Align nucleoside permease nupG (characterized)
to candidate BWI76_RS07365 BWI76_RS07365 MFS transporter
Query= CharProtDB::CH_088596 (418 letters) >FitnessBrowser__Koxy:BWI76_RS07365 Length = 413 Score = 202 bits (513), Expect = 2e-56 Identities = 124/404 (30%), Positives = 209/404 (51%), Gaps = 22/404 (5%) Query: 6 QLKILSFLQFCLWGSWLTTLGSYMFVTLKFDGASIGAVYSSLGIAAVFMPALLGIVADKW 65 +L ++ F+QF +WGSW TLG M T IG +S+ IA++ P +LG++ D++ Sbjct: 21 RLSLMMFMQFFIWGSWSVTLGLVM--TRYEMSLLIGDAFSAGPIASILSPFVLGMLVDRF 78 Query: 66 LSAKWVYAICHTIGAITLFMAAQVTTPE--AMFLVILIN-SFAYMPTLGLINTISYYRLQ 122 +++ V A+ H GA+ L+ Q + A+ + +L + YMPTL L N I+++ L Sbjct: 79 FASQKVMAVMHLAGAVILWFVPQALVAQNGALLIGLLFGYTLCYMPTLALTNNIAFHSLA 138 Query: 123 NAGMDIVTDFPPIRIWGTIGFIMAMWVVSLSGFELSHMQLYIGAALSAILVLFTLTLPHI 182 N + FP +R++GTIG+I+A + ++G + + A S L +++LTLPH Sbjct: 139 N----VDKTFPVVRVFGTIGWIIAGIFIGVTGISDTTGIFSVAALCSVALAVYSLTLPHT 194 Query: 183 PVAKQQANQSWTTLLGLDAFALFKNKRMAIFFIFSMLLGAELQITNMFGNTFLHSFDKDP 242 P + + LL DAFAL K + IF + + L+ L + ++L Sbjct: 195 PAPAKGTPVQFRDLLCADAFALLKTRHFLIFSLCATLISIPLGTYYAYTASYL------- 247 Query: 243 MFASSFIVQHASIIMSISQISETLFILTIPFFLSRYGIKNVMMISIVAWILRFALFAYGD 302 + + S MS Q+SE F+L IP R G+K +++I + AW +R+A FA G Sbjct: 248 ---ADAGIADVSTAMSFGQMSEIFFMLVIPLLFRRLGVKYMLLIGMAAWFVRYAFFALG- 303 Query: 303 PTPFGTVLLVLSMIVYGCAFDFFNISGSVFVEKEVSPAIRASAQGMFLMMTNGFGCILGG 362 + G LL L ++++G +DFF + G ++ ++ ++ AQ M +M T G G +LG Sbjct: 304 VSEEGRFLLYLGILLHGVCYDFFFVVGFIYTDRVAGEKVKGQAQSMIVMFTYGIGMLLGS 363 Query: 363 IVSGKVVE--MYTQNGITDWQTVWLIFAGYSVVLAFAFMAMFKY 404 +SG + + Q+ W W I A + V+A F+ F+Y Sbjct: 364 QISGALYNHLVAGQSVPQAWVAFWWIPAVAAAVIALIFLFSFQY 407 Lambda K H 0.331 0.141 0.436 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: 512 Number of extensions: 31 Number of successful extensions: 8 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: 418 Length of database: 413 Length adjustment: 31 Effective length of query: 387 Effective length of database: 382 Effective search space: 147834 Effective search space used: 147834 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 50 (23.9 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