GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Pseudovibrio axinellae Ad2

Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_068010715.1 PsAD2_RS22100 sugar porter family MFS transporter

Query= reanno::Korea:Ga0059261_1777
         (458 letters)



>NCBI__GCF_001623255.1:WP_068010715.1
          Length = 450

 Score =  217 bits (552), Expect = 7e-61
 Identities = 144/438 (32%), Positives = 229/438 (52%), Gaps = 13/438 (2%)

Query: 26  AAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADR 85
           A  A L G L+G++ AV+ GA   L+  F       G  VA+  +G ++G+ +    +D 
Sbjct: 6   ACVAVLCGFLYGYNEAVVGGAYDLLEAYFVFPPYWRGILVAALPLGGLVGAFLCAHLSDA 65

Query: 86  FGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARF 145
           +GR+  ++   + +V+ SL +GLA +L      R + G+AIG +S+    Y+AE+SP + 
Sbjct: 66  YGRRSALIISGLLFVLGSLLSGLALELYLLSCARLLVGIAIGISSLAALQYLAEISPPKA 125

Query: 146 RGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA---WRWMFGIVAVPSTIFLLVTLLL 202
           RGRL+A  QL + LGIL A+LS  +I  +         W+ ++ +  + +   L  +L  
Sbjct: 126 RGRLLAAFQLLVSLGILSAYLSEALINRVPLTGDPFNHWQLLYLMSGIAAVAMLAGSLAS 185

Query: 203 PESPRWLAIHGQADRARDVMQRL------GFADPRAELARIELAEAREEAAGKPRLFQRS 256
            ESPRWLA+ G+A  A     +L       +A  + +L R + A A +E  G   L   +
Sbjct: 186 LESPRWLAMVGKAGHAEATFIKLEPTQTPDWAIRQVKLLRQD-AIATQEKRGWRELLSAN 244

Query: 257 HFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSA-LLQSIAVGGTNLVFTVAA 315
                  A+   +  QLSG+  LL+YAP I E  G    S   L ++      ++ +  +
Sbjct: 245 MRPITGFALMCFLLQQLSGVYVLLFYAPSILEEFGLPESSVHTLTTLGFAAALILGSALS 304

Query: 316 LFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLI-LFGLLGFIAAFAMSQGAV 374
           +FLIDR GRRPL+ +G   CAATLLL+ W ++   PDG  I L G+  F+  FA S G +
Sbjct: 305 VFLIDRIGRRPLMVMGYPCCAATLLLIIWGMDMPAPDGIWITLTGIFLFVVNFAFSIGPL 364

Query: 375 IWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQL 433
            WV+++E+FPS +R KG AL  + +W++     +AFP     V    +  FF        
Sbjct: 365 PWVYMAELFPSHLRAKGMALAVSLNWILTFLAVFAFPKIYQFVSVNQILLFFVVTSFFGA 424

Query: 434 LWTWKFMPETNGIALEDM 451
           ++  +  PETN + LE++
Sbjct: 425 VYMVRKAPETNTLTLENI 442


Lambda     K      H
   0.327    0.139    0.420 

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: 541
Number of extensions: 30
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: 458
Length of database: 450
Length adjustment: 33
Effective length of query: 425
Effective length of database: 417
Effective search space:   177225
Effective search space used:   177225
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: 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