GapMind for catabolism of small carbon sources

 

Aligments for a candidate for exuT in Sphingomonas koreensis DSMZ 15582

Align Hexuronate transporter (characterized)
to candidate Ga0059261_1901 Ga0059261_1901 Sugar phosphate permease

Query= SwissProt::P0AA78
         (432 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1901 Ga0059261_1901 Sugar
           phosphate permease
          Length = 423

 Score =  253 bits (645), Expect = 1e-71
 Identities = 136/410 (33%), Positives = 230/410 (56%), Gaps = 10/410 (2%)

Query: 6   GLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQPVA 65
           G RW++I+L+ + TV+ Y+ RN +A   P + +++    + Y+ ++  +   Y + Q + 
Sbjct: 4   GFRWWIISLIAVATVINYIDRNALAVMWPAVAKDIGAGKEDYALLVTIFMVFYALGQSLF 63

Query: 66  GYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKASSE 125
           G + DV+GT++G+A+  ++W++   A ++  S   L V RG +G +EA   P   KA++ 
Sbjct: 64  GKIFDVVGTRMGFAISIIVWSLSIAAHSMVRSMAMLGVLRGTLGISEAGNWPGAAKANAT 123

Query: 126 WFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWLIFY 185
           WFP  ER+ A G FN G+S+GA+++ PLV     +  W+ AF+I G L F+W + W+  Y
Sbjct: 124 WFPRSERAFAQGIFNAGASLGAIVSAPLVAILFGLVGWRTAFLIVGVLGFLWLLPWIWVY 183

Query: 186 K-HPRDQKHLTDEERDYIINGQEAQHQVS--TAKKMSVGQILRNRQFWGIALPRFLAEPA 242
           K  P     L+  ERD+I+   E     +       S+GQ+LR++Q W +   RF  +P 
Sbjct: 184 KSDPDAHPWLSKAERDHILGANERVDGDARPAGYAPSMGQLLRHKQAWAVMAGRFFLDPI 243

Query: 243 WGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLP-PLFQRWFGVNLIVS 301
           W  F +W+P+++ + +GF++K+I MFAW+P + A LG + GG+L   L QR  G +   +
Sbjct: 244 WWLFVSWLPIYLNESFGFDVKQIGMFAWVPFVGAMLGSLSGGWLSGKLIQR--GWSADKA 301

Query: 302 RKMVVTLGAVLMIGPGMI--GLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEV 359
           RK+ +TLG V+M+ P ++     + P  A++L+    F  Q     + TL SD FG   V
Sbjct: 302 RKLAITLGCVIML-PALLLTATASTPLYAVLLIAAILFGFQVAINNIQTLPSDWFGGGAV 360

Query: 360 ATANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIW 409
            +  G++G +A +A TL    +  +     F+P+F + A    L  L IW
Sbjct: 361 GSLAGISGTAA-VAGTLVTTWLVPVMTKTSFAPIFILGAALVPLSLLCIW 409


Lambda     K      H
   0.326    0.138    0.437 

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: 675
Number of extensions: 30
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: 432
Length of database: 423
Length adjustment: 32
Effective length of query: 400
Effective length of database: 391
Effective search space:   156400
Effective search space used:   156400
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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