GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate 209322 DVU0386 amino acid ABC transporter, periplasmic amino acid-binding protein

Query= reanno::pseudo3_N2E3:AO353_03055
         (258 letters)



>MicrobesOnline__882:209322
          Length = 249

 Score =  108 bits (270), Expect = 1e-28
 Identities = 80/244 (32%), Positives = 117/244 (47%), Gaps = 12/244 (4%)

Query: 9   ALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWV 68
           AL L+  S+   A+EK    GI+A YPPFA    DG   GFD D  N +  +M  K V  
Sbjct: 12  ALVLAFASVAA-AEEKTYINGIDANYPPFAYVDKDGKPAGFDVDSMNWIAAKMGFKVVHK 70

Query: 69  EQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAE 128
             ++DG++P+L  +KID + S MSITD RKK + F+  Y+      V K  +++S +   
Sbjct: 71  PMDWDGIVPSLLAKKIDMVCSGMSITDARKKQITFSEPYWTVSQVFVAKKDSKLSVDDVY 130

Query: 129 LKGKKIGVQRGSIHNRFAEEVLKPLG--AEIKPYGSQNEIYLDVAAGRLDGTVADATLLD 186
              KK+GVQRG+      ++     G   E++ Y S      DV  GR+D    D    +
Sbjct: 131 KGKKKLGVQRGTSEADALQKQAPEKGWNFELRFYDSAPLAIEDVLNGRIDAAGMDILPAE 190

Query: 187 DGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQI 246
           D   K    K    +G     E +     G+A R  D     KIN     + A+  ++Q+
Sbjct: 191 DAAAK----KPVKILGTFGEPEDF-----GVATRNEDTELRGKINEGYKLLMADPYWQQL 241

Query: 247 QDKY 250
           +DKY
Sbjct: 242 KDKY 245


Lambda     K      H
   0.318    0.138    0.395 

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: 180
Number of extensions: 9
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: 258
Length of database: 249
Length adjustment: 24
Effective length of query: 234
Effective length of database: 225
Effective search space:    52650
Effective search space used:    52650
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: 47 (22.7 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