GapMind for catabolism of small carbon sources

 

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

Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate Pf6N2E2_3917 High-affinity choline uptake protein BetT

Query= SwissProt::Q87NZ5
         (553 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3917
          Length = 667

 Score =  363 bits (932), Expect = e-104
 Identities = 185/500 (37%), Positives = 286/500 (57%), Gaps = 24/500 (4%)

Query: 45  VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104
           VF  +   I+LF +  +    Q   +    + W  + + W+++ +  ++++  +V  ++ 
Sbjct: 18  VFYFAATFILLFGLVVIAMPAQAGAWLLAAQNWAANTVGWYYMLAMTLYLVFVVVTALSG 77

Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164
            G++++G     P++SY  W  MLFAAG+ I L FF VSEP++H                
Sbjct: 78  YGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMVQ------------- 124

Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224
              P  G  G T  A+   M     HW LH W ++A + + LA F++   LPL +RS  Y
Sbjct: 125 ---PPQGEAGGTAEAARQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALY 181

Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIV 284
           PL G+R+ G +G+ +D   ++ATVFGL   +G+G     +GL++LFG+  T   QV LIV
Sbjct: 182 PLIGKRINGPIGYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLIV 241

Query: 285 VITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNI 344
           ++   A+I  VAG+D GV+ +S+INM+LA  LL FV+  GPT  +L     NI  Y+  +
Sbjct: 242 LMMGAAIIVAVAGVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNIGDYLGAL 301

Query: 345 PALSMPFERED--VNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPS 402
           P  S      D   ++  GWT FYWAWWI+WSPFVG+FIAR+SRGR++REF+  V+LIP 
Sbjct: 302 PMKSFDLYAYDKPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPL 361

Query: 403 TVCVLWMTAFGGTAISQYVNDGYEAVFNAEL---PLKLFAMLDVMPFAEITSVVGIILVV 459
              + WM+ FG +AI Q +N G  A+  + L    + L+ +L+  P+++    V + +  
Sbjct: 362 GFTLAWMSIFGNSAIDQVLNHGMSALGMSALENPSMSLYLLLETYPWSKTVIAVTVFISF 421

Query: 460 VFFITSSDSGSLVIDTIAA-GGKVDAPTPQ--RVFWCTFEGLVAIALMLGGGLAAAQAMA 516
           VFF+TS+DSG++V+ T++A GG  D   P+  RVFW     LV  AL+  G + A ++  
Sbjct: 422 VFFVTSADSGTVVLSTLSAKGGNPDEDGPKWLRVFWGAMTALVTSALLFSGSIDALKSAV 481

Query: 517 VTTGLPFTIVLLVATVSLIK 536
           V T LPF+++LL+    L K
Sbjct: 482 VLTSLPFSLILLLMMWGLHK 501


Lambda     K      H
   0.327    0.141    0.435 

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: 1042
Number of extensions: 80
Number of successful extensions: 5
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: 553
Length of database: 667
Length adjustment: 37
Effective length of query: 516
Effective length of database: 630
Effective search space:   325080
Effective search space used:   325080
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 (21.7 bits)
S2: 53 (25.0 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