GapMind for catabolism of small carbon sources

 

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

Align Putrescine transport system permease protein PotI (characterized)
to candidate Pf1N1B4_3025 Spermidine Putrescine ABC transporter permease component potC (TC_3.A.1.11.1)

Query= SwissProt::P0AFL1
         (281 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3025
          Length = 274

 Score =  134 bits (338), Expect = 2e-36
 Identities = 86/253 (33%), Positives = 136/253 (53%), Gaps = 11/253 (4%)

Query: 19  GFTFLYAPMLMLVIYSFNSSKLVTVWA--GWSTRWYGELLRDDAMMSAVGLSLTIAACAA 76
           G  FL+ P+L++ +Y+FN+      +   G++ +W G       ++ A+ LSL IAA A 
Sbjct: 22  GLVFLHFPILIIFLYAFNTEDAAFSFPPKGFTLKWIGVAFSRPDVLEAIKLSLQIAAVAT 81

Query: 77  TAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWPA 136
             A ILGT+A+  L R   F G  G + M+  P+ +P +ITG++LL  F  L        
Sbjct: 82  LIALILGTLASAALYRRDFF-GKQGISLMLILPIALPGIITGIALLATFKTLG------I 134

Query: 137 DRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMPA 196
           + GM TI + H TFC   V   + +RLR    S+ EA+MDLGA   + F  I LP +  A
Sbjct: 135 EPGMFTIIVGHATFCVVIVYNNVIARLRRTSYSLIEASMDLGADGWQTFRYIVLPNLGSA 194

Query: 197 IISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSV-RMGVNPEINALATLILGAVGI 255
           +++G +LAF LS D++++ +F +G    TLP+ + + + R    P  N +A L++    +
Sbjct: 195 MLAGGMLAFALSFDEIIVTTFTAG-HERTLPLWLLNQLSRPRDVPVTNVVAMLVMMVTML 253

Query: 256 VGFIAWYLMARAE 268
               A+YL    E
Sbjct: 254 PILGAYYLTRGGE 266


Lambda     K      H
   0.330    0.140    0.430 

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: 197
Number of extensions: 10
Number of successful extensions: 3
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: 281
Length of database: 274
Length adjustment: 25
Effective length of query: 256
Effective length of database: 249
Effective search space:    63744
Effective search space used:    63744
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 (21.9 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