GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Echinicola vietnamensis KMM 6221, DSM 17526

Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate Echvi_3767 Echvi_3767 Gluconolactonase

Query= metacyc::MONOMER-13276
         (356 letters)



>FitnessBrowser__Cola:Echvi_3767
          Length = 344

 Score =  204 bits (520), Expect = 2e-57
 Identities = 117/300 (39%), Positives = 175/300 (58%), Gaps = 11/300 (3%)

Query: 58  ILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPSGHAE 117
           ++     IE +AS   W EGP+W+  G++LLFSD P N + K T +   S +L  SG++ 
Sbjct: 52  VISRDATIERMASGFDWVEGPLWIGKGDYLLFSDIPRNKVYKMTSEGDTSTYLNRSGYSG 111

Query: 118 PIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKV----DPVTRQRSVVVDNYKGKRFN 173
                  REPGSN + +  D ++ +   G R + K+    D      + +V +Y+GKR N
Sbjct: 112 E--GAYSREPGSNALLLDKDNQLVLMQHGNRKVAKMKGGLDAPAPDFTSLVHDYQGKRLN 169

Query: 174 SPNDLFFSKSGAVYFTDPPYGLTNLDESDIKEMNYNGVFRLSPDGRLDLIEAGLSRPNGL 233
           SPND  F K G +YFTDPPYGL        KE+++ G++ L  +G L L+++ LSRPNG+
Sbjct: 170 SPNDGIFDKQGNLYFTDPPYGLPPRFAG--KELSFQGIYCLKTNGTLVLLDS-LSRPNGI 226

Query: 234 ALSPDETKLYVSNSDRASPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNID 293
           ALSPDE  L+V+NSD  +   + Y L++ G   +R+L  +  +E    G  GLPDGM + 
Sbjct: 227 ALSPDEKHLFVANSDEKNAAWFQYPLEAPGEVDTRSLFYDATEEVLPGGRNGLPDGMKVH 286

Query: 294 KQGNLFASAPGGIYIFAPDGECLGLISGNPGQPLSNCCFGEKGQTLFISASHNVVRVRTK 353
            +G LFA+ P GI+IF   G+ LG I  + GQ  SNC F +  + L+++A  +++RV  K
Sbjct: 287 PKGYLFATGPDGIWIFDLKGKVLGKI--HTGQLTSNCTFTDDYKHLYVTAHRDILRVDLK 344


Lambda     K      H
   0.317    0.135    0.409 

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: 402
Number of extensions: 32
Number of successful extensions: 5
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: 356
Length of database: 344
Length adjustment: 29
Effective length of query: 327
Effective length of database: 315
Effective search space:   103005
Effective search space used:   103005
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 (21.6 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