Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 191 bits (484), Expect = 3e-53 Identities = 110/300 (36%), Positives = 176/300 (58%), Gaps = 24/300 (8%) Query: 51 MNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAV 110 M LV ++ ++ G+LAI T VIIT+GIDLS G+++ A++A V Sbjct: 58 MEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAG-----------V 106 Query: 111 FPSLTDLPVWIPVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQ 170 + +P+ + + A + G L+G I+G +IA +PPFIATLGMM+ +GL+ + + Sbjct: 107 VLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTR 166 Query: 171 PVSML-SDSYTAIGHGAM------------PVIIFLVVAVIFHIALRYTKYGKYTYAIGG 217 P+ ++ ++AI ++ V+I +VA+ I L T +G+YT+A+G Sbjct: 167 PIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGS 226 Query: 218 NMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIG 277 N +A R SG+ V V VY+ +G + G+AG++ ++R + Q +G YELDAIAA VIG Sbjct: 227 NEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIG 286 Query: 278 GTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYRNKRK 337 GTSL+GG G I GT+IGA I+ V+ +G + V Q ++ G+II++AV +D R +R+ Sbjct: 287 GTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRRR 346 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: 242 Number of extensions: 11 Number of successful extensions: 4 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: 347 Length adjustment: 29 Effective length of query: 311 Effective length of database: 318 Effective search space: 98898 Effective search space used: 98898 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