GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Flavobacterium glycines Gm-149

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_066330220.1 BLR17_RS12195 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_900100165.1:WP_066330220.1
          Length = 369

 Score =  187 bits (476), Expect = 3e-52
 Identities = 124/378 (32%), Positives = 203/378 (53%), Gaps = 19/378 (5%)

Query: 9   LLALAPLTGVAPQAQAASLYNLLVGTYTEG-SSEGIQVYRFDGADGSVKGPLRVAHTSNP 67
           L+ L  L+ +  QAQ    +NL++GTYT+   S+GI VY F+   G  +      +  NP
Sbjct: 6   LITLLLLSCICIQAQEKK-FNLIIGTYTKSCESKGIYVYDFNAETGDFQFKSSTENVINP 64

Query: 68  SYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSL 127
           S+++ + +   ++ VNE+G           +++++D  + +++ +++ +     P Y  +
Sbjct: 65  SFVSVSKNNDFIYSVNEDG------PKSTVSAFKYDTSNAKIEFVNKQEIHNPGPCY--I 116

Query: 128 SHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSVVS 186
            +D + +  ANY+    GSVAV     +GSL  + Q+  H    ++P RQ   HVHSV  
Sbjct: 117 INDDKNVITANYT---GGSVAVFGKNKNGSLTELKQLIKHSGKGINPARQEKSHVHSVQF 173

Query: 187 SPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAY 246
           SPD Q++ A DLG DK+++Y+Y P+ A +PL+  D   +    GSGPRH  FS +G+  Y
Sbjct: 174 SPDHQFVLATDLGTDKMYLYQYNPKVA-KPLELKDS--IKVKAGSGPRHFAFSKNGQQLY 230

Query: 247 LTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDN 306
           L  EL G + VF +   G+L  +Q   +    F+G   A  +H+S D RFL   NR + N
Sbjct: 231 LLQELDGTLSVFNY-NKGKLVLVQETTVLAPDFKGTSTAADIHISPDQRFLYATNRKEAN 289

Query: 307 QLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQ 366
            +  F +    G+L    R S  G  PR FA  P G F+LV +Q ++ + VF R+ ++G 
Sbjct: 290 TISCFKI-LKDGKLALASRTSSLGDGPRNFAIDPTGNFLLVGHQYTNNVVVFKRNKETGA 348

Query: 367 VGKTLQSVEVGSPSDLRF 384
           +  T + +E+ +P  L F
Sbjct: 349 LTDTGKRIELCAPVCLVF 366



 Score = 25.0 bits (53), Expect = 0.004
 Identities = 13/49 (26%), Positives = 27/49 (55%)

Query: 338 FSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFVA 386
           FSP  +FVL  +  +D++ ++  +P+  +  +   S++V + S  R  A
Sbjct: 173 FSPDHQFVLATDLGTDKMYLYQYNPKVAKPLELKDSIKVKAGSGPRHFA 221


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: 397
Number of extensions: 29
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 388
Length of database: 369
Length adjustment: 30
Effective length of query: 358
Effective length of database: 339
Effective search space:   121362
Effective search space used:   121362
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