GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS24055
          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:

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