Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 153 bits (386), Expect = 7e-42 Identities = 118/347 (34%), Positives = 180/347 (51%), Gaps = 32/347 (9%) Query: 11 DAVPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGT---SNFASAENTM 67 +AV P A +++ W R +P+LV L L + ++G G F + + + Sbjct: 2 NAVAPAATSAAAGRRPWWRRR-AQVPLLVTLVLF-----VAMAGAGGVLYHGFLTPQVFL 55 Query: 68 NILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGW----AIPMF 123 N+L A ++A GMTFVIL GIDLSVG+V+A S VL L GW AI + Sbjct: 56 NLLIDNAFLCIVAVGMTFVILAGGIDLSVGAVVAFSTVL--LAELVQRHGWPPLAAIALV 113 Query: 124 IFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGT---------TVLNNDI 174 + G G G ++ + FVVTL M RG A L++ + +V N + Sbjct: 114 LAVGTGFGAGMGVLIQRFRLQPFVVTLAGMFLARGVATLISVDSIDIDQPWLASVANLRL 173 Query: 175 PSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGL 234 P +G G L V L VA+AVV ++ + G +YAIGG+ +ARL G+ V Sbjct: 174 P----LGGGSMLSVGAL--VALAVVAAGALLAGASSFGRTVYAIGGSESSARLMGLPVDA 227 Query: 235 VLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGT 294 ++ VY++SG + LAG + + G ELDAIAAVV+GGT L GG G + GT Sbjct: 228 TVVRVYALSGFCAALAGVVYTLYMLSGYSQHALGLELDAIAAVVIGGTVLAGGSGYVLGT 287 Query: 295 VVGALIIGVMNNGLTILG-LSSFWQYVAKGAVIVLAVILDK-WRQKD 339 ++G L++G++ + G LSS+W + GA+++ +L + +R+K+ Sbjct: 288 LLGVLVLGLIQTLIVFDGELSSWWTRIVIGALLLAFCLLQRLFRRKE 334 Lambda K H 0.324 0.138 0.417 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: 330 Number of extensions: 19 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: 344 Length of database: 337 Length adjustment: 28 Effective length of query: 316 Effective length of database: 309 Effective search space: 97644 Effective search space used: 97644 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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