GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcP in Pedobacter sp. GW460-11-11-14-LB5

Align D-fructose transporter, sugar porter family (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter

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



>lcl|FitnessBrowser__Pedo557:CA265_RS23325 CA265_RS23325 MFS
           transporter
          Length = 443

 Score =  314 bits (804), Expect = 4e-90
 Identities = 170/424 (40%), Positives = 252/424 (59%), Gaps = 6/424 (1%)

Query: 29  AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88
           AA GG LFGFD AVISG+   L+ QF LT    GF   S  +G ++G LIAG  +D +GR
Sbjct: 18  AAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGAMVGCLIAGYVSDAYGR 77

Query: 89  KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148
           K  ++  A  ++ SSL   +AP+ + F+V RF  G+ +G AS+++P+YIAE++P +FRGR
Sbjct: 78  KPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASMLSPMYIAELAPPKFRGR 137

Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208
           LVA+NQL IVLGILI  L NY +      + AWRWMFG+ A+PS IFL+   +LPESPRW
Sbjct: 138 LVAINQLTIVLGILITNLINYTLRN--TGEDAWRWMFGLGAIPSGIFLIGISILPESPRW 195

Query: 209 LAIHGQADRARDVMQRLGFADPRAE-LARIELAEAREEAAGKPRLFQRSHFTPVACAIAI 267
           L   G+ ++A  V+ ++G  +  A+ L  IE    R+       +F + +F  V   I +
Sbjct: 196 LVQKGKNEKALKVLNKIGNHEFAADALKNIEQTLQRKSNVEHESIFNKMYFPAVMIGIGL 255

Query: 268 AMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRRPL 327
           A+F Q  GIN +  YAP++FE  G   D  LLQ++ +G  N++FT++A+FL+D+ GR+PL
Sbjct: 256 AIFQQFCGINTVFNYAPKLFESIGTSQDDQLLQTVFIGAVNVIFTISAMFLVDKIGRKPL 315

Query: 328 LFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPSAV 387
           + +G+   A   +L+   L S     T++ + LL  I  +A+S   V WV ISE+FP+ V
Sbjct: 316 MLIGAGGLAVLYVLISQLLASG---STMVSWFLLSAIGVYAVSLAPVTWVLISEIFPNKV 372

Query: 388 RGKGQALGSTTHWVMAAAITWAFPVFAASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIA 447
           R K         W     + + FP+    +   +F  + A+  L  +  WKF+ ET G  
Sbjct: 373 RVKATTWAILCLWGAYFVLVFTFPILFDWLKESIFYIYAAICTLGCIGIWKFVKETKGKT 432

Query: 448 LEDM 451
           LE++
Sbjct: 433 LEEI 436


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: 508
Number of extensions: 23
Number of successful extensions: 4
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: 443
Length adjustment: 33
Effective length of query: 425
Effective length of database: 410
Effective search space:   174250
Effective search space used:   174250
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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