GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Caulobacter crescentus NA1000

Align L-arabinonolactonase (characterized, see rationale)
to candidate CCNA_01882 CCNA_01882 SMP-30/gluconolaconase/LRE-like protein

Query= uniprot:A0A1I2AUG6
         (300 letters)



>FitnessBrowser__Caulo:CCNA_01882
          Length = 293

 Score =  149 bits (375), Expect = 1e-40
 Identities = 105/282 (37%), Positives = 136/282 (48%), Gaps = 12/282 (4%)

Query: 13  LGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALCEADGWLLLGLA 72
           LGE  LW      LYW D  A  +WR+ P     RS   P+ +G + L    G L+ GLA
Sbjct: 15  LGESPLWDADAGVLYWVDSMAPAIWRYDPFTSEQRSIPAPKPIGSVVLGRP-GELIAGLA 73

Query: 73  TRLAFFRPEDDLLLPLVSVEPDLPT-RLNDGACDRQGRFVFGTLHEPAAGETRQPIGAFY 131
             +   + +     P+   +   P  R NDG  DRQGRFV GT+   A       IG  Y
Sbjct: 74  DGVYRVQLDTGAFTPIALPDTLAPIERFNDGKADRQGRFVTGTM---AMHNETGRIGKLY 130

Query: 132 RLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDRCG---EPRVFA 188
           R +A    E L    I I+NS  FSP G T+YF DS   ++    Y  + G   E R F 
Sbjct: 131 RFSAGGAWEVLPTEPIEIANSTCFSPSGDTLYFADSLRHMVWAFSYDPKTGAVGEKRDFF 190

Query: 189 RVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQPTRPAFGDSPL 248
                   PDG+ VDA+G +W A     +++R +PDGR+DR+VE PA   + PAFG   L
Sbjct: 191 DTTGFNSAPDGATVDAEGHIWLALVQAQKLIRISPDGRLDRVVESPAPFCSCPAFGGEDL 250

Query: 249 DTLYITSARDGLSSAALATQ-PLAGALFAADA-GASGLPEPR 288
           D LY+TS  D  S   L T    +G L A    G  G+ E R
Sbjct: 251 DILYVTSISD--SGGRLKTDVDASGRLMAFHGLGVRGIAETR 290


Lambda     K      H
   0.321    0.139    0.451 

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: 305
Number of extensions: 17
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: 300
Length of database: 293
Length adjustment: 26
Effective length of query: 274
Effective length of database: 267
Effective search space:    73158
Effective search space used:    73158
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