GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Pseudomonas putida KT2440

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate PP_4750 PP_4750 Amino acid ABC transporter, permease protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3432
         (229 letters)



>FitnessBrowser__Putida:PP_4750
          Length = 213

 Score =  115 bits (287), Expect = 9e-31
 Identities = 67/199 (33%), Positives = 113/199 (56%), Gaps = 12/199 (6%)

Query: 8   VILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67
           ++L+G+  T+ + + +  + +VLG    ALR+S ++ L+ L  +    +R IP +V +  
Sbjct: 7   MLLNGIPWTIAVTVLAFCVGVVLGFPICALRMSRVKVLSILAAMLVLTLRSIPPIVWLFF 66

Query: 68  IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127
           IF+G            G   YI L+P  A +  LG I  A++SE +RGAF AIP GQ EA
Sbjct: 67  IFFG-----------IG-GGYISLSPFTAAVVGLGLITAAHMSEVYRGAFAAIPAGQFEA 114

Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187
                +S+ Q FF V++PQ++R+AIP      + L K +A+ S +G+ ++ F+A Q +  
Sbjct: 115 AYVLNLSAPQRFFDVVLPQLVRIAIPTSATYAIGLLKDSAVASTIGVGEISFQAYQVSQQ 174

Query: 188 TREPFTFFLAVAAMYLVIT 206
           T +  + + A A +YLV++
Sbjct: 175 TFQGLSVYTAAAVVYLVLS 193


Lambda     K      H
   0.329    0.144    0.428 

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: 174
Number of extensions: 11
Number of successful extensions: 2
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: 229
Length of database: 213
Length adjustment: 22
Effective length of query: 207
Effective length of database: 191
Effective search space:    39537
Effective search space used:    39537
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 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