHQASKVHP 174
            +    P + ++  D + +F+ANYS    GS+AVLPV  DGS+ P  QV +      V  
Sbjct: 114 LSQGADPCFVAVDKDQKNIFIANYS---SGSLAVLPVNKDGSIRPASQVIQDAGTGPVKD 170

Query: 175 RQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPR 234
           RQ   HVH    SP+ +YL   DLG DK+ V RY   + + PL  A+PAFV   PG+GPR
Sbjct: 171 RQEGPHVHMAALSPNEKYLLYTDLGTDKINVQRYKASKPQ-PLSPAEPAFVSVAPGNGPR 229

Query: 235 HLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADG 294
           H++FSADG++ YL  E+ G V  + ++ NG+L Q+Q+ D+    F G +G+ A+ +S DG
Sbjct: 230 HMVFSADGKYVYLLQEIGGFVNAYTYD-NGKLTQIQSVDMKRPEFGGNIGSAAIKISPDG 288

Query: 295 RFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQ 354
           RFL   NRG+ N++V +A++  +GQL FV R    G  PR+F+  P G+F++V+NQNSD 
Sbjct: 289 RFLYASNRGNANEIVQYAINAENGQLSFVARVPSLGKGPRDFSIDPQGKFLIVSNQNSDT 348

Query: 355 LRVFARDPQSGQVGKTLQSVEVGSPSDLRFVA 386
           + V+  D +SG +G  + ++++G+P  L+ V+
Sbjct: 349 IYVYRIDQKSGWIGSVVSTLKIGNPVCLKIVS 380


Lambda     K      H
   0.318    0.135    0.395 

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: 487
Number of extensions: 38
Number of successful extensions: 13
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: 388
Length of database: 382
Length adjustment: 30
Effective length of query: 358
Effective length of database: 352
Effective search space:   126016
Effective search space used:   126016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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