GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Kocuria turfanensis HO-9042

Align The glucose uptake porter, GluP (characterized)
to candidate WP_062735750.1 AYX06_RS10665 sugar porter family MFS transporter

Query= TCDB::Q0SE66
         (483 letters)



>NCBI__GCF_001580365.1:WP_062735750.1
          Length = 471

 Score =  559 bits (1441), Expect = e-164
 Identities = 286/458 (62%), Positives = 354/458 (77%), Gaps = 4/458 (0%)

Query: 20  TSVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAML 79
           TS  +RI+++AA GG LFGYDSAVINGAVSAI+ +F V    LGFA+ASALLGAAAGA  
Sbjct: 16  TSAVLRISIIAAFGGFLFGYDSAVINGAVSAIQEEFGVSPGPLGFAVASALLGAAAGAFF 75

Query: 80  AGRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIA 139
            GRIAD+ GR+  M+ AAV+FL+SAIG G   +   L+ +RIVGG+GVG+AS+IAPAYIA
Sbjct: 76  GGRIADQLGRVPVMKIAAVLFLVSAIGCGVVDSFGWLIFWRIVGGVGVGVASIIAPAYIA 135

Query: 140 EISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCV 199
           EI+PA VRGRLGSLQQ+ IV GIFVSL VD  LAA+AGGS +ELW+GLEAWRWMF+A  +
Sbjct: 136 EIAPAAVRGRLGSLQQMGIVLGIFVSLAVDAWLAALAGGSTQELWWGLEAWRWMFMAEAI 195

Query: 200 PALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSI 259
           PALAY + + TIPESPRYL+  GR  EA+ +LA L G      ++  I+ +L  E +P +
Sbjct: 196 PALAYLIGAFTIPESPRYLVEDGRPDEAQAVLANLQGSASATERVRLIKESLRSEHKPRL 255

Query: 260 RDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVV 319
            DLKG   GL PIVW+GIGL+  QQFVGINVIFYYS+VLWQ+VGF E  S  ITVITSV 
Sbjct: 256 SDLKGRMAGLKPIVWVGIGLAALQQFVGINVIFYYSNVLWQSVGFTEADSFTITVITSVT 315

Query: 320 NIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQG 379
           N+A T++AIA ++RVGRR LL+IGSAGMA++L T++ +F TA   VVDG   P L    G
Sbjct: 316 NVAVTIVAIALVERVGRRRLLLIGSAGMALSLGTLSVLFATAD--VVDG--APVLGPTAG 371

Query: 380 PIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSM 439
           P+ALVAANLFVV FG+SWGP++WVLLGE FPNRIR AAL++A   QW ANWL+TVTFP++
Sbjct: 372 PVALVAANLFVVFFGVSWGPMMWVLLGEMFPNRIRGAALAVAGFVQWIANWLVTVTFPAL 431

Query: 440 KDFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAM 477
             FSLG++YG Y   A++SL+F L+ V+ET G+ELE M
Sbjct: 432 AAFSLGVAYGLYTFFALVSLLFTLKMVRETTGIELEDM 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: 736
Number of extensions: 24
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.

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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