Align Inner-membrane translocator (characterized, see rationale)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 315 bits (808), Expect = 8e-91 Identities = 162/313 (51%), Positives = 220/313 (70%) Query: 4 RRFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63 R +PL +T L + M G + GF + +V NLL DNAFL I A+GMT VI++GGID Sbjct: 22 RAQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIVAVGMTFVILAGGID 81 Query: 64 LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123 LSVGAV+A S V+ + L+ + W PL A ++L +GT FGA MG +I ++LQPF+VTLA Sbjct: 82 LSVGAVVAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVLIQRFRLQPFVVTLA 141 Query: 124 GMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHY 183 GMFLARG+AT +S +SI ID P+ +VA + + L G L + +L+ + A++ Sbjct: 142 GMFLARGVATLISVDSIDIDQPWLASVANLRLPLGGGSMLSVGALVALAVVAAGALLAGA 201 Query: 184 TRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIG 243 + FG VYAIGG++ SA LMG+ + T + +YA+S F A LAG+V+T Y SGY+ A+G Sbjct: 202 SSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYSQHALG 261 Query: 244 VELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLF 303 +ELDAIAAVVIGGT+L GGSG+VLGT+LGV+++G+IQT I FDG LSSWWT+IVIG LL Sbjct: 262 LELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWTRIVIGALLL 321 Query: 304 FFILLQKLLNGRK 316 F LLQ+L ++ Sbjct: 322 AFCLLQRLFRRKE 334 Lambda K H 0.330 0.145 0.424 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: 433 Number of extensions: 14 Number of successful extensions: 4 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: 320 Length of database: 337 Length adjustment: 28 Effective length of query: 292 Effective length of database: 309 Effective search space: 90228 Effective search space used: 90228 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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