GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Caulobacter crescentus NA1000

Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate CCNA_01282 CCNA_01282 gluconolactonase

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



>FitnessBrowser__Caulo:CCNA_01282
          Length = 347

 Score =  293 bits (751), Expect = 4e-84
 Identities = 157/354 (44%), Positives = 213/354 (60%), Gaps = 16/354 (4%)

Query: 7   SRRECLSAAVMVPIAAMTATATITGSAQAAKNNMNGSTIGKITKFSPRLDAILDVSTPIE 66
           +RR  L A V +   A    A   G+            IG+I + SP LDA++D + PIE
Sbjct: 3   TRRAMLGAGVALIAGAQGFAAQARGAGSPK--------IGRIRRLSPELDAVVDANAPIE 54

Query: 67  VIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPSGHAEPIPAGQFRE 126
            +   I W+EGP WV NG++LLFSD P N+M +W    G + FL+PSG+  P P   FRE
Sbjct: 55  QLTDGITWAEGPAWVANGSYLLFSDVPGNVMHRWDAKGGKTDFLRPSGYDGP-PTKIFRE 113

Query: 127 PGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFNSPNDLFFSK---- 182
            G+NG  +   G++ V D G RA+ ++D  TR+++++   + GK+FNSPNDL   +    
Sbjct: 114 AGTNGAIISTAGELLVCDCGNRAVARIDLSTRKKTLLATTFNGKKFNSPNDLVEVRHGPL 173

Query: 183 SGAVYFTDPPYGLTNLDESDIKEMNYNGVFRLSPDGRLDLIEAGLSRPNGLALSPDETKL 242
            G++YFTDPPYGL   D S  KE  +NGV+ L P+G + L++  LS PNG+ LSPD  +L
Sbjct: 174 KGSLYFTDPPYGLEGGDASPAKEQAFNGVYLLRPNGEVALVDGSLSFPNGVGLSPDGRRL 233

Query: 243 YVSNSDRASPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNIDKQGNLFASA 302
           YV+ SD   P I  Y L ++GLPT+  +  +   +    G  GLPDGM +D QG LFAS 
Sbjct: 234 YVAISDPKRPVIMAYDLGADGLPTASRVFFD-ASDLLKAGGPGLPDGMKVDAQGRLFASG 292

Query: 303 PGGIYIFAPDGECLGLISGNPGQPLSNCCFGEKGQTLFISASHNVVRVRTKTFG 356
           PG I I  PD + LG+I    G P +NC FGE G TLFI+++H V RVRTKT G
Sbjct: 293 PGCIMILTPDAKLLGVI--ETGFPAANCVFGEDGGTLFITSNHLVARVRTKTKG 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: 493
Number of extensions: 43
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: 347
Length adjustment: 29
Effective length of query: 327
Effective length of database: 318
Effective search space:   103986
Effective search space used:   103986
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