Align Inositol transport system permease protein (characterized)
to candidate BPHYT_RS22740 BPHYT_RS22740 ABC transporter permease
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS22740 Length = 328 Score = 186 bits (472), Expect = 7e-52 Identities = 105/304 (34%), Positives = 175/304 (57%), Gaps = 19/304 (6%) Query: 41 GWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASL 100 G+ + S ++ Q L L++ Q ++ ++AIG T +++T GIDLS G V+A ++I Sbjct: 35 GFFISQSSRFLSFQNLSLILQQTMVVAVIAIGQTLIVLTGGIDLSCGMVMAFGSIIMTKF 94 Query: 101 AQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSAR 160 A T +P + + G+G L GA+NG +I +P FI TLG + A Sbjct: 95 AVT-----------LGVPPVLAILCGVGASALFGALNGVLITRIKLPAFIVTLGTLNIAF 143 Query: 161 GLARYYTEGQPVSMLSDSYTAIGH----GAMPVIIFLVVAVIFHIA----LRYTKYGKYT 212 L + Y+ + VS L D+ +G+ G V V+ ++ ++A LR T G++ Sbjct: 144 ALTQIYSNAESVSNLPDAIMFLGNTFKLGPADVTYGTVLTLLMYLATWFVLRDTVPGRHL 203 Query: 213 YAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIA 272 YA+G N +AAR G++ ++ L+ VYS+AG + G+A +++ +R G G + LD+I Sbjct: 204 YALGNNPEAARLMGLSSQKILLTVYSLAGAIYGIAALLSVSRTGVGDPQAGQTENLDSIT 263 Query: 273 AAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQY 332 A V+GGTSL GG G I+GT++GALI+GV +G T +GV + Q +I G+++++AV D+ Sbjct: 264 AVVLGGTSLFGGRGSISGTLLGALIVGVFRNGLTLIGVSSVYQVLITGMLVILAVAADKL 323 Query: 333 RNKR 336 ++R Sbjct: 324 SHRR 327 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: 211 Number of extensions: 10 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: 340 Length of database: 328 Length adjustment: 28 Effective length of query: 312 Effective length of database: 300 Effective search space: 93600 Effective search space used: 93600 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