GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Pseudomonas fluorescens FW300-N2C3

Align L-Arginine ABC transporter, periplasmic substrate-binding component (characterized)
to candidate AO356_26125 AO356_26125 ABC transporter substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5660
         (257 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26125
          Length = 260

 Score =  313 bits (803), Expect = 2e-90
 Identities = 155/258 (60%), Positives = 193/258 (74%), Gaps = 1/258 (0%)

Query: 1   MKKLVL-LGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCE 59
           +K++ L LG ++L        A E  L+IGIEAAYPPFASK PD +IVGFDYDIG ALC 
Sbjct: 3   VKRIALNLGFISLLAFGASLQAAESSLRIGIEAAYPPFASKTPDNAIVGFDYDIGQALCA 62

Query: 60  EMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAG 119
           EMKV+CVW EQEFDGLIPALKV+K+DA++SSMSIT +R KSVDFT++YY  PARLV + G
Sbjct: 63  EMKVRCVWQEQEFDGLIPALKVKKVDAVISSMSITPERLKSVDFTDRYYRIPARLVFRKG 122

Query: 120 TQVSDNLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVSAGRLDGTV 179
           + +SD  A+LKGK IGVQR +  +R+  +  AP GAE+  YGSQNEI+LD+  GRLD T+
Sbjct: 123 SAISDIPAQLKGKRIGVQRATNFDRYVTDHFAPAGAEVVRYGSQNEIFLDLLGGRLDATM 182

Query: 180 ADATLLDDGFLKTDAGKGFAFVGPAFTDEKYFGDGIGIAVRKGDALKDKINGAITAIREN 239
           A + ++D+  LK   GK F FVGP FT+E+YFG GIGIAVRK DAL  + N A+  IR N
Sbjct: 183 ASSVVIDESLLKRPEGKDFEFVGPNFTEEQYFGTGIGIAVRKNDALAGRFNQALATIRAN 242

Query: 240 GKYKQIQDKYFAFDIYGK 257
           G Y +I+ KYF FDIYG+
Sbjct: 243 GTYDRIRQKYFDFDIYGE 260


Lambda     K      H
   0.318    0.138    0.396 

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: 261
Number of extensions: 10
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: 257
Length of database: 260
Length adjustment: 24
Effective length of query: 233
Effective length of database: 236
Effective search space:    54988
Effective search space used:    54988
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