Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 274 bits (701), Expect = 2e-78 Identities = 157/314 (50%), Positives = 210/314 (66%), Gaps = 12/314 (3%) Query: 18 WPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVI 77 WP L+ L+L+L + L P F + +DG L+G+ IDI +RAAP+AL+++GMTLVI Sbjct: 32 WP-----LLTLILLLAGNGLFNPGFLALQWRDGHLYGNLIDIAHRAAPLALVSLGMTLVI 86 Query: 78 ATGGIDLSVGAVMAIAGATTAAMTVAGFS------LPIVLLSALGTGILAGLWNGILVAI 131 A G+D+SVGAV+AIA AT AA T+ S L + + +AL G L GLWNG LV Sbjct: 87 ALRGLDISVGAVLAIA-ATVAAWTIGHVSNDGLLPLWLAIAAALAAGALCGLWNGWLVVG 145 Query: 132 LKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLIL 191 +QP VATLILMVAGRG+AQ I+ GQI+T S+ G+G +L LP + + L Sbjct: 146 AGMQPIVATLILMVAGRGIAQSISGGQILTLYYAPYSFLGNGFVLGLPFSLFVVAAVFAL 205 Query: 192 FWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGA 251 L RKTALG+F+ A+G N +AA AGV R I + YV G+ AA+AG++V++++ A Sbjct: 206 LQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSSNVNSA 265 Query: 252 DANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQV 311 DANNAGL LELDAILAV +GG L GGRF+L S++GALIIQ + T I G PP++N Sbjct: 266 DANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIGVPPQVNLA 325 Query: 312 VKAVVVLCVLIVQS 325 VKAV+V V+++QS Sbjct: 326 VKAVLVFAVMLLQS 339 Lambda K H 0.327 0.142 0.416 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: 353 Number of extensions: 17 Number of successful extensions: 2 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: 341 Length of database: 358 Length adjustment: 29 Effective length of query: 312 Effective length of database: 329 Effective search space: 102648 Effective search space used: 102648 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 (21.7 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