Align Inositol transport system permease protein (characterized)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 224 bits (572), Expect = 2e-63 Identities = 135/304 (44%), Positives = 180/304 (59%), Gaps = 37/304 (12%) Query: 56 LVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLT 115 L+ + LQV+ I L + T VIIT GIDLS GSVLAL+ + AA L + Sbjct: 53 LMTVALQVTSIAYLGVAATCVIITGGIDLSVGSVLALAGVAAALLVKAG----------- 101 Query: 116 DLPVWIPVAM--GLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVS 173 V IPVAM G+ VG G +NG + G+PPFIATLGMM+ ARGLA T +PVS Sbjct: 102 ---VPIPVAMLGGMLVGAACGWVNGICVTRMGLPPFIATLGMMLVARGLALQITGARPVS 158 Query: 174 MLSDSYTAIGHGAM---------------------PVIIFLVVAVIFHIALRYTKYGKYT 212 L D++ +G+GA+ PV+I +V+ I L T G++ Sbjct: 159 GLGDAFGELGNGALFRISHIGADGFPDTVFPGIPYPVVIMVVLFAAVSILLSRTSLGRHI 218 Query: 213 YAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIA 272 YA+G N +AAR SG+NV+ + Y ++GLLAG G V +R T Q G+ YELDAIA Sbjct: 219 YAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIA 278 Query: 273 AAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQY 332 +AVIGGTSL GGVG I+GT IGA ++GV+ +G GV ++IQ II G++I+ V IDQ Sbjct: 279 SAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQL 338 Query: 333 RNKR 336 RN++ Sbjct: 339 RNRK 342 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: 254 Number of extensions: 8 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: 343 Length adjustment: 29 Effective length of query: 311 Effective length of database: 314 Effective search space: 97654 Effective search space used: 97654 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