Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS01810 Length = 319 Score = 187 bits (474), Expect = 4e-52 Identities = 121/326 (37%), Positives = 188/326 (57%), Gaps = 38/326 (11%) Query: 17 RRRLPTELSIFLVLIGIGLV-FEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQ 75 ++ LP L++ L+ GLV +E FG SF + S+ L+++G+ Sbjct: 2 KKNLPILLAL-AALVVFGLVRYEHFGSAYNITSFWRYN----------SMFALISVGMAF 50 Query: 76 VIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGA 135 VIIT GIDLS G+V AL++++AA TS + W+ V+AG G GL G Sbjct: 51 VIITGGIDLSVGTVAALASVVAAL---TSVYGG-----------WVAVLAGCGAGLAVGV 96 Query: 136 INGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDS-YTAIGHGAM-----PV 189 +NG II I PFI TL + A G+A + VS+ ++S + G G + P Sbjct: 97 LNGLIITRLKILPFIVTLATSLGAHGVALLLGKNDAVSIAAESNFGNFGQGDLFGLPIPG 156 Query: 190 IIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGV 249 I+ +V AV +ALR T++G+++ AIGG+ +AAR G+NV R LV+ Y+++GLLAG+AGV Sbjct: 157 IVAVVAAVAGWLALRSTRFGRHSLAIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGV 216 Query: 250 VASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVM------AS 303 + +A+ GQ G+ +EL AI+A V+GGT L GG G I T+ G L+LG++ + Sbjct: 217 ILAAQFGAGQPNEGVGWELFAISAVVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFEN 276 Query: 304 GFTFVGVDAYIQDIIKGLIIVIAVVI 329 G F+ + AY Q +I+G+ +++ +V+ Sbjct: 277 GLGFISLSAYWQSVIRGVFLLLVIVL 302 Lambda K H 0.326 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: 244 Number of extensions: 13 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: 319 Length adjustment: 28 Effective length of query: 312 Effective length of database: 291 Effective search space: 90792 Effective search space used: 90792 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