GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolT in Klebsiella michiganensis M5al

Align Inositol transporter 1 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= SwissProt::Q8VZR6
         (509 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS24055 BWI76_RS24055 MFS
           transporter
          Length = 464

 Score =  285 bits (730), Expect = 2e-81
 Identities = 162/441 (36%), Positives = 250/441 (56%), Gaps = 14/441 (3%)

Query: 38  AGIGGLLFGYDTGVISGALLYIKDDFEVVKQSSFLQETIVSMALVGAMIGAAAGGWINDY 97
           A + GLLFG D GVI+GAL +I ++F++   S+  QE +VS  + GA +GA   GW++  
Sbjct: 22  AALAGLLFGLDIGVIAGALPFIANEFQI---SAHTQEWVVSSMMFGAAVGAVGSGWLSFK 78

Query: 98  YGRKKATLFADVVFAAGAIVMAAAPDPYVLISGRLLVGLGVGVASVTAPVYIAEASPSEV 157
            GRKK+ +   ++F AG++  AAAP+  VL+  R+L+GL VGVAS TAP+Y++E +P ++
Sbjct: 79  LGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAPLYLSEIAPEKI 138

Query: 158 RGGLVSTNVLMITGGQFLSYLVNSAFTQVPGTWRWMLGVSGVPAVIQFILMLFMPESPRW 217
           RG ++S   LMIT G   +YL ++AF+   G WRWMLGV  +PAV+  I ++F+P+SPRW
Sbjct: 139 RGSMISMYQLMITIGILGAYLSDTAFS-YSGAWRWMLGVIIIPAVLLLIGVVFLPDSPRW 197

Query: 218 LFMKNRKAEAIQVLARTYDIS-RLEDEIDHLSAAEEEEKQRKRTVGYLDVFRSKELRLAF 276
              K R  +A +VL R  D S   + E+D     E  E  + +  G+     +   R A 
Sbjct: 198 FAAKRRFVDAERVLLRLRDTSAEAKRELD-----EIRESLKVKQSGWSLFKENSNFRRAV 252

Query: 277 LAGAGLQAFQQFTGINTVMYYSPTIVQMAGFHSNQLALFLSLIVAAMNAAGTVVGIYFID 336
             G  LQ  QQFTG+N +MYY+P I ++AG+ +    ++ ++IV   N   T + I  +D
Sbjct: 253 FLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTVIVGLTNVLATFIAIGLVD 312

Query: 337 HCGRKKLALSSLFGVIISLLILSVSFFKQSETSSDGGLYGWLAVLGLALYIVFFAPGMGP 396
             GRK   +     + + + IL                  + AVL L ++IV FA   GP
Sbjct: 313 RWGRKPTLILGFIVMALGMGILG----SMMHIGIHSATAQYFAVLMLLMFIVGFAMSAGP 368

Query: 397 VPWTVNSEIYPQQYRGICGGMSATVNWISNLIVAQTFLTIAEAAGTGMTFLILAGIAVLA 456
           + W + SEI P + R      S   NWI+N+IV  TFLT+  + G+  TF +  G+ +L 
Sbjct: 369 LIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLGSANTFWVYGGLNILF 428

Query: 457 VIFVIVFVPETQGLTFSEVEQ 477
           +   +  +PET+ ++   +E+
Sbjct: 429 IFLTLWLIPETKNVSLEHIER 449


Lambda     K      H
   0.323    0.138    0.406 

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: 538
Number of extensions: 25
Number of successful extensions: 5
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: 509
Length of database: 464
Length adjustment: 34
Effective length of query: 475
Effective length of database: 430
Effective search space:   204250
Effective search space used:   204250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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 preprint 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