Align D-mannose and D-mannitol transporter (characterized)
to candidate BWI76_RS16940 BWI76_RS16940 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Koxy:BWI76_RS16940 Length = 439 Score = 210 bits (534), Expect = 8e-59 Identities = 134/406 (33%), Positives = 208/406 (51%), Gaps = 14/406 (3%) Query: 9 IIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAAD 68 I+ +L + +INYLDR+ L +AAP + + G+ MG++FS+F YA GG D Sbjct: 26 ILALLAVGTMINYLDRTVLGIAAPQLTAELGIDAAMMGIVFSAFAWTYALAQIPGGIFLD 85 Query: 69 RYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPK 128 R+G K T LA+ LWSLF+ + VG SL+L R G+ E P S++V+ W+ + Sbjct: 86 RFGNKVTYFLALTLWSLFTLFHGMAVGLKSLLLCRFGLGVSEAPCFPVNSRVVSAWFPQQ 145 Query: 129 RRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKERPE 188 RA+A G LG A P++ +I ++GW+ FI + G+++A VW++ +E E Sbjct: 146 ERAKATAVYTVGEYLGLACFAPLLFWIMGSFGWRALFISVGAAGVLFALVWWRCYREPHE 205 Query: 189 GE-----GAEDILRAEGQGELAAQPV---FPL-RFYLKQPTVLFTSLAFFSYNYTLFFFL 239 + E I+ G A Q +PL R L + +L S+ F+ N L FFL Sbjct: 206 DKHLNQLEREHIINGGGMSTGAEQHTAFSWPLVRQLLAKRQILGASIGQFAGNTVLVFFL 265 Query: 240 TWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVT 299 TWFP+YL + + ++P++ G+ GG++SD + K TG RK+ ++ Sbjct: 266 TWFPTYLATERHMPWIKVGFFAIMPFLAAAGGVMFGGWVSDKLLKATGSANLGRKLPIIA 325 Query: 300 CLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMH 359 LL + IA + + L AVILV FF + W +I D P G G + Sbjct: 326 GLLMASTIIAANWLTSDL--AVILVMSFAFFGQGMVGLGWTLISDIAPKGLGGLTGGLFN 383 Query: 360 FLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARYV 405 F AN +GI+ P + GF+V +G+F A + G ++G VA Y+ Sbjct: 384 FCANLAGILTPLIIGFIVAASGNFFYALIYIGGAALLG---VAAYL 426 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: 539 Number of extensions: 30 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: 439 Length adjustment: 32 Effective length of query: 398 Effective length of database: 407 Effective search space: 161986 Effective search space used: 161986 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