Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 213 bits (541), Expect = 7e-60 Identities = 134/333 (40%), Positives = 194/333 (58%), Gaps = 34/333 (10%) Query: 13 PAKSRRR------LPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSII 66 PA S RR L + S+ +L+ I +V M F +N+ L ++ Q S+ Sbjct: 4 PAVSGRRYFTKAWLMEQKSLIALLVLIAIVSTM-----SPNFFTVNN--LFNILQQTSVN 56 Query: 67 GLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAG 126 ++A+G+T VI+T+GIDLS GS+LAL+ +AAS+ ++ + V A Sbjct: 57 AIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGI------------EVNALVAVAAA 104 Query: 127 LGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSM----LSDSYTAI 182 L +G GA+ G I+A + FIATL MM+ RG+ YT G PV+ +D + Sbjct: 105 LALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWF 164 Query: 183 GHGA-----MPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVY 237 G G PV I +V + L +T+ G+Y YA+GGN A R SGI+V + +IVY Sbjct: 165 GIGRPLGIPTPVWIMAIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVY 224 Query: 238 SIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALI 297 S+ G+LA LAG++ AR ++ Q G YELDAIAA V+GGTSLAGG GRI GT+IGALI Sbjct: 225 SLCGMLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALI 284 Query: 298 LGVMASGFTFVGVDAYIQDIIKGLIIVIAVVID 330 LG + +G +GV +Y Q I+K ++I++AV++D Sbjct: 285 LGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317 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: 258 Number of extensions: 8 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: 321 Length adjustment: 28 Effective length of query: 312 Effective length of database: 293 Effective search space: 91416 Effective search space used: 91416 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 Apr 09 2024. 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