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

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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