GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Sphingomonas indica Dd16

Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate WP_085219373.1 B9N75_RS03075 ABC transporter ATP-binding protein

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



>NCBI__GCF_900177405.1:WP_085219373.1
          Length = 233

 Score =  127 bits (320), Expect = 2e-34
 Identities = 89/221 (40%), Positives = 126/221 (57%), Gaps = 19/221 (8%)

Query: 12  LAVQDIHKRYGDN----EVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQ 67
           + ++ + K YG      + LKGV L+  +G+ ++++G SGSGKST +  +  L+ P  G 
Sbjct: 7   IRLKGVTKTYGTGATAFQALKGVDLDVAQGEFLAVMGPSGSGKSTAMNILGCLDVPTGGN 66

Query: 68  IVVDGEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVL 127
            +  G  V+T  DR       D + L R R  L  VFQ FNL A  + LEN VE P+   
Sbjct: 67  YLFRGVPVET-LDR-------DQRALLR-RKYLGFVFQGFNLLARTSALEN-VELPLLYR 116

Query: 128 GLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTS 187
           G  ++E        LEKVGLA   +   P+ LSGGQQQRVAIARA+  +PDV+L DEPT 
Sbjct: 117 GETKEERHKAGMAALEKVGLADWWDHT-PAELSGGQQQRVAIARAIVTHPDVLLADEPTG 175

Query: 188 ALDPELVGEVLKVMQKL-AEEGRTMIVVTHE---MGFARNV 224
            LD E   E+++++  L    G T+++VTHE     FAR++
Sbjct: 176 NLDSERSVEIMELLTDLNRNAGITVLMVTHEPEMAAFARSI 216


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: 151
Number of extensions: 8
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: 263
Length of database: 233
Length adjustment: 24
Effective length of query: 239
Effective length of database: 209
Effective search space:    49951
Effective search space used:    49951
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