Align D-mannose and D-mannitol transporter (characterized)
to candidate H281DRAFT_03217 H281DRAFT_03217 MFS transporter, ACS family, D-galactonate transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Burk376:H281DRAFT_03217 Length = 455 Score = 211 bits (538), Expect = 3e-59 Identities = 130/411 (31%), Positives = 203/411 (49%), Gaps = 19/411 (4%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R I+ +L + +INYLDR+ L +AAP + K+ G++ MG++FS F Y A GG Sbjct: 31 RYQILGLLAVGTMINYLDRTVLGIAAPQLTKELGINAAMMGLLFSVFSWSYVASQIPGGL 90 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWY 125 DR+G+K T L+M WSL + L G A L + R+ G+ E P T S++V W+ Sbjct: 91 FLDRFGSKLTYFLSMTFWSLCTLAQGLVHGIAGLFVFRLGLGVSEAPCFPTNSRVVATWF 150 Query: 126 TPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKE 185 RA A G G +G A P + + +GW+ F ++ +G+V+ +W+ +E Sbjct: 151 PQSERAMATGTYTVGEYIGLAFFSPFLFMLMGAFGWRSLFYVVGGVGIVFGVIWWLMYRE 210 Query: 186 ---RPEGEGAE-DILRAEG-------QGELAAQPV---FPLRF---YLKQPTVLFTSLAF 228 P AE D + A G G AA P F R LK + L Sbjct: 211 PRDHPSANQAELDYIEAGGGLTHRHKDGGAAAAPAKGGFEWRTIGRLLKHRQLTGICLGQ 270 Query: 229 FSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGR 288 F+ N TL FFLTWFP+YL + + ++P++ +G+ GG SD++ ++ Sbjct: 271 FAGNSTLVFFLTWFPTYLATERHMGWLKIGFFAIMPFIAASIGVMFGGLFSDWLLRRGKS 330 Query: 289 MMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPA 348 +RK+ ++ LL + I + + + AVI + FF A+ W ++ D P Sbjct: 331 ANVARKLPIIAGLLLASTIILANYVESNV--AVIAILSVAFFAQGMAALGWTLVSDIAPE 388 Query: 349 ARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAV 399 +G G +F AN +GIV P + GF+V TGSF A + G++ +IGA+ Sbjct: 389 GLLGVTGGIFNFAANLAGIVTPLVVGFIVAATGSFVGALVFIGVIALIGAL 439 Lambda K H 0.329 0.142 0.439 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: 555 Number of extensions: 32 Number of successful extensions: 3 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: 430 Length of database: 455 Length adjustment: 32 Effective length of query: 398 Effective length of database: 423 Effective search space: 168354 Effective search space used: 168354 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 (21.8 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