Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate BWI76_RS07245 BWI76_RS07245 ABC transporter
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__Koxy:BWI76_RS07245 Length = 343 Score = 457 bits (1175), Expect = e-133 Identities = 226/321 (70%), Positives = 278/321 (86%) Query: 17 RRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQV 76 R RLP + IF+V++ I L FE+ GW VRDQSFL+N+ RL+L++LQV+IIG++A+GVTQV Sbjct: 22 RHRLPKDTGIFIVMLVIALTFEIAGWYVRDQSFLLNTNRLILIVLQVAIIGIIAVGVTQV 81 Query: 77 IITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAI 136 IITTGIDLSSGSV+AL+A++AASLAQTSD +FPSL ++P IP+ AG+GVGLL G Sbjct: 82 IITTGIDLSSGSVIALAAVVAASLAQTSDSLSPMFPSLVNMPAIIPIGAGIGVGLLCGLT 141 Query: 137 NGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVIIFLVVA 196 NG ++ TGIPPFIATLGMMVSARGLA+YYT+G P+S LSDS+TAIG GAMPVIIF VVA Sbjct: 142 NGFLVTRTGIPPFIATLGMMVSARGLAQYYTQGNPISFLSDSFTAIGQGAMPVIIFFVVA 201 Query: 197 VIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAA 256 +FHIAL++T+YGKY YAIGGNM +A+ SGINV ++LVIVY+IAG L+GLAGVV +AR + Sbjct: 202 AVFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLVIVYAIAGALSGLAGVVLAARVS 261 Query: 257 TGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQD 316 +GQ+ MGMSYELDAIAAAVIGG+SL GGVGRITGT+IGA+ILG++ SGFTFVGVDAY+QD Sbjct: 262 SGQSSMGMSYELDAIAAAVIGGSSLMGGVGRITGTLIGAMILGLIKSGFTFVGVDAYVQD 321 Query: 317 IIKGLIIVIAVVIDQYRNKRK 337 IIKG+IIV AV ID RN++K Sbjct: 322 IIKGIIIVAAVTIDMRRNRKK 342 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: 368 Number of extensions: 11 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: 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