Align D-mannose and D-mannitol transporter (characterized)
to candidate RR42_RS00375 RR42_RS00375 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Cup4G11:RR42_RS00375 Length = 432 Score = 178 bits (451), Expect = 3e-49 Identities = 126/417 (30%), Positives = 196/417 (47%), Gaps = 19/417 (4%) Query: 8 LIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAA 67 + ++MLFL INY+DR++LSVA P I K++ LS G+I SSFF YA GG A Sbjct: 21 IFLMMLFLIA-INYIDRASLSVAMPLIAKEFDLSPTMQGLILSSFFWTYAVMQIPGGMLA 79 Query: 68 DRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTP 127 D+Y + + A V W F + + +L+L R+ G E P+ K+ W T Sbjct: 80 DKYKPRIVIATATVFWGAFQAMAAVCTSAGALLLTRLGLGAAEAPIYPAGGKLNAIWMTQ 139 Query: 128 KRRARAIGASMSGTPLGGAISGPVVGFIAVTYG-WKISFIIIMLIGLVWAAV--WFKFVK 184 R R G PLG A+ ++ ++ G W+++F++ +G V A + W+ +V+ Sbjct: 140 NERGRGATLLDGGAPLGAALGAIIITWLITALGSWRLAFVVAG-VGTVLAGMLAWY-YVR 197 Query: 185 ERP-EGEGAEDI----LRAEGQGELAAQPV---FPLRFYLKQPTVLFTSLAFFSYNYTLF 236 P E G ++ + A E A+P +LK +V + + +N + Sbjct: 198 NSPREHRGVNELEASYIEAAQASEHRAEPANLSGRSLDFLKYRSVWCMATGWMCFNSVFY 257 Query: 237 FFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVV 296 LTW P+YL HG ++K M A+ I + GF+G +GG+I+D G + + Sbjct: 258 GLLTWMPNYLNKVHGFDIKQMGGASFIIFFSGFIGELIGGWIADKWKAAGGAPNLVMRTL 317 Query: 297 LVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSG 356 + V I V V L++ +FFL G +YW I +VG + G Sbjct: 318 FGIAAVVATVSIFSVAYVKDPVVVVALLSSTLFFLRWCG-LYWCIPSILGTRNKVGVLGG 376 Query: 357 FMHFLANTSGIVGPTLTGFLVQFTGSFTSA---FLLAGLLTVIGAVCVARYVKPLSV 410 M+ N GI P + G +VQFTGS+ A F AG+ +I + + Y K L V Sbjct: 377 IMNLGGNIGGITVPIIVGMIVQFTGSYFLALMFFAAAGVGLLISSTAI-DYEKKLPV 432 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: 533 Number of extensions: 35 Number of successful extensions: 5 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: 432 Length adjustment: 32 Effective length of query: 398 Effective length of database: 400 Effective search space: 159200 Effective search space used: 159200 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