Aligments for a candidate for fruI in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruI in Desulfovibrio vulgaris Miyazaki F

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

Query= TCDB::Q9HY55
         (956 letters)



>FitnessBrowser__Miya:8501869
          Length = 846

 Score =  447 bits (1151), Expect = e-129
 Identities = 335/850 (39%), Positives = 444/850 (52%), Gaps = 73/850 (8%)

Query: 155 LGQNAEDLDELAWLGARLLKKAGCVENGF-------AAVLQQTEPLPLGDG---LCWLHS 204
           LGQ  ++L E    G   L  AG +++           V+   E +  GDG   L  L S
Sbjct: 13  LGQGVKELVEQMTQGRVPLAVAGGIDDPEHPIGTDPMRVMAAIEEVQQGDGVLVLMDLGS 72

Query: 205 EQLVKRPGLAFVTP---AQPLQHQGQLVTGLFCLASLGEAHQALLERLCDLLLEGRGAEL 261
             +     L  + P   AQ       LV G+   A       ++   L  +L E + A  
Sbjct: 73  ALMSAETALDLLPPEVAAQVRLRPAPLVEGVMAAA----VQASIGADLDTVLREAQSALA 128

Query: 262 VRATSSRSVLAALGG---ELPPDWPSARAVLANPH----------GLHARPAQALAQLAK 308
            +A      L   GG   E  P  P+A A  A  H          GLHARPA  +     
Sbjct: 129 AKAELLGMALPQDGGGVDEAAP--PAAGATPAASHELTLMVPNRLGLHARPAARIVTALG 186

Query: 309 GFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPALLAAVREG 368
            F  +  V+LA  E   VSA+S++++  L  R G+T+ F A    AE AL AL     E 
Sbjct: 187 PFVAD--VQLARGERV-VSARSVNRIATLAVRGGETITFRAAGTDAEQALKALADLAAEN 243

Query: 369 LGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQA-----------IAASPGIASGPA 417
            G+         LPDA   +       P   GE+ +A           + ASPGIA GPA
Sbjct: 244 FGD---------LPDATKSSGRTGVEGPEGPGEQGRAGVAGVPAAKGGVPASPGIAVGPA 294

Query: 418 HVQVAQRFEFQP---RGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIR---EIFVTH 471
            V     F+  P       P  E  RL  A  A  +E+  L  R+   A +   EIFV H
Sbjct: 295 -VWHRPAFDAPPPDLAAGDPDSEAARLDGALDAARKELAALERRTAAMAGKQEAEIFVMH 353

Query: 472 REMLDDPELAEQVQLRL-NRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRR 530
           R +LDD  +A   + R+  R E AEAAW  V++ +A     L +  + ERAADL D+G R
Sbjct: 354 RLLLDDATIAGDARQRIAERREPAEAAWYAVIDQAAESFRQLPEGYMRERAADLVDVGAR 413

Query: 531 VLARLCGVEAPREP--EQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARA 588
           VL  L G   P  P  E+P +L+  ++GPSD+A LD   V GI+TA+GGATSH+AI+AR+
Sbjct: 414 VLRLLTGAP-PSGPRLERPSVLLAADLGPSDMAHLDPALVLGIVTAQGGATSHAAILARS 472

Query: 589 LGIPALVGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQ 648
           +GIPA+ GAGA    +  G  + LDG  G + +AP+ + L    + R +    +  A A 
Sbjct: 473 MGIPAVAGAGALAASVADGVTVALDGSTGEVWIAPAPDVLSTIESRRASWLAVRQAALAG 532

Query: 649 RLEPARTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAE 708
              PA T DG  + V AN+G    AA A++ GAEGVGL RTEF+F++   APD   Q A 
Sbjct: 533 AARPAVTVDGRHMHVHANIGSPMDAAPALQNGAEGVGLFRTEFLFLDRVAAPDEEEQRAA 592

Query: 709 YRRVLDALDGRPLVARTLDVGGDKPLPYWP--IPHEENPYLGLRGIRLTLQRPQILETQL 766
           Y     A+ G P+V RTLD+GGDKP+PY       EENP+LGLRGIR  L R ++  TQL
Sbjct: 593 YVAAAAAMPGLPVVVRTLDIGGDKPVPYLGDFAAGEENPFLGLRGIRFCLARRELFLTQL 652

Query: 767 RALFRAAGERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLADLQLGIMVEVPSA 821
           RAL RAA E PLRVMFPMV    E   A+ L    R     + +P   +++GIMVEVP+A
Sbjct: 653 RALLRAAAEHPLRVMFPMVAHPGELAAAKALLEEARAALAAQGLPHGPVEVGIMVEVPAA 712

Query: 822 ALLAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAE 881
             LA  LARE  FFS+GTNDL QY +A DRG+ +++  +D LHPAVL+++  TV A  A 
Sbjct: 713 VALADQLARESAFFSIGTNDLAQYVMAADRGNAAVADLSDALHPAVLRMVRDTVAAGKAA 772

Query: 882 GKWVGVCGELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGL 941
           G  V +CGELA +  A+PLLVGLG+DELS++  +I   K  VR   + A   LA +AL L
Sbjct: 773 GIPVAMCGELAGNADAIPLLVGLGLDELSMNGPAIPRAKDVVRGCDMTACVRLAGRALEL 832

Query: 942 ASAAEVRALV 951
             AA VR L+
Sbjct: 833 PDAAAVRRLL 842


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: 1671
Number of extensions: 67
Number of successful extensions: 8
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: 846
Length adjustment: 43
Effective length of query: 913
Effective length of database: 803
Effective search space:   733139
Effective search space used:   733139
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: 56 (26.2 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