GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Kocuria flava HO-9041

Align The glucose uptake porter, GluP (characterized)
to candidate WP_058857557.1 AS188_RS02770 sugar porter family MFS transporter

Query= TCDB::Q0SE66
         (483 letters)



>NCBI__GCF_001482365.1:WP_058857557.1
          Length = 471

 Score =  557 bits (1435), Expect = e-163
 Identities = 285/457 (62%), Positives = 351/457 (76%), Gaps = 4/457 (0%)

Query: 21  SVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAMLA 80
           S  +RI+++AA GG LFGYDSAVINGAVSAI+ +F V    LGFA+ASALLGAAAGA   
Sbjct: 17  SAVLRISIIAAFGGFLFGYDSAVINGAVSAIQEEFGVSPGPLGFAVASALLGAAAGAFFG 76

Query: 81  GRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAE 140
           GRIADR GR+  M+ AAV+FL+SAIG G   + E L+ +R+VGG+GVG+AS+IAPAYIAE
Sbjct: 77  GRIADRLGRVPVMKIAAVLFLVSAIGCGVVESFEWLIFWRVVGGVGVGVASIIAPAYIAE 136

Query: 141 ISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCVP 200
           I+PA VRGRLGSLQQ+ IV GIF+SL VD  LAA+AGGS E LW+GLEAWRWMF+A  VP
Sbjct: 137 IAPASVRGRLGSLQQMGIVLGIFISLAVDAWLAALAGGSGEPLWWGLEAWRWMFMAEAVP 196

Query: 201 ALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSIR 260
           ALAY + + TIPESPRYL+A+GR  EAR +L  L GE     ++  I+ TL  E +P + 
Sbjct: 197 ALAYLIGAFTIPESPRYLVAEGRADEARAVLTDLQGEASATERVRLIQQTLRTERKPRMS 256

Query: 261 DLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVVN 320
           DLKG   GL PIVW+GIGL+  QQFVGINVIFYYS+VLWQ+VGF E  S  ITVITSV N
Sbjct: 257 DLKGRMAGLKPIVWVGIGLAALQQFVGINVIFYYSNVLWQSVGFTEADSFTITVITSVTN 316

Query: 321 IATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQGP 380
           +  T++AIA ++RVGRR LL+IGS GM + L T+A IF TA   +VDG   P L    GP
Sbjct: 317 VVVTVVAIALVERVGRRRLLLIGSGGMTLMLGTLAVIFATA--PLVDG--APVLGPTAGP 372

Query: 381 IALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSMK 440
           +ALVAANLFVV FG+SWGP++WVLLGE FPN+IR AAL++A   QW ANW++TVTFP++ 
Sbjct: 373 VALVAANLFVVFFGVSWGPMMWVLLGEMFPNQIRGAALAVAGFVQWIANWVVTVTFPALA 432

Query: 441 DFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAM 477
             SLG++YG YA  A++SL+F +R V+ET G+ELE M
Sbjct: 433 AASLGLAYGLYAFFALVSLLFTIRMVRETTGIELEDM 469


Lambda     K      H
   0.324    0.138    0.405 

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: 746
Number of extensions: 29
Number of successful extensions: 2
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: 483
Length of database: 471
Length adjustment: 33
Effective length of query: 450
Effective length of database: 438
Effective search space:   197100
Effective search space used:   197100
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: 51 (24.3 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