GapMind for catabolism of small carbon sources

 

Alignments 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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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