GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Erythrobacter marinus HWDM-33

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_047094318.1 AAV99_RS11970 ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_001013305.1:WP_047094318.1
          Length = 240

 Score =  132 bits (333), Expect = 5e-36
 Identities = 85/228 (37%), Positives = 129/228 (56%), Gaps = 15/228 (6%)

Query: 4   LEVQDLHKRYG----SHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59
           +E++ + K +G    + + LKGV +K   GD ++I+G SGSGKST +  +  L+ P  G 
Sbjct: 7   IELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLDVPTDGI 66

Query: 60  ILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVL 119
                 E++ +          D + L R R  L  VFQ FNL +  TA+EN+ E P+   
Sbjct: 67  FRFRGIEVQALTR--------DQRSLLRRRY-LGFVFQGFNLLARTTALENV-ELPLLYR 116

Query: 120 GMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSA 179
           G +K + R  AE  L+KVG+       P  +SGG+QQRVAIARAL  +P+V+L DEPT  
Sbjct: 117 GETKKQRRIAAERSLDKVGLLPWASHTPAELSGGQQQRVAIARALVTDPDVLLADEPTGN 176

Query: 180 LDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVV 227
           LD E   ++++++  L+  G T+++VTHE   A E +  +V    G+V
Sbjct: 177 LDTERSLEIMELLTDLSDTGITVLMVTHEEEMA-EYARTIVHFRDGLV 223


Lambda     K      H
   0.317    0.131    0.366 

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: 139
Number of extensions: 8
Number of successful extensions: 3
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: 254
Length of database: 240
Length adjustment: 24
Effective length of query: 230
Effective length of database: 216
Effective search space:    49680
Effective search space used:    49680
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: 46 (22.3 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