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.
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:
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