GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Herbaspirillum seropedicae SmR1

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 HSERO_RS10775 HSERO_RS10775 cysteine ABC transporter substrate-binding protein

Query= TCDB::Q9HU31
         (250 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS10775 HSERO_RS10775 cysteine
           ABC transporter substrate-binding protein
          Length = 267

 Score =  142 bits (359), Expect = 5e-39
 Identities = 100/266 (37%), Positives = 144/266 (54%), Gaps = 26/266 (9%)

Query: 2   KNYKKILLAA--AATLAFALDASAAD---------KLRIGTEGAYPPFNGIDA-SGQAVG 49
           KN K+ LLA   AA LA +L  SAAD          L++  EG YPPFN  D  +G+  G
Sbjct: 3   KNIKQWLLAGVGAALLASSLSVSAADLLQSVKSSGTLKVALEGNYPPFNFKDPKTGELTG 62

Query: 50  FDLDIGKALCAKMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYY 109
           F++D+ K L AK+  +    T++W GI+  L A K+D I+  + ITDER++A DF+DPY 
Sbjct: 63  FEVDVAKLLAAKLGVKPVFTTTEWSGILAGLGAGKYDVIINQVGITDERQKAFDFSDPYT 122

Query: 110 TNKLQFVAPKSV--DFKTDKDSLKGKVIGAQRATIAGTWLEDNMADV--VTIKLYDTQEN 165
            +  Q +  K    +FK+ +D LKGK +G  +    GT  E     V  + ++ Y     
Sbjct: 123 LSSAQLIVRKDEKREFKSLED-LKGKKLGLGQ----GTNFEQKAKAVPGIDVRTYPGSPE 177

Query: 166 AYLDLSSGRLDGVLADKFVQYDWLKSDAGKEFEFK-GEPVFDNDKIGIAVRKGDP-LREK 223
              DL++GR+D  L D  +    LKS        K G P+   DKIGI  RKG+P  +  
Sbjct: 178 YLADLAAGRIDAALNDSLLVGYILKS---TNLPLKAGSPIGAVDKIGIPFRKGNPEFKAA 234

Query: 224 LNAALKEIVADGTYKKINDKYFPFSI 249
           LN AL +I ADG++K  ++K+F   +
Sbjct: 235 LNKALADIKADGSFKAASEKWFGIDV 260


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: 210
Number of extensions: 15
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: 250
Length of database: 267
Length adjustment: 24
Effective length of query: 226
Effective length of database: 243
Effective search space:    54918
Effective search space used:    54918
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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