Align Inositol transport system permease protein (characterized)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 150 bits (380), Expect = 4e-41 Identities = 99/316 (31%), Positives = 172/316 (54%), Gaps = 23/316 (7%) Query: 24 LSIFLVLIGIGLV---FELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITT 80 L++ L+L G GL F W RD N L+ + + + + L+++G+T VI Sbjct: 35 LTLILLLAGNGLFNPGFLALQW--RDGHLYGN---LIDIAHRAAPLALVSLGMTLVIALR 89 Query: 81 GIDLSSGSVLALSAMIAA-SLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGS 139 G+D+S G+VLA++A +AA ++ S+ LP+W+ +A L G L G NG Sbjct: 90 GLDISVGAVLAIAATVAAWTIGHVSNDGL--------LPLWLAIAAALAAGALCGLWNGW 141 Query: 140 IIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHG---AMPVIIFLVVA 196 ++ G+ P +ATL +MV+ RG+A+ + GQ +++ Y+ +G+G +P +F+V A Sbjct: 142 LVVGAGMQPIVATLILMVAGRGIAQSISGGQILTLYYAPYSFLGNGFVLGLPFSLFVVAA 201 Query: 197 V--IFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASAR 254 V + +ALR T G + AIG N QAA +G+ + + Y G+ A LAG++ S+ Sbjct: 202 VFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSSN 261 Query: 255 AATGQA-GMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAY 313 + A G+ ELDAI A +GG+ L GG + G+++GALI+ + + +GV Sbjct: 262 VNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIGVPPQ 321 Query: 314 IQDIIKGLIIVVAVVI 329 + +K +++ +++ Sbjct: 322 VNLAVKAVLVFAVMLL 337 Lambda K H 0.325 0.140 0.394 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: 218 Number of extensions: 7 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: 340 Length of database: 358 Length adjustment: 29 Effective length of query: 311 Effective length of database: 329 Effective search space: 102319 Effective search space used: 102319 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