GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolT in Mariniradius saccharolyticus AK6

Align Inositol transporter 1 (characterized)
to candidate WP_008629477.1 C943_RS15175 sugar porter family MFS transporter

Query= SwissProt::Q8VZR6
         (509 letters)



>NCBI__GCF_000330725.2:WP_008629477.1
          Length = 447

 Score =  244 bits (622), Expect = 6e-69
 Identities = 158/452 (34%), Positives = 243/452 (53%), Gaps = 19/452 (4%)

Query: 29  SYILGLTVTAGIGGLLFGYDTGVISGALLYIKDDFEVVKQSSFLQETIVSMALVGAMIGA 88
           +Y L L++TA +GG LFG+DT VISGA   I++ +E+   S  L    V+MAL G ++GA
Sbjct: 5   NYALFLSITAALGGFLFGFDTAVISGAERDIQNLWELDDWSHGLA---VAMALYGTVLGA 61

Query: 89  AAGGWINDYYGRKKATLFADVVFAAGAIVMAAAPDPYVLISGRLLVGLGVGVASVTAPVY 148
             GG   D YGRK   ++  + +   A+  A   D Y  +  R + GLGVG +SV AP+Y
Sbjct: 62  LLGGIPADKYGRKVTLIWIGIFYFVSALGSALVDDVYSFMFYRFIGGLGVGASSVVAPMY 121

Query: 149 IAEASPSEVRGGLVSTNVLMITGGQFLSYLVNSAF--TQVPGTWRWMLGVSGVPAVIQFI 206
           I+E +P++ RG LV+     I  G  ++Y  N       +   WRWMLGV  +PA+I  I
Sbjct: 122 ISEIAPAKSRGQLVALYQFNIVFGILMAYFSNYLIGTANLDEAWRWMLGVEAIPALIYSI 181

Query: 207 LMLFMPESPRWLFMKNRKAE-AIQVLARTYDISRLEDEIDHLSAAEEEEKQRKRTVGYLD 265
           L+L +P+SPRWL  K +  + A ++L RT D   +++ I     A EE K  K       
Sbjct: 182 LILKVPKSPRWLIAKKQDYQTAREILTRT-DPEGVDEAI---KLAIEESKSIKGKTSVAA 237

Query: 266 VFRSKELRLAFLAGAGLQAFQQFTGINTVMYYSPTIVQMAGFHSNQLALFLSLIVAAMNA 325
           +F S+  +++F A   +  F Q +GIN ++Y++P I + AG  S + ALF ++ +  +N 
Sbjct: 238 LFDSRFRKISFFAFL-MAFFNQMSGINAIIYFAPRIFESAGI-STEDALFSTIGIGVINL 295

Query: 326 AGTVVGIYFIDHCGRKKLALSSLFGVIISLLILSVSFFKQSETSSDGGLYGWLAVLGLAL 385
             T+ G+Y ID  GRKKL      G IISL +++ S+F        G +   L    + +
Sbjct: 296 IATMAGLYLIDKLGRKKLMYIGSVGYIISLSLMAYSYF-------GGMISSNLLPYFVFV 348

Query: 386 YIVFFAPGMGPVPWTVNSEIYPQQYRGICGGMSATVNWISNLIVAQTFLTIAEAAGTGMT 445
           +I   A G G V W   +EI+P + R     + +  +WI   ++A  F   A   G G  
Sbjct: 349 FIASHAIGQGSVIWVFIAEIFPNELRAFGQSLGSFTHWILAALIANVFPFFANTFGAGSI 408

Query: 446 FLILAGIAVLAVIFVIVFVPETQGLTFSEVEQ 477
           F   A + VL +++V   +PET+G +  E++Q
Sbjct: 409 FAFFALMMVLQLLWVAFRMPETKGKSLEEIQQ 440


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: 509
Number of extensions: 25
Number of successful extensions: 6
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: 447
Length adjustment: 33
Effective length of query: 476
Effective length of database: 414
Effective search space:   197064
Effective search space used:   197064
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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