GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylC in Caulobacter crescentus NA1000

Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate CCNA_01882 CCNA_01882 SMP-30/gluconolaconase/LRE-like protein

Query= metacyc::MONOMER-20628
         (289 letters)



>FitnessBrowser__Caulo:CCNA_01882
          Length = 293

 Score =  127 bits (320), Expect = 2e-34
 Identities = 98/289 (33%), Positives = 133/289 (46%), Gaps = 23/289 (7%)

Query: 1   MTAQVTCVWDLKATLGEGPIWHGDT--LWFVDIKQRKIHNYHPATGERFSFDAPDQVTFL 58
           MT  V  +   +  LGE P+W  D   L++VD     I  Y P T E+ S  AP  +  +
Sbjct: 1   MTFTVEIIGKERCRLGESPLWDADAGVLYWVDSMAPAIWRYDPFTSEQRSIPAPKPIGSV 60

Query: 59  APIVGATG-FVVGLKTGIHRFHPATG-FSLLLEVEDAALNNRPNDATVDAQGRLWFGTMH 116
             ++G  G  + GL  G++R    TG F+ +   +  A   R ND   D QGR   GTM 
Sbjct: 61  --VLGRPGELIAGLADGVYRVQLDTGAFTPIALPDTLAPIERFNDGKADRQGRFVTGTMA 118

Query: 117 -DGEENNSGSLYRMDLTGVARM--DRDICITNGPCVSPDGKTFYHTDTLEKTIYAFDL-A 172
              E    G LYR    G   +     I I N  C SP G T Y  D+L   ++AF    
Sbjct: 119 MHNETGRIGKLYRFSAGGAWEVLPTEPIEIANSTCFSPSGDTLYFADSLRHMVWAFSYDP 178

Query: 173 EDGLLSNKRVFVQFALGDDVYPDGSVVDSEGYLWTALWGGFGAVRFSPQGDAVTRIELPA 232
           + G +  KR F     G +  PDG+ VD+EG++W AL      +R SP G     +E PA
Sbjct: 179 KTGAVGEKRDFFD-TTGFNSAPDGATVDAEGHIWLALVQAQKLIRISPDGRLDRVVESPA 237

Query: 233 PNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAVPVDVAGQ 281
           P  + P FGG DL  LY T+    +SD        +GG     VD +G+
Sbjct: 238 PFCSCPAFGGEDLDILYVTS----ISD--------SGGRLKTDVDASGR 274


Lambda     K      H
   0.321    0.139    0.442 

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: 324
Number of extensions: 26
Number of successful extensions: 6
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: 289
Length of database: 293
Length adjustment: 26
Effective length of query: 263
Effective length of database: 267
Effective search space:    70221
Effective search space used:    70221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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