GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Galbibacter marinus ck-I2-15

Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_008991179.1 I215_RS06545 sugar porter family MFS transporter

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



>NCBI__GCF_000300875.1:WP_008991179.1
          Length = 444

 Score =  366 bits (939), Expect = e-106
 Identities = 198/428 (46%), Positives = 278/428 (64%), Gaps = 10/428 (2%)

Query: 29  AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTV-ASALIGTVLGSLIAGAPADRFG 87
           AAL G LFGFDT VISGA + LQ  +G TDA  G  V A AL GTV+G++  G P ++FG
Sbjct: 11  AALAGFLFGFDTVVISGADKQLQELWGTTDAFHGSVVMAMALWGTVVGAIFGGIPTNKFG 70

Query: 88  RKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRG 147
           R+  +  +   Y+VS++G+ L  D  +F  FRF+GGL +GA+++  P YI+E++P + RG
Sbjct: 71  RRNTLFFIGALYLVSAIGSALVNDPVSFAAFRFIGGLGVGASTIAAPTYISEIAPPKNRG 130

Query: 148 RLVAMNQLNIVLGILIAFLSNYII--AGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPES 205
           RLV+M Q NIVLGIL+AFLSNY++  AG    +  WRWM G+ A+P+ I++L  L +P+S
Sbjct: 131 RLVSMYQFNIVLGILMAFLSNYLLRDAG----NQPWRWMLGVEAIPAFIYMLFVLFIPKS 186

Query: 206 PRWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTPVACAI 265
           PRWL    +   A+ V+Q++       +L+   + +++ +      +F + +  P+  A 
Sbjct: 187 PRWLLSKSKIAEAKQVLQKMNIGMDIDQLSE-NIQQSKGDRTTAESIFLKRYRFPLMLAF 245

Query: 266 AIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRR 325
            +A FNQ+SGINA LYYAPRIFE+AG   DS+LL SI +G  NL+FT+  +FLID+ GR+
Sbjct: 246 LVAFFNQMSGINAFLYYAPRIFEIAGLEQDSSLLSSIGIGVVNLIFTLIGVFLIDKAGRK 305

Query: 326 PLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPS 385
            L+ VGS+    +LLLV       +  G  +   L  FIA+ A+ QGAVIWVFISE+FP+
Sbjct: 306 QLMLVGSIGYIISLLLVACAF-FFQWGGLWVPIFLFIFIASHAVGQGAVIWVFISEIFPN 364

Query: 386 AVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTWKFMPETN 444
            +R  GQA GS+ HWV+AA I    PV   S+G G+VF FF  MM  QLL+    MPET 
Sbjct: 365 HLRASGQAFGSSVHWVLAAIIPSFVPVLFTSIGAGYVFLFFAIMMFFQLLFVLFMMPETK 424

Query: 445 GIALEDMN 452
           G +LED++
Sbjct: 425 GKSLEDLS 432


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: 592
Number of extensions: 29
Number of successful extensions: 7
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: 444
Length adjustment: 33
Effective length of query: 425
Effective length of database: 411
Effective search space:   174675
Effective search space used:   174675
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