Align Inositol transport system permease protein (characterized)
to candidate 3607867 Dshi_1275 Monosaccharide-transporting ATPase (RefSeq)
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Dino:3607867 Length = 374 Score = 593 bits (1528), Expect = e-174 Identities = 292/370 (78%), Positives = 326/370 (88%) Query: 4 APTQFAEDERIKTRSKFREAMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQI 63 AP DERIK SKFR+A+IRPELGGI GT+ VF F + A DSGMF QGV+NW+ + Sbjct: 5 APPAPVVDERIKQTSKFRQALIRPELGGICGTVIVFVFFFLTAFDSGMFTPQGVLNWTLV 64 Query: 64 SAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAI 123 SAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGM+IA+F V L WP+W+AIL+TFAI +I Sbjct: 65 SAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMMIAVFGVVLAWPMWIAILITFAICLSI 124 Query: 124 GALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFG 183 GALNG IV+RTGLPSFIVTLAFLFILRGF I++PQT+E KTIIGG+ DAAEGDWLA +FG Sbjct: 125 GALNGAIVIRTGLPSFIVTLAFLFILRGFTIFIPQTLESKTIIGGIRDAAEGDWLAPVFG 184 Query: 184 GKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNW 243 GKI G FQW GD G I F RG R G+ V++GLPML++WA+LL+ GH++LT+TRFGNW Sbjct: 185 GKIGNGFFQWLGDIGVIETFSRGNRAGEAVIDGLPMLVIWALLLIAFGHILLTRTRFGNW 244 Query: 244 IFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAI 303 IFAAGGDAEAARNSGVPVN+VKILMFMFTAFCA VFATCQVMEFG AG+DRGLLKEFEAI Sbjct: 245 IFAAGGDAEAARNSGVPVNKVKILMFMFTAFCACVFATCQVMEFGSAGADRGLLKEFEAI 304 Query: 304 IAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNT 363 IAVVIGGALLTGGYGSV+GAALGALIFGVVQQGLFFAGVESSLFRVFLG+ILL AVILNT Sbjct: 305 IAVVIGGALLTGGYGSVIGAALGALIFGVVQQGLFFAGVESSLFRVFLGVILLGAVILNT 364 Query: 364 YIRRVITGER 373 YIRR+ITGER Sbjct: 365 YIRRMITGER 374 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: 728 Number of extensions: 40 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: 373 Length of database: 374 Length adjustment: 30 Effective length of query: 343 Effective length of database: 344 Effective search space: 117992 Effective search space used: 117992 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: 50 (23.9 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