Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate WP_004129777.1 RHSP_RS32465 ribose ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >NCBI__GCF_000359745.1:WP_004129777.1 Length = 320 Score = 251 bits (640), Expect = 2e-71 Identities = 151/338 (44%), Positives = 202/338 (59%), Gaps = 24/338 (7%) Query: 1 MNAILENKPAMAPAKSRRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMI 60 MN I KP A R + SI LV L+ F + + M + ++ Sbjct: 1 MNTIAAAKPGNFRAGEMIR---QFSIVLVFF---LIVAFFAFA---NQYFMTWLNWLNLV 51 Query: 61 LQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW 120 Q SI G+LAIGVT VI+T GIDLS GSV+AL+ MIAASL ++ +F Sbjct: 52 RQSSINGILAIGVTFVILTKGIDLSVGSVMALAGMIAASLVTETNEQFVLFG-------- 103 Query: 121 IPVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT 180 + AGL G G +NG ++A +PPF+ TLGM+ ARGL ++EG+P+ LSD + Sbjct: 104 --IFAGLAAGAGLGLVNGVLVAAVKVPPFVVTLGMLSVARGLTLIFSEGRPIPNLSDPFK 161 Query: 181 AIGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVI 235 IG G + P++I VV +I L YT +G+Y YA+GGN +AARTSGI+ K + Sbjct: 162 WIGSGQIMYIPVPIVILFVVFLIGWTVLNYTTFGRYVYAVGGNEKAARTSGISTKVIVGA 221 Query: 236 VYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295 Y I+GLLAGLAG+V +AR G+ YELDAIAA VIGGTSLAGG G + GT+IGA Sbjct: 222 TYVISGLLAGLAGLVLTARTTAALPQAGIGYELDAIAAVVIGGTSLAGGRGSLLGTLIGA 281 Query: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYR 333 LI+G + +G +GV +Y Q ++KG IIV+AV+ DQ R Sbjct: 282 LIIGTINNGMDLMGVSSYYQQVLKGTIIVVAVIADQIR 319 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: 293 Number of extensions: 17 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: 320 Length adjustment: 28 Effective length of query: 312 Effective length of database: 292 Effective search space: 91104 Effective search space used: 91104 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 24 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