GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC2A2 in Kocuria flava HO-9041

Align Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized)
to candidate WP_058857557.1 AS188_RS02770 sugar porter family MFS transporter

Query= SwissProt::P11168
         (524 letters)



>NCBI__GCF_001482365.1:WP_058857557.1
          Length = 471

 Score =  183 bits (465), Expect = 1e-50
 Identities = 140/419 (33%), Positives = 210/419 (50%), Gaps = 31/419 (7%)

Query: 100 SVSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRS 159
           +V+S  +G    +FFGG + D LGR+  M +A +L LV A+  G  +   S   +I  R 
Sbjct: 61  AVASALLGAAAGAFFGGRIADRLGRVPVMKIAAVLFLVSAIGCGVVE---SFEWLIFWRV 117

Query: 160 ISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGL----------E 209
           + G+  G+ S + P YI EIAP ++RG LG+  Q+ IV GI IS  +            E
Sbjct: 118 VGGVGVGVASIIAPAYIAEIAPASVRGRLGSLQQMGIVLGIFISLAVDAWLAALAGGSGE 177

Query: 210 FILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDV 269
            +    + W  +     V A+   +  F  PESPRYL  +   + +A+  L  L+G    
Sbjct: 178 PLWWGLEAWRWMFMAEAVPALAYLIGAFTIPESPRYLVAEGRAD-EARAVLTDLQGEASA 236

Query: 270 TKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPIL-VALMLHVAQQFSGINGIFYYSTS 328
           T+ +   R  ++   +E+K  +  L    +  +PI+ V + L   QQF GIN IFYYS  
Sbjct: 237 TERV---RLIQQTLRTERKPRMSDLKGRMAGLKPIVWVGIGLAALQQFVGINVIFYYSNV 293

Query: 329 IFQTAGISKPVYATIGV--GAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFV-----CAI 381
           ++Q+ G ++    TI V     N+V T V++ LVE+ GRR L LIG  GM +       I
Sbjct: 294 LWQSVGFTEADSFTITVITSVTNVVVTVVAIALVERVGRRRLLLIGSGGMTLMLGTLAVI 353

Query: 382 FMSVGLV----LLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALA 437
           F +  LV    +L   +    V+++A  LFV FF +  GP+ W ++ E F    R AALA
Sbjct: 354 FATAPLVDGAPVLGPTA--GPVALVAANLFVVFFGVSWGPMMWVLLGEMFPNQIRGAALA 411

Query: 438 IAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIA 496
           +A F  W  N++V + F  +A       + L+A   L   LFT   V ET G   E++A
Sbjct: 412 VAGFVQWIANWVVTVTFPALAAASLGLAYGLYAFFALVSLLFTIRMVRETTGIELEDMA 470


Lambda     K      H
   0.326    0.140    0.418 

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: 614
Number of extensions: 42
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 524
Length of database: 471
Length adjustment: 34
Effective length of query: 490
Effective length of database: 437
Effective search space:   214130
Effective search space used:   214130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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