GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocF in Haloterrigena daqingensis JX313

Align arginase (EC 3.5.3.1) (characterized)
to candidate WP_076582366.1 BB347_RS07370 agmatinase family protein

Query= metacyc::MONOMER-14987
         (338 letters)



>NCBI__GCF_001971705.1:WP_076582366.1
          Length = 335

 Score = 92.8 bits (229), Expect = 1e-23
 Identities = 91/297 (30%), Positives = 132/297 (44%), Gaps = 30/297 (10%)

Query: 62  SLLGVPLGHNSSFLQGPAFAPPRIREAM--WC-------GSTNSTTEEGKELDDPRI-LT 111
           ++LG P     S   G  + P  IR A   W        G TN   + GK++D  R  + 
Sbjct: 46  AVLGAPYDGAVSNRPGARYGPEAIRRASAWWAYLSGYKGGLTNM--DSGKQVDFSRFAVA 103

Query: 112 DVGDVPVQELRDAGVDDDRLMSIISESVKLVMEENPLRPLVLGGDHSISYPVVRAVSEKL 171
           D GDVPV  +       DR  +  S +  +        P+VLGGDH  +YP V   +E +
Sbjct: 104 DCGDVPVFPM-------DRETTAESITAHVATAAERAFPVVLGGDHYCTYPSVTGFAEGI 156

Query: 172 GGP-IDILHLDAHPD-IYHAFEGNKYSHASSFARIMEGGYA--RRLLQVGIRSINKEGR- 226
               I  + +DAH D +  +    ++ H S    I +  YA    +  VGIR        
Sbjct: 157 DADSIGFVQIDAHTDTVSESAVFGEHFHGSPTHHIADSEYAAYENVSHVGIRGYEGPAFF 216

Query: 227 EQGKRFGVEQYEMRTFSQD--RQFLENL--KLGEGVKGVYISVDVDCMDPAFAPGVSHIE 282
           E     G+  + M    +   R  + +      +GV  VY++ D+D +DPA APG     
Sbjct: 217 EFADESGLNLFTMADVRERGIRSVVTDAIDAAADGVDAVYVTFDIDGVDPAVAPGTGTPV 276

Query: 283 PGGLSFRDVLNILHNLQA-DVVGA-DVVEFNPQRDTVDGMTAMVAAKLVRELTAKIS 337
           PGGLS R+ L ++  L A D VGA D++E  P  D  +G   + A  LVR L  K +
Sbjct: 277 PGGLSAREALTVMDILGARDSVGAVDLMEVAPTYDPTEGTQRLAAYLLVRFLEQKFA 333


Lambda     K      H
   0.318    0.136    0.389 

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: 302
Number of extensions: 18
Number of successful extensions: 2
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: 338
Length of database: 335
Length adjustment: 28
Effective length of query: 310
Effective length of database: 307
Effective search space:    95170
Effective search space used:    95170
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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