Align Hexuronate transporter (characterized)
to candidate Ga0059261_2977 Ga0059261_2977 Sugar phosphate permease
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__Korea:Ga0059261_2977 Length = 432 Score = 230 bits (587), Expect = 6e-65 Identities = 125/402 (31%), Positives = 213/402 (52%), Gaps = 7/402 (1%) Query: 8 RWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQPVAGY 67 RW ++AL+ TV+ Y+ R + PTLM++L+ S + ++ +I + AY + G Sbjct: 21 RWMIVALLFAATVINYIDRQMIGVLKPTLMQDLHWSERDFAGVIIWFQIAYAIGYIGFGK 80 Query: 68 VLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKASSEWF 127 +D++G ++GYA+ V+W + A A S A+AR +G E+ PAG+KA +EWF Sbjct: 81 FVDMVGARVGYAVAFVIWQLAHIAHGGAYSMTQFAMARFGLGIGESGNFPAGIKAVTEWF 140 Query: 128 PAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWLIFYKH 187 PAKER+ A+G FN G++IGA+I P +V ++ W+MAF+++G +SF+W +AW Y+ Sbjct: 141 PAKERAFAIGVFNAGANIGAVITPLVVPLMVIAWGWRMAFVVTGVISFVWLIAWWAMYRS 200 Query: 188 PRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPAWGTFN 247 PR +++ E +I Q K + +L ++ W +L +F +P W F Sbjct: 201 PRQHPKVSEGELAWI-----EQDPADPVKPIGYATVLTRKETWAYSLGKFFIDPIWWFFL 255 Query: 248 AWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSRKMVVT 307 W+P ++FK Y NL + L +D+G + GG++ + G + +RK+ + Sbjct: 256 FWLPGYLFKQYDLNLLTFGIPLAAIYLISDVGSVFGGWMSSKLMK-AGKSANYARKLTMF 314 Query: 308 LGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVATANGLTG 367 + A L++ T+ +VA++++ + HQA S L L SD+F R V + G+ G Sbjct: 315 VCACLVLPVVFAESITSVWVAVLVIGVATAGHQAFSANLYALPSDLFPRGAVGSVVGIGG 374 Query: 368 MSAWLASTLFALVVGALADTIG-FSPLFAVLAVFDLLGALVI 408 + L A G + D +G + PLF V + LV+ Sbjct: 375 TVGAVGGILMAFYAGEILDRLGVYWPLFWVAGSAYFVALLVV 416 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: 667 Number of extensions: 40 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 432 Length of database: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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