Aligments for a candidate for ectP in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for ectP in Pseudomonas simiae WCS417

Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate GFF221 PS417_01120 choline transporter

Query= SwissProt::Q87NZ5
         (553 letters)



>FitnessBrowser__WCS417:GFF221
          Length = 666

 Score =  359 bits (921), Expect = e-103
 Identities = 183/500 (36%), Positives = 287/500 (57%), Gaps = 25/500 (5%)

Query: 45  VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104
           VF  +   I+LF +  +   QQ   +    + W  + + W+++ +  ++++  +V  ++ 
Sbjct: 18  VFYFAATFILLFGITVIAIPQQAGAWLLAAQNWAANTVGWYYMLAMTLYLVFVVVTALSG 77

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

Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224
              P  GA  + DAA    M     HW LH W ++A + + LA F++   LPL +RS  Y
Sbjct: 125 ---PPQGAPMNADAARQ-AMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALY 180

Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIV 284
           PL G+R+ G +G+ +D   ++ATVFGL   +G+G     +GL++LFG+  T   QV LI 
Sbjct: 181 PLIGKRINGPIGYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLIT 240

Query: 285 VITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNI 344
           ++   A+I  VAG+D GV+ +S+INM+LA  LL FV+  GPT  +L     NI  Y+  +
Sbjct: 241 LMMGAAIIVAVAGVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNIGDYLGAL 300

Query: 345 PALSMPFERED--VNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPS 402
           P  S      D   ++  GWT FYWAWWI+WSPFVG+FIAR+SRGR++REF+  V+LIP 
Sbjct: 301 PTKSFDVYAYDKPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPL 360

Query: 403 TVCVLWMTAFGGTAISQYVNDGYEAVFNAEL---PLKLFAMLDVMPFAEITSVVGIILVV 459
              + WM+ FG +AI Q +N G  A+  + +    + L+ +L+  P+++    V + +  
Sbjct: 361 GFTLAWMSIFGNSAIDQVLNHGLVALGQSAIDDPSMSLYLLLETYPWSKTVIAVTVFISF 420

Query: 460 VFFITSSDSGSLVIDTIAA-GGKVDAPTPQ--RVFWCTFEGLVAIALMLGGGLAAAQAMA 516
           VFF+TS+DSG++V+ T+++ GG  D   P+  RVFW     LV  AL+  G + + ++  
Sbjct: 421 VFFVTSADSGTVVLSTLSSKGGNADEDGPKWLRVFWGAMTALVTSALLFAGSIDSLKSAV 480

Query: 517 VTTGLPFTIVLLVATVSLIK 536
           V T LPF+++LL+    L K
Sbjct: 481 VLTSLPFSMILLLMMWGLHK 500


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: 1021
Number of extensions: 67
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: 666
Length adjustment: 37
Effective length of query: 516
Effective length of database: 629
Effective search space:   324564
Effective search space used:   324564
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources