GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Desulfovibrio vulgaris Hildenborough

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 206413 DVU0981 multiphosphoryl transfer protein, putative

Query= TCDB::Q9HY55
         (956 letters)



>MicrobesOnline__882:206413
          Length = 854

 Score =  449 bits (1155), Expect = e-130
 Identities = 331/844 (39%), Positives = 441/844 (52%), Gaps = 51/844 (6%)

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

Query: 205 EQLVKRPGLAFVTP---AQPLQHQGQLVTGLFC---LASLGEAHQALLERLCDLL----- 253
             +     L  + P   +Q       LV GL     LAS G    A+ E     L     
Sbjct: 73  ALMSAETALDLLPPEVASQVRLSAAPLVEGLMAAAVLASTGADLGAVAEEAQSALAAKRE 132

Query: 254 LEGRGAELVRATSSRSVLAALGGELP----PDWPSARAVLANPHGLHARPAQALAQLAKG 309
           L G  A    A  S     A    +P    P       V+ N  GLHARPA  +      
Sbjct: 133 LLGAAAPAAPAMPSAHPEGARDSTVPSSAMPAGEELTLVVPNRLGLHARPAARIVTALGP 192

Query: 310 FAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPALLAAVREGL 369
           FA ++++   D     VSA+S++++  L  R G+T+ F A    A  AL A+ A      
Sbjct: 193 FAADVQLVRGDRV---VSARSVNRIATLAVRGGETVTFRAVGGDAALALRAIEALAAAHF 249

Query: 370 GEEVEALAEEALPDAV-----GEAEEDARPAPLRAGERLQAIAASPGIASGPAHVQVAQR 424
           G+  EA ++   P        G+  E A  A ++ G  L+  AASPG+  G A V     
Sbjct: 250 GDAPEAPSKGEAPSPAEAPKDGDMAEAAVSADVQGGGVLRGAAASPGLTVGNA-VWYRPA 308

Query: 425 FE---FQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIR---EIFVTHREMLDDP 478
           F+     P  + PA E  RL  A  A   E+V L  R+   A R   EIF  HR +LDD 
Sbjct: 309 FDAPDVAPLADDPATEVTRLDAALGAARTELVELERRTVAAAGRKEAEIFAMHRLLLDDV 368

Query: 479 ELAEQVQLRL-NRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLCG 537
            +A   + R+ +R E+AE+AW  V+ D+AA    L +  + ER AD+ D+G RVL  L G
Sbjct: 369 TIAGAARQRIMDRREAAESAWYEVISDAAATFRQLPEGYMREREADMVDVGARVLRLLTG 428

Query: 538 VEA--PREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALV 595
           V A  PR    P +L+  ++GPSD+A LD   V GI+T +GGATSH+AI+AR+LGIPA+ 
Sbjct: 429 VAAVGPRLGG-PSVLLATDLGPSDMATLDPSLVIGIVTVQGGATSHAAILARSLGIPAVA 487

Query: 596 GAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPART 655
           G G A+ G+  G  + LDG  G + V P+        A RDA    +  A A    PA T
Sbjct: 488 GLGPALQGVGEGDIVALDGGTGDVWVNPAPGVRAAVEARRDAWLAGREAALAGAAAPAVT 547

Query: 656 RDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDA 715
            DG AV + AN+G +A A  A++ GAEGVGL RTEF+F++    P    Q   Y     A
Sbjct: 548 ADGRAVHILANIGSSADAGAALKNGAEGVGLFRTEFLFLDRTSPPGEEEQLTAYVTAAAA 607

Query: 716 LDGRPLVARTLDVGGDKPLPYWP--IPHEENPYLGLRGIRLTLQRPQILETQLRALFRAA 773
           + GRP+V RTLD+GGDKP+ Y       E+NP+LGLRGIR  L+R  +  TQLRAL RAA
Sbjct: 608 MQGRPVVVRTLDIGGDKPVSYLEGFATGEDNPFLGLRGIRFCLERKPLFMTQLRALLRAA 667

Query: 774 GERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLADLQLGIMVEVPSAALLAPVL 828
              PL+VMFPMV    E   A+ L    R     E +P   L +GIM+EVP+A  LA  L
Sbjct: 668 AVHPLKVMFPMVAHPGELAAAKALLDEARATLDAEGMPHGQLDVGIMIEVPAAVALADQL 727

Query: 829 AREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVC 888
           AR+  FFS+GTNDL QY +A DRG+ S++A +D LHPAVL+++  TVRA HA G  V +C
Sbjct: 728 ARDAAFFSIGTNDLAQYVMAADRGNASVAALSDALHPAVLRMVRDTVRAGHAAGIPVAIC 787

Query: 889 GELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVR 948
           GEL  +P A+PLLVGL +DELS++  +I   K  VR         LA +A+ L  AA VR
Sbjct: 788 GELGGNPEAIPLLVGLELDELSMNGPAIPRAKEVVRGCDTGTCAVLADRAMALPDAAAVR 847

Query: 949 ALVE 952
            L++
Sbjct: 848 RLLQ 851


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: 1717
Number of extensions: 78
Number of successful extensions: 9
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: 854
Length adjustment: 43
Effective length of query: 913
Effective length of database: 811
Effective search space:   740443
Effective search space used:   740443
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