GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMIT1 in Dinoroseobacter shibae DFL-12

Align Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)

Query= SwissProt::Q8K0E3
         (673 letters)



>FitnessBrowser__Dino:3610523
          Length = 526

 Score =  260 bits (664), Expect = 1e-73
 Identities = 153/473 (32%), Positives = 250/473 (52%), Gaps = 41/473 (8%)

Query: 28  DIAVLVLYFLFVLAVGLWSTVRTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGHFIGL 87
           D  V+ +Y   V+A+G+W   +T+  T +  FLAG  + W  +G SLFASN+ +   +GL
Sbjct: 13  DYGVIAVYLAIVIAIGVWVARKTR--TGEDLFLAGRSLGWAAIGFSLFASNISTSTLVGL 70

Query: 88  AGSGAAVGISVAAYELNGLFSVLMLAWVFLPIYIAGQVTTMPEYLRRRFGGNRISITLAV 147
            GS    G++V++YE      +L +A++F P+++  +++T PEYL  R+   R+ +  + 
Sbjct: 71  TGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYS-RRVRLYFSG 129

Query: 148 LYLFIYIFTKISVDMYAGAIFIQQSL-HLDLYLAIVGLLAITALYTVAGGLAAVIYTDAL 206
           L +   +    +  +YAGA+ ++     LD++++ V +     +YT  GGL AV+YTD L
Sbjct: 130 LTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGLRAVVYTDIL 189

Query: 207 QTVIMLIGAFILMGYSFAAVGGMEGLKDQYFLALASNRSENSSCGLPREDAFHIFRDPLT 266
           Q V+++ G  +     + +V            +  S RS+     L           P+ 
Sbjct: 190 QAVVLICGTGLTAFLMYQSVD----------FSWESVRSQVPEGHLS-------IVQPID 232

Query: 267 SD-LPWPGILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKVLPLFLMVF 325
            D LPWPG+  G+ +   WYW T+Q IVQR L AK+LS+A+ G+++   LK+LP F ++ 
Sbjct: 233 DDTLPWPGLFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTFFIIL 292

Query: 326 PGMVSRVLFPDQVACAHPDICQRVCSNPSGCSDIAYPKLVLELLPTGLRGLMMAVMVAAL 385
           PG+++ V  PD               N    SD  +P ++ E+LP+GL GL+MA ++AA+
Sbjct: 293 PGVMALVTLPD-------------IQN----SDQVFPIIITEVLPSGLTGLVMAGLIAAI 335

Query: 386 MSSLTSIFNSASTIFTMDLWNHIRPRASERELMIVGRIFVFALVLVSILWIPIVQASQGG 445
           MS++ S  NS+ST+   D                 G +     ++++I W P++Q    G
Sbjct: 336 MSTVDSTLNSSSTLLINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPLIQ--YFG 393

Query: 446 QLFIYIQSISSYLQPPVAMVFIMGCFWKRTNEKGAFSGLILGLLLGLVRLILD 498
            L+ YIQ   S L PP+ + F +G  W R  E  AF  LI+G  LGLV  +L+
Sbjct: 394 GLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGLVVFMLN 446


Lambda     K      H
   0.325    0.139    0.426 

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: 861
Number of extensions: 43
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: 673
Length of database: 526
Length adjustment: 37
Effective length of query: 636
Effective length of database: 489
Effective search space:   311004
Effective search space used:   311004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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