GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|MicrobesOnline__882:206413 DVU0981 multiphosphoryl transfer
           protein, putative
          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 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