GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0327 in Pseudomonas fluorescens FW300-N2C3

Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate AO356_05190 AO356_05190 sugar ABC transporter permease

Query= TCDB::Q72KX3
         (369 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05190
          Length = 302

 Score =  121 bits (304), Expect = 2e-32
 Identities = 82/226 (36%), Positives = 130/226 (57%), Gaps = 19/226 (8%)

Query: 155 WLATREQVLVFDWNRLPFYTALVVGLVL-LYVAYTAYREGERRRA-LWGLASA----GVL 208
           W+A++  VL   +  +     LV+G++L +++     REG  R   L+ +A +    G  
Sbjct: 75  WVASKNLVL---FGGMFIGITLVIGVLLAVFLDQRIRREGFIRTIYLYPMALSMIVTGTA 131

Query: 209 LLWAFAFGQGL-RLLPYPEVHGFSL--------ALVGVILAAVWQMSGYTMALYLAGLRG 259
             W    G GL +LL      GF L         +  +++AAVWQ SG+ MA++LAGLRG
Sbjct: 132 WKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRG 191

Query: 260 IPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIALKIFDLVFAM-AGLDYA 318
           +   ++ AA++DGAS  +++ +V+ P L P+  SA+++L HIA+K FDLV AM AG    
Sbjct: 192 VDQSIIRAAQIDGASMPRIYWKVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGY 251

Query: 319 PTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQLR 364
            +D+PA++MY   F   Q   G+A  IL+L  +  ++VPYL ++LR
Sbjct: 252 SSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELR 297



 Score = 88.6 bits (218), Expect = 2e-22
 Identities = 57/160 (35%), Positives = 85/160 (53%), Gaps = 11/160 (6%)

Query: 4   RILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYRELF 63
           R L  LVL PS+  V V  YG+I   LW  +  +           P  ++ GL  Y  L 
Sbjct: 18  RWLPKLVLAPSMFIVLVGFYGYI---LWTFVLSFTTS-----TFLPNYKWAGLAQYARLM 69

Query: 64  TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123
               + R+  +  NL+ F   F+  +L +G+LLA+ +D+  R EGF RT++L+PMALS +
Sbjct: 70  D---NDRWWVASKNLVLFGGMFIGITLVIGVLLAVFLDQRIRREGFIRTIYLYPMALSMI 126

Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVL 163
           VTGT W+WLL P  G++ L   +G       WL   ++V+
Sbjct: 127 VTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVV 166


Lambda     K      H
   0.331    0.146    0.458 

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: 337
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 369
Length of database: 302
Length adjustment: 28
Effective length of query: 341
Effective length of database: 274
Effective search space:    93434
Effective search space used:    93434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 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