GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Tatumella morbirosei LMG 23360

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_038017558.1 HA49_RS11685 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_000757425.2:WP_038017558.1
          Length = 364

 Score =  217 bits (552), Expect = 5e-61
 Identities = 145/355 (40%), Positives = 202/355 (56%), Gaps = 19/355 (5%)

Query: 36  TEGSSEGIQVYRFDG-ADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTV 94
           T   SEGI  YR    ADGS++   R+  T NPS++  + DQR L+  NE+         
Sbjct: 23  TAHPSEGI--YRLQLLADGSLQVVDRLK-TDNPSWIVLSQDQRFLYTTNES-------ET 72

Query: 95  GRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSV-QPEGSVAVLPVR 153
           GR ++    P  G L+ ++  QT   HPT++ L+ DGRYL  ANYS         V P+ 
Sbjct: 73  GRVSAIEITP-QGPLRLLNSQQTRGAHPTHACLTPDGRYLLAANYSDGMNNAGFIVFPLV 131

Query: 154 ADGSLAPVVQVE--SHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPE 211
             G +   VQ    +  ++ V  RQ SGH HSV  SPDG+ L+  DLGAD V +Y Y P 
Sbjct: 132 DSGEIGEAVQHVRFAEGSAVVAERQQSGHAHSVNISPDGKILYVADLGADIVRIYHYQP- 190

Query: 212 QAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQT 271
           Q + P        +  P G+GPRH+ FS DGRF  +  E+S QV +F     G+L  +QT
Sbjct: 191 QNDTPFLHQPQDDIRLPGGAGPRHIAFSDDGRFVCVVSEMSAQVHLF-QMNEGQLNAIQT 249

Query: 272 HDLAPA-GFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEG 330
            +LA +   + K GAG L+ S DGRFL V NR   N++V F+VDP SG+L   ++ S  G
Sbjct: 250 LELADSDSAEDKAGAGVLY-SPDGRFLYVGNRQQRNEIVVFSVDPHSGRLSDRQQFSSGG 308

Query: 331 TEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFV 385
            EPR FAF   G F+LVAN  S+++ V ARDP +G +  T  S+++G+P+D++F+
Sbjct: 309 IEPRAFAFDNTGHFLLVANVWSNRVTVLARDPHNGGLRPTGNSLDIGTPTDIKFL 363


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: 529
Number of extensions: 38
Number of successful extensions: 10
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: 364
Length adjustment: 30
Effective length of query: 358
Effective length of database: 334
Effective search space:   119572
Effective search space used:   119572
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