Align Inositol transport system permease protein (characterized)
to candidate SMa0217 SMa0217 ABC transporter permease
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Smeli:SMa0217 Length = 359 Score = 134 bits (337), Expect = 4e-36 Identities = 93/298 (31%), Positives = 134/298 (44%), Gaps = 37/298 (12%) Query: 70 IAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGF 129 +A+GA +LMIAGEFDLS+GS+ F +L+A V G ++A + IG+LNG Sbjct: 95 LALGAGVLMIAGEFDLSIGSVYTFTAVLMASL-VNAGLSAFIAAPIAILTGLLIGSLNGH 153 Query: 130 IVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTG 189 I +R GLPSFIVTL L RG + ++ + V +LF G + Sbjct: 154 ITLRFGLPSFIVTLGGLLFWRGAVLLYNGAVQVRFDPEPV--------FTSLFSGTLF-- 203 Query: 190 LFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGG 249 G+ +W +L V H++L + RFGN +FA GG Sbjct: 204 --------------------------GVNAAFIWIVLFVTGFHLLLHRHRFGNHVFATGG 237 Query: 250 DAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIG 309 + AA G+ +RVK++ F A V G +G E +AI A VIG Sbjct: 238 NRGAAEAIGINTSRVKLIAFAIAGGMAAVAGILATARVGSVQPGQGAGLELQAIAACVIG 297 Query: 310 GALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTYIRR 367 G L GG GS++G LG L+ + L +F+ +++ A I N I R Sbjct: 298 GLSLRGGRGSIIGIFLGVLLIHTITDVLLLLRAPGFYLDMFIATLIVLAAIFNHLIER 355 Lambda K H 0.330 0.145 0.443 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: 455 Number of extensions: 35 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 373 Length of database: 359 Length adjustment: 30 Effective length of query: 343 Effective length of database: 329 Effective search space: 112847 Effective search space used: 112847 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 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