GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Sinorhizobium meliloti 1021

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate SMa0495 SMa0495 ABC transporter substrate-binding protein

Query= TCDB::Q9HU31
         (250 letters)



>FitnessBrowser__Smeli:SMa0495
          Length = 272

 Score =  162 bits (409), Expect = 9e-45
 Identities = 97/265 (36%), Positives = 148/265 (55%), Gaps = 18/265 (6%)

Query: 1   MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60
           MKN++  L      +  +   + AD LR+G E  Y PFN   + G+  G+D+D+ K +  
Sbjct: 4   MKNWQTSLTGLITAVLLSAAPANADTLRVGMECTYAPFNYRTSDGKLEGYDVDVAKGISE 63

Query: 61  KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120
            +  + E V  +WDG+IPAL A KFD I+ASMSITD+RK+ +DF+ PY  +  + V P  
Sbjct: 64  IIGVDFEYVCQEWDGMIPALLANKFDLIIASMSITDKRKEQIDFSSPYRNSVGRIVGPVG 123

Query: 121 VDFKTDKD-------SLKGKVIGAQRATIAGTWLEDNM--ADVVTIKLYDTQENAYLDLS 171
            D K   D       +  G  IG +RA+    W    +  AD+V   LYD+ E  YLDL 
Sbjct: 124 KDLKLFDDKGQPVVGNFDGLRIGVERASTYFEWFSAKLPKADLV---LYDSNEAMYLDLK 180

Query: 172 SGRLDGVLADKFVQYDWLKSDAGK-EFEFKG----EPVFDNDKIGIAVRKG-DPLREKLN 225
           +GR+D ++ +    +    S  GK ++EF G    EP F    +G+ +RKG D LR+K++
Sbjct: 181 NGRVDVIMTNPMKAHLSFLSGEGKGKYEFIGPEVNEPKFFGPGVGVGLRKGNDELRDKIS 240

Query: 226 AALKEIVADGTYKKINDKYFPFSIY 250
           AA+++++ +G  K+   K FPF I+
Sbjct: 241 AAIRKLIREGKLKEYALKIFPFQIH 265


Lambda     K      H
   0.317    0.135    0.392 

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: 237
Number of extensions: 16
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: 250
Length of database: 272
Length adjustment: 25
Effective length of query: 225
Effective length of database: 247
Effective search space:    55575
Effective search space used:    55575
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