GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB in Pseudomonas fluorescens FW300-N2E2

Align BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Pf6N2E2_1799 ABC transporter permease protein

Query= TCDB::P73544
         (530 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1799
          Length = 292

 Score =  137 bits (344), Expect = 7e-37
 Identities = 76/202 (37%), Positives = 117/202 (57%), Gaps = 9/202 (4%)

Query: 313 GSILTVLLTAFSVFFGLIGGTGVAIALISDIKPLQLIFRIYVEFFRGTPMLVQLFIIYFG 372
           G + TV++   ++  G++ G   AI  +S    L+ +  IY   FRGTP+++QL +++F 
Sbjct: 75  GLLNTVVMAVLAMALGIVFGVITAIMRMSANPILRYVALIYTWLFRGTPLILQL-LLWFN 133

Query: 373 LPALFKEIGLGITIDR--------FPAAIIALSLNVAAYLAEIIRGGIQSIDQGQWEACE 424
           L  +F  IG+    +         F AA++ LS+N  AY AE++R G+ S+D GQ+EA +
Sbjct: 134 LALIFPTIGIPGLFEMDTVSLMTPFVAALLGLSINQGAYTAEVVRAGLLSVDTGQYEAAK 193

Query: 425 SLGMSPWQTMKEVIFPQAFRRILPPLGNEFITLIKDTSLTAVIGFQELFREGQLIVATTY 484
           S+GM   Q ++ +I PQA R I+PP+GNEFI ++K TSL +VI + EL    Q I     
Sbjct: 194 SIGMPRLQALRRIILPQAMRIIIPPVGNEFIGMVKMTSLASVIQYSELLYNAQNIYYANA 253

Query: 485 RAFEVYIAVALVYLLLTTISSF 506
           R  E+ I   + YL   T+ SF
Sbjct: 254 RVMELLIVAGIWYLATVTVLSF 275


Lambda     K      H
   0.322    0.139    0.403 

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: 312
Number of extensions: 16
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: 530
Length of database: 292
Length adjustment: 31
Effective length of query: 499
Effective length of database: 261
Effective search space:   130239
Effective search space used:   130239
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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