GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Malonomonas rubra DSM 5091

Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= reanno::BFirm:BPHYT_RS07685
         (263 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  149 bits (376), Expect = 9e-41
 Identities = 96/280 (34%), Positives = 149/280 (53%), Gaps = 38/280 (13%)

Query: 7   TEACKLAVQDIHKRYG--------------DNEVL----------KGVSLNANKGDVISI 42
           TE  K+ V++++K +G              D E +          +  S    KG++  I
Sbjct: 2   TEPVKIEVKNLYKIFGPQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVI 61

Query: 43  IGASGSGKSTFLRCINFLERPNAGQIVVDGEMVKTKTDRAGNLEVADHKQLQRIR-TKLA 101
           +G SGSGKST +R +N L  P +GQ+++DGE +    D           QL ++R  KL+
Sbjct: 62  MGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMND----------DQLVKVRRAKLS 111

Query: 102 MVFQHFNLWAHMNVLENIVEAPIHVLGLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSG 161
           MVFQ F L  HM VL+N     + + G+ ++  E RA + LE+VGL    E   P  LSG
Sbjct: 112 MVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVGLEAWAESM-PDELSG 169

Query: 162 GQQQRVAIARALAMNPDVMLFDEPTSALDPELVGEVLKVMQKL-AEEGRTMIVVTHEMGF 220
           G QQRV +AR LA++PD++L DE  SALDP +  E+   + KL A+  RT++ ++H++  
Sbjct: 170 GMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDE 229

Query: 221 ARNVSNHVMFLHQGRTEEEGLPAEVLSAPRSERLKQFLSG 260
           A  + + +  +  GR  + G P E+L  P  + ++ F  G
Sbjct: 230 AMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRG 269


Lambda     K      H
   0.318    0.133    0.374 

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: 226
Number of extensions: 12
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: 263
Length of database: 415
Length adjustment: 28
Effective length of query: 235
Effective length of database: 387
Effective search space:    90945
Effective search space used:    90945
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 Apr 09 2024. 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