Align Inositol transport system permease protein (characterized)
to candidate H281DRAFT_03379 H281DRAFT_03379 monosaccharide ABC transporter membrane protein, CUT2 family
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Burk376:H281DRAFT_03379 Length = 343 Score = 145 bits (365), Expect = 2e-39 Identities = 106/334 (31%), Positives = 167/334 (50%), Gaps = 37/334 (11%) Query: 33 IGTITVFAMFLIFAGDSGMFNSQGVMNWSQISAQFMIIA---VGACLLMIAGEFDLSVGS 89 +G++ V + + F+ S F S G N ++ Q IA V A ++I G DLSVGS Sbjct: 30 LGSLVV--LIVAFSLTSAAFFSVG--NLMTVALQVTSIAYLGVAATCVIITGGIDLSVGS 85 Query: 90 MIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSFIVTLAFLFIL 149 ++ AG+ A+ V G PV +A+ + A G +NG V R GLP FI TL + + Sbjct: 86 VLALAGVAAALL-VKAGVPVPVAMAGGMLVGAACGWVNGICVTRMGLPPFIATLGMMLVA 144 Query: 150 RGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGLFQWFGDNGWIAVFERGT-- 207 RG A+ + G + ++GL FG+ G A+F+ Sbjct: 145 RGLALQIT-------------------------GARPVSGLGDAFGELGNGALFKVSHIG 179 Query: 208 RKGQP--VVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNSGVPVNRVK 265 G P V G+P +V ++L + V+L++T G I+A G +AEAAR SGV V VK Sbjct: 180 ADGFPDTVFPGIPYPVVIMVILFVAVSVLLSRTSLGRHIYAVGSNAEAARLSGVNVQGVK 239 Query: 266 ILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGYGSVLGAAL 325 + ++ + A + A + G++ E +AI + VIGG L GG G++ G A+ Sbjct: 240 LFTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAI 299 Query: 326 GALIFGVVQQGLFFAGVESSLFRVFLGLILLFAV 359 GA + GV++ GL GV S + ++ +G+++L V Sbjct: 300 GAFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTV 333 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: 406 Number of extensions: 36 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: 373 Length of database: 343 Length adjustment: 29 Effective length of query: 344 Effective length of database: 314 Effective search space: 108016 Effective search space used: 108016 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