GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1901
          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:

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