GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Chryseobacterium viscerum 687B-08

Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_103233202.1 C1634_RS24605 sugar porter family MFS transporter

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



>NCBI__GCF_002899945.2:WP_103233202.1
          Length = 436

 Score =  357 bits (915), Expect = e-103
 Identities = 195/433 (45%), Positives = 274/433 (63%), Gaps = 7/433 (1%)

Query: 22  IILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVAS-ALIGTVLGSLIAG 80
           I++ +  AAL G LFGFD  VISGA + LQ  +  +DA  G  V   AL GTV+G++  G
Sbjct: 4   ILMWSITAALAGFLFGFDVVVISGADKKLQTLWNSSDAFHGAVVMGMALWGTVIGAIFGG 63

Query: 81  APADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEV 140
            P +  GRK  +L + + Y  S++GT L+ D   F  FRFMGGL +GA+++  P YI+E+
Sbjct: 64  IPTNTLGRKKTLLIIGVLYAFSAIGTALSNDPYLFAFFRFMGGLGVGASTIAAPAYISEI 123

Query: 141 SPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTL 200
           +PA+ RG++V++ Q NIVLGILIAFLSNY+++G+   D  WRWM G+ A+P+ I+ L  L
Sbjct: 124 APAKDRGKMVSLYQFNIVLGILIAFLSNYLLSGIGDND--WRWMLGVQAIPAAIYTLCVL 181

Query: 201 LLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTP 260
            +PESPRWL  H + + A+ VM+ L   D  ++    ++ +   E+  K  +F + +  P
Sbjct: 182 TIPESPRWLVSHSRIEEAKKVMKILS-PDQDSDTLITQMEDDHAESP-KENIFMKKYRFP 239

Query: 261 VACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLID 320
           +  A  +A FNQ+SGINA LYYAPRIF  AG G  +ALL SI +G  N+VFT+  + LID
Sbjct: 240 LMLAFLVAFFNQMSGINAFLYYAPRIFGEAGLGEKTALLSSIGIGVVNMVFTLVGVNLID 299

Query: 321 RFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFIS 380
           + GRR L+++GSV    +L LV          G  I   L  FIA+ A+ QG VIWVFIS
Sbjct: 300 KVGRRTLMYLGSVGYIISLGLVSMAF-YFHWSGLAIPIFLFLFIASHAIGQGTVIWVFIS 358

Query: 381 EVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTWKF 439
           E+FP+ +R  GQA GS+THW++AA I    P   +++G G VF  F   M+ QLL+    
Sbjct: 359 EIFPNHLRASGQAFGSSTHWLLAAIIPSLIPTLFSTIGAGTVFLVFTVAMVFQLLFVMFM 418

Query: 440 MPETNGIALEDMN 452
           MPET GI+LE ++
Sbjct: 419 MPETKGISLEKLS 431


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: 571
Number of extensions: 36
Number of successful extensions: 9
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: 436
Length adjustment: 33
Effective length of query: 425
Effective length of database: 403
Effective search space:   171275
Effective search space used:   171275
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