Align Inositol transport system permease protein (characterized)
to candidate Pf6N2E2_1457 Xylose ABC transporter, permease protein XylH
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1457 Length = 378 Score = 144 bits (363), Expect = 4e-39 Identities = 110/371 (29%), Positives = 180/371 (48%), Gaps = 63/371 (16%) Query: 18 RRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVI 77 ++L + + ++I + L++ F W + + + + L ++ Q+SI G+LA G+ VI Sbjct: 5 KQLFSRYKMLALVIAVALIWLFFSW--QTEGGFVTPRNLSNLLRQMSITGILACGMVLVI 62 Query: 78 ITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAG--- 134 I+ IDLS GS+L L +AA L SL L + +GLG G + Sbjct: 63 ISGEIDLSVGSLLGLLGGLAAILDVVYHIPLLANLSLVAL---CGLVIGLGNGYMTAYLR 119 Query: 135 ------------AINGSIIAVTG------------------IPPFIAT-LGMMVSARGLA 163 A G ++ VTG +P + T LG+++ A L Sbjct: 120 IPSFIVGLGGMLAFRGVLLGVTGGTTIAPVSPELVYVGQGYLPHTVGTGLGILLFALTLF 179 Query: 164 RYYTEGQ--------PVSMLSDSYTAIGHGAM----------------PVIIFLVVAVIF 199 + + + S++ D + GA+ PV++ L++ +F Sbjct: 180 LTWKQRRNRALHGLAAHSLVRDVLRVVVIGAVLAGFVYTLNSYDGIPVPVLLLLILLGVF 239 Query: 200 HIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQ 259 T +G+ Y++G NM+A R SGINV+ + ++ I G++ LAGVV +AR A G Sbjct: 240 SYVTSQTVFGRRVYSVGSNMEATRLSGINVQAVKLWIFGIMGVMCALAGVVNTARLAAGS 299 Query: 260 AGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIK 319 G ELDAIAA IGGTS+ GG G + G ++GAL++ + +G + + VD+Y Q I+K Sbjct: 300 PSAGNMGELDAIAACFIGGTSMRGGSGTVYGALLGALVITSLDNGMSMLDVDSYWQMIVK 359 Query: 320 GLIIVVAVVID 330 G I+V+AV +D Sbjct: 360 GSILVLAVWVD 370 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: 301 Number of extensions: 13 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: 340 Length of database: 378 Length adjustment: 29 Effective length of query: 311 Effective length of database: 349 Effective search space: 108539 Effective search space used: 108539 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