GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Shewanella oneidensis MR-1

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 201387 SO2237 phosphoenolpyruvate-protein phosphotransferase (NCBI ptt file)

Query= TCDB::Q9HY55
         (956 letters)



>FitnessBrowser__MR1:201387
          Length = 567

 Score =  319 bits (817), Expect = 4e-91
 Identities = 203/550 (36%), Positives = 297/550 (54%), Gaps = 14/550 (2%)

Query: 403 LQAIAASPGIASGPA----HVQVAQRFEFQPRGESPAHERERLLRAKRAVDEEI-VGLVE 457
           +  I  S GIA G A    H +    +   P    P  ++ + L+A +A+ +++ +   +
Sbjct: 3   ITGIIVSSGIAFGKALHLNHCENHLDYRPIPLSRIPL-QQSKFLKALQALKQQLSLSQAK 61

Query: 458 RSTVKAIREIFVTHREMLDDPELAEQVQLRLNRGE-SAEAAWSRVVEDSAAQQEALHDAL 516
                   ++      +LDD EL EQV+  +   + SA  A  R+    A + E+L D  
Sbjct: 62  LDPESENYQLIEADLLLLDDDELIEQVKEAIRTLQLSASVAVERIFAHQANELESLDDPY 121

Query: 517 LAERAADLRDLGRRVLARLCG--VEAPREPEQPYILVMDEVGPSDVARLDAQRVAGILTA 574
           LA RA D+R LG+R++  + G   +   +  +  IL+  ++ P++ A L  + ++GI+  
Sbjct: 122 LANRAQDVRCLGQRIVTAINGRLEQGLADLSEATILLAQDLTPAEFALLPKEHISGIVLK 181

Query: 575 RGGATSHSAIIARALGIPALVGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAE 634
            GG TSH+AI+ARA GIPA++        +   T L+LD   G L V P  EQ  +    
Sbjct: 182 TGGLTSHTAILARAAGIPAMLSCQFDAEFIPNNTPLVLDALSGVLYVNPEPEQQARLTVT 241

Query: 635 RDARQQRQARADAQRLEPARTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFM 694
               Q R+      R  PA+T+DGH V + AN+G+        + GA+G+GL RTEF+ M
Sbjct: 242 LHHEQARRQALQTYRDVPAQTQDGHHVGLLANVGNLNEITHVKDEGADGIGLFRTEFMLM 301

Query: 695 NNARAPDLATQEAEYRRVLDALDGRPLVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRL 754
           N +  PD   Q   Y   L ALDG+    RTLD+G DK LP      E+NP LG RG+R 
Sbjct: 302 NTSTLPDEKAQYNLYCEALHALDGKTFTIRTLDIGADKELPCLCQNIEDNPALGQRGVRY 361

Query: 755 TLQRPQILETQLRALFRAAGERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLAD 809
           TL  P++ +TQLRA+ RAA   P+R+MFPMV  ++E  +   L    +     EE    +
Sbjct: 362 TLAHPELFKTQLRAILRAANHGPIRLMFPMVNQVEELDEIFKLIAECQDALEEEEKGYGE 421

Query: 810 LQLGIMVEVPSAALLAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQ 869
           L  GI+VE P+A L    +   +DF S+GTNDLTQY +A DR +P L+     L PA+L 
Sbjct: 422 LSYGIVVETPAAVLNLASMLPRLDFVSIGTNDLTQYAMAADRTNPQLTKDYPSLSPAILH 481

Query: 870 LIDMTVRAAHAEGKWVGVCGELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLV 929
           LI+MT+  A A G  V +CGELA+ P   PLLVG+G+DELSV+  S+  VKA + + +L 
Sbjct: 482 LINMTITQAKATGVTVSLCGELASSPQMAPLLVGMGLDELSVNLSSLLEVKAAICQGELA 541

Query: 930 AARGLARKAL 939
               LA  A+
Sbjct: 542 KFSELAHTAM 551


Lambda     K      H
   0.318    0.134    0.382 

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: 892
Number of extensions: 31
Number of successful extensions: 2
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: 956
Length of database: 567
Length adjustment: 40
Effective length of query: 916
Effective length of database: 527
Effective search space:   482732
Effective search space used:   482732
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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