GapMind for catabolism of small carbon sources

 

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

Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate Pf1N1B4_2220 Glycerol-3-phosphate transporter

Query= TCDB::Q9Z7N9
         (455 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2220
          Length = 449

 Score =  345 bits (886), Expect = 1e-99
 Identities = 187/455 (41%), Positives = 267/455 (58%), Gaps = 20/455 (4%)

Query: 7   FFQPPKHIKEIEDQEVVKKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFD 66
           FF+P  H   + ++++    Y+  R +IF  +FIGY  YY  RK+FT A P LIA  G+ 
Sbjct: 4   FFRPAAHQAPLPEEKI-DSTYRRLRWQIFAGIFIGYAGYYLLRKNFTLAFPDLIAQ-GYT 61

Query: 67  KAQLGIIGSTLYFSYGISKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGMS----SSIV 122
           K QLG+  S +  +YG+SKF+ G++SD+SNPRYF+  GL+++      FG +    SS+ 
Sbjct: 62  KGQLGVAMSAIAIAYGLSKFLMGIVSDRSNPRYFLPFGLIVSAGVMFVFGFAPWATSSVT 121

Query: 123 LFALWWGLNGWFQGWGWPPCARLLTHWYAKSERGTWWSVWSTSHNIGGALI-PILTGFII 181
           +  +   +NGW QG GWPP  R + HW+++ ERG   SVW+T+HN+GG LI P+    + 
Sbjct: 122 MMFILLFINGWAQGMGWPPSGRTMVHWWSQKERGGVVSVWNTAHNVGGGLIGPLAILGMG 181

Query: 182 DYSGWRGAMYVPGILCIGMGLVLINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASEGT 241
            ++ W    YVP  + + + +     +RDTPQS GLPPIEKYK D    + EG  AS   
Sbjct: 182 WFNDWHSKFYVPAAVALLVAVFAFIVMRDTPQSTGLPPIEKYKND----YPEGYDASH-- 235

Query: 242 EEIERELSTREILFTYVLTNQWLWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVKAN 301
              E E S ++I   YVL N+ LWF+A A+ F+Y++R  + DW+  +L E KH+   K +
Sbjct: 236 ---EEEFSAKDIFVKYVLRNKMLWFIALANVFVYLLRYGILDWAPTYLKEVKHFDFDKTS 292

Query: 302 FCVSLFEIGGLFGMLVAGWLSDKISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWVDG 361
           +   L+E  G+ G L+ GW+SDKI +GNRG   ++F   +  A +  W +   N   VD 
Sbjct: 293 WAYFLYEWAGIPGTLLCGWMSDKIFRGNRGLTGMVFMALVTVATIVYWLNPPGNP-MVDM 351

Query: 362 TLLFVIGFFLYGPQMMIGLAAAELSHKKAAGTASGFTGWFAYFGATFAGYPL-GKVTDVW 420
             LF IGF +YGP M++GL A EL  KKAAGTA+GFTG F Y G + A   L G   D +
Sbjct: 352 ISLFAIGFLIYGPVMLVGLQALELVPKKAAGTAAGFTGLFGYLGGSVAASALMGYTVDYF 411

Query: 421 GWKGFFIALLACASIALLLFLPTWNATEKNTRSKA 455
           GW G FI L+    +A+    PT     KN  S++
Sbjct: 412 GWDGGFILLVVACLLAMAFLAPTLG--HKNVASQS 444


Lambda     K      H
   0.327    0.141    0.476 

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: 816
Number of extensions: 43
Number of successful extensions: 7
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: 455
Length of database: 449
Length adjustment: 33
Effective length of query: 422
Effective length of database: 416
Effective search space:   175552
Effective search space used:   175552
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: 51 (24.3 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