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_074882195.1 PsAD2_RS21425 sugar porter family MFS transporter

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



>NCBI__GCF_001623255.1:WP_074882195.1
          Length = 448

 Score =  239 bits (610), Expect = 1e-67
 Identities = 154/437 (35%), Positives = 236/437 (54%), Gaps = 21/437 (4%)

Query: 31  LGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASAL-IGTVLGSLIAGAPADRFGRK 89
           L G L G++  V+SGA   L  QF  T   LG  VASAL +G +LGS+ A   +D  GR+
Sbjct: 11  LCGFLSGYNGGVVSGAYSLLVQQFHFTP-FLGGVVASALPLGGLLGSIFASYSSDHMGRR 69

Query: 90  GVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGRL 149
             +L  A  +VV +L +G    +   ++ RF+ G A G  + + P Y++E++P   RGR+
Sbjct: 70  TSILISASLFVVGALMSGTTNHVETLIIARFLVGFATGIVTPIGPQYLSEIAPPLVRGRM 129

Query: 150 VAMNQLNIVLGILIAFLSNYIIAGL-VQYDVAWRW--MFGIVAVPSTIFLLVTLLLPESP 206
           +   Q+    G+L A+++N II+G+   +DV  RW  MF +  +P+ + L+  L  P SP
Sbjct: 130 IGAYQMMTSGGVLSAYVANQIISGISADFDVINRWQLMFALSGIPAVVLLVGMLFAPRSP 189

Query: 207 RWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTP-----V 261
           RWL + G+   AR+V   LG         +       EE + +     R    P      
Sbjct: 190 RWLLLRGRNQDAREVFYMLGSKGAEDWGEKAVNTAINEERSTRGTCRWRDLIGPELRSIT 249

Query: 262 ACAIAIAMFNQLSGINALLYYAPRIF-ELAGAGADSALLQSIAVGGTNLVFTVAALFLID 320
             AIAI +  QLSGIN ++YYAP+I  +L  A  +++LL + ++G    + ++ ALFL D
Sbjct: 250 IFAIAIFVIQQLSGINVVIYYAPQILSQLGFALHETSLLATTSLGVVMFLTSIPALFLFD 309

Query: 321 RFGRRPLLFVGSVIC--AATLLLVGWQLESAKPDGTLILFGLLG---FIAAFAMSQGAVI 375
           +FGRR LL +G  +C  A  L +V   LE    +G L   G LG   ++AAFA+S G + 
Sbjct: 310 KFGRRSLLIIGLPLCGFAEILAMVPVYLE----NGELAWLGALGLCLYMAAFALSIGPLP 365

Query: 376 WVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLL 434
           W++I+E+FP   R KG  +G  T+W+    +   FPV  AS G  W+FA F     L + 
Sbjct: 366 WIYIAEIFPVQARAKGMVIGVMTNWIFNFGVVLMFPVLIASFGIFWMFAMFITTCFLGMC 425

Query: 435 WTWKFMPETNGIALEDM 451
           +  ++ PET G+ +E +
Sbjct: 426 YAVRYAPETKGVPIEQI 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: 590
Number of extensions: 33
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: 448
Length adjustment: 33
Effective length of query: 425
Effective length of database: 415
Effective search space:   176375
Effective search space used:   176375
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