Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 294 bits (752), Expect = 2e-84 Identities = 160/312 (51%), Positives = 213/312 (68%), Gaps = 10/312 (3%) Query: 3 KRNLPLMITIGVFVL-----GYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVIL 57 + +PL++T+ +FV G LY GF + +V N+L DNAFL I+AVGMTFVIL Sbjct: 22 RAQVPLLVTLVLFVAMAGAGGVLY-----HGFLTPQVFLNLLIDNAFLCIVAVGMTFVIL 76 Query: 58 SGGIDLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAF 117 +GGIDLSVG+V+AF+ V LA+++ G PL A LVL +G FGA MG+LI ++ F Sbjct: 77 AGGIDLSVGAVVAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVLIQRFRLQPF 136 Query: 118 IITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGI 177 ++TLAGMF RGV+ L+S +SI I+ P ++++L + GG LS L+ LAVV G Sbjct: 137 VVTLAGMFLARGVATLISVDSIDIDQPWLASVANLRLPLGGGSMLSVGALVALAVVAAGA 196 Query: 178 FLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYA 237 LA + FG VYAIGG+ +SA LMG+ +T +R+Y LS A LAG+V+++Y +GY+ Sbjct: 197 LLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYS 256 Query: 238 LAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAI 297 +G+ELDAIA+VVIGGT+L+GG G VLGTL GV + GLIQT I FDG LSSWWT+I I Sbjct: 257 QHALGLELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWTRIVI 316 Query: 298 GILLFIFIALQR 309 G LL F LQR Sbjct: 317 GALLLAFCLLQR 328 Lambda K H 0.329 0.145 0.428 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: 376 Number of extensions: 20 Number of successful extensions: 1 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: 331 Length of database: 337 Length adjustment: 28 Effective length of query: 303 Effective length of database: 309 Effective search space: 93627 Effective search space used: 93627 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