GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS23325
          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:

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