GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Pseudomonas fluorescens FW300-N1B4

Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate Pf1N1B4_5844 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein

Query= CharProtDB::CH_003045
         (260 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5844
          Length = 259

 Score =  236 bits (601), Expect = 5e-67
 Identities = 118/260 (45%), Positives = 172/260 (66%), Gaps = 3/260 (1%)

Query: 1   MKKTVLALSLLIG-LGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEM 59
           MKK V+  +L +  L  TA +  A P  +R+G +  Y PFS K+  G+  GFD+D+G+ +
Sbjct: 1   MKKRVMFGALALSMLSLTAMADDAKP--IRLGIEAGYPPFSMKNPDGKLTGFDVDIGDAL 58

Query: 60  CKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAA 119
           C++M+VKCTWV  +FD LIP+LK KKIDAI+SS++ITD R++ + F+ K Y   +R +  
Sbjct: 59  CEQMKVKCTWVEQEFDGLIPALKVKKIDAILSSMTITDDRKKNVDFTIKYYHTPARFVMK 118

Query: 120 KGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDA 179
           +G+ ++  L  LKGK VGVL+ ST + +A +     G+++V Y +Q     D+ AGRLDA
Sbjct: 119 EGTDVKDPLTELKGKKVGVLRASTHDRFATEVLVPAGINLVRYGSQQEANLDMVAGRLDA 178

Query: 180 ALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTEL 239
            L D V   +GFLK  AGK +AF GP+ +D KYFG G G+ +RK D EL   F+ A+TE+
Sbjct: 179 MLADSVNLDDGFLKTDAGKGFAFVGPTYEDAKYFGGGAGIAVRKGDKELADKFNTAITEI 238

Query: 240 RQDGTYDKMAKKYFDFNVYG 259
           R +G Y ++  KYF+F+VYG
Sbjct: 239 RANGKYKQVQDKYFNFDVYG 258


Lambda     K      H
   0.315    0.132    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: 221
Number of extensions: 7
Number of successful extensions: 1
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: 260
Length of database: 259
Length adjustment: 24
Effective length of query: 236
Effective length of database: 235
Effective search space:    55460
Effective search space used:    55460
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 (21.6 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