GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Sphingopyxis indica DS15

Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_089216652.1 CHB69_RS14085 sugar porter family MFS transporter

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



>NCBI__GCF_900188185.1:WP_089216652.1
          Length = 455

 Score =  372 bits (955), Expect = e-107
 Identities = 214/445 (48%), Positives = 277/445 (62%), Gaps = 10/445 (2%)

Query: 9   AGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASA 68
           AG+P +  R T+A  +  A  AL GLLFGFDTAVI+G T  L   F LT   LG TV++A
Sbjct: 12  AGSP-QGGRITLAAAIGTA--ALAGLLFGFDTAVIAGVTHDLTRLFALTPETLGLTVSAA 68

Query: 69  LIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGA 128
           L GT+ G+L AG P D FG +  +  +A  Y V+ LG  LAP    FL FRF+ GLAIG 
Sbjct: 69  LWGTLAGALFAGKPGDAFGSRDSLRVLAAFYFVAGLGCALAPSWTLFLFFRFLCGLAIGG 128

Query: 129 ASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIV 188
           +SV+ P+YIAE++P R RG LV + QL IV+GIL A+LSN +IAGLV     WRW  GI 
Sbjct: 129 SSVLAPVYIAEIAPPRRRGLLVGLFQLMIVIGILTAYLSNAVIAGLVDGGAGWRWKLGIT 188

Query: 189 AVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFAD--PRAELARIELAEAREEA 246
           A P+ +F ++   +P SPRWL + G+A  AR+ + R+G A     AELAR+E A  R+  
Sbjct: 189 AAPALLFFILLFAIPHSPRWLVVKGRASEAREALARIGMAPDAAAAELARVEQALMRDPP 248

Query: 247 AGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGG 306
               +L  R H  P+  AI +AMFNQL+GINA+LYY   IF  A AG+ S   Q++ +G 
Sbjct: 249 --NEKLSWRRHRRPMTLAILVAMFNQLAGINAVLYYLNDIF--ARAGSLSPDRQAVLIGL 304

Query: 307 TNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAA 366
            NL+FT+  + LIDR GR+ LL  G+   A  L +    L  A     L+L  L+GFIA 
Sbjct: 305 ANLIFTLVGMALIDRIGRKTLLLAGAAGMALCLSIAAGVLFGAL-GNALMLPALVGFIAF 363

Query: 367 FAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGWVFAFFG 426
           FA SQGAVIWV+ISEVFP+ VR +G ALG++THW+M A I   FP+  A   G  FA F 
Sbjct: 364 FATSQGAVIWVYISEVFPTPVRARGSALGASTHWLMNALIAGVFPILVAWSPGAPFAIFA 423

Query: 427 AMMLLQLLWTWKFMPETNGIALEDM 451
           A M+LQ +      PET G+ L+ M
Sbjct: 424 AAMVLQFVVVAAIFPETRGVDLDAM 448


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: 619
Number of extensions: 24
Number of successful extensions: 5
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: 455
Length adjustment: 33
Effective length of query: 425
Effective length of database: 422
Effective search space:   179350
Effective search space used:   179350
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