GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Azospirillum brasilense Sp245

Align galactaro-1,5-lactonase (characterized)
to candidate AZOBR_RS22710 AZOBR_RS22710 gluconolactonase

Query= reanno::WCS417:GFF3393
         (291 letters)



>FitnessBrowser__azobra:AZOBR_RS22710
          Length = 296

 Score =  271 bits (692), Expect = 2e-77
 Identities = 138/285 (48%), Positives = 171/285 (60%), Gaps = 5/285 (1%)

Query: 8   DARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGNWV 67
           D RN  GE PVW     +  W+DIP   + R   ++G    WT P+M+  +     G  V
Sbjct: 8   DLRNGTGENPVWDAERGSWTWIDIPARTIHRLDPSSGAHRRWTLPEMIGSLVLRPDGGVV 67

Query: 68  AGMETGFFQLT-PHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLNA 126
              ETG F +  P   G    T LA    P++ MR NDGRCDRQGRFW  SMV+++    
Sbjct: 68  CACETGVFDVDLPGEGGEAVVTALATHRFPKEGMRFNDGRCDRQGRFWLSSMVMDISKGD 127

Query: 127 AEGTLYRYT-SGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGT 185
           + G  +R+T +         G+I  NG AFSPDGRT+YASDSH  V+ +WA+DYD DTGT
Sbjct: 128 SSGLWHRFTRADGLTETGTGGYIIPNGSAFSPDGRTLYASDSHRDVRMVWAWDYDTDTGT 187

Query: 186 PSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTM 245
             NRR FVDM   +GRPDGAAVD DGCYWIC  D G I RF+P+G LDR + VP++KPTM
Sbjct: 188 ADNRRPFVDMRAMVGRPDGAAVDIDGCYWICCLDEGCIKRFTPNGDLDRRIEVPMRKPTM 247

Query: 246 CAFGGSRLDTLFVTSIR---DDQSEQSLSGGVFALNPGVVGLPEP 287
           CAFGG  L T+ VTS+     D +E    G V   +PG  GLPEP
Sbjct: 248 CAFGGPDLRTMLVTSLSRGPADLAEDPHGGRVLMFDPGAQGLPEP 292


Lambda     K      H
   0.321    0.137    0.443 

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: 423
Number of extensions: 32
Number of successful extensions: 4
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: 291
Length of database: 296
Length adjustment: 26
Effective length of query: 265
Effective length of database: 270
Effective search space:    71550
Effective search space used:    71550
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.

Links

Downloads

Related tools

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