Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 205 bits (522), Expect = 1e-57 Identities = 125/345 (36%), Positives = 193/345 (55%), Gaps = 27/345 (7%) Query: 5 LENKPAMAPAKSRRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVS 64 L NK + ++R PT L L + L+ F + M ++ ++ + Sbjct: 10 LGNKKTFSGLRARVFTPTALQKLLAFGSLILLLVFFSFA---SPAFMQMDNMLGILQATA 66 Query: 65 IIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVI 124 + G+LAI T VIIT GIDLS G+++ +A+I VF + LP+W V+ Sbjct: 67 VNGVLAIACTFVIITGGIDLSVGTLMTFTAVICG-----------VFLTYWHLPMWTGVL 115 Query: 125 AGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLAR--------YYTEGQPVSMLS 176 A +G G + G ++G++ A IPPFIATLGMM+ +GL+ Y+T+ + M+S Sbjct: 116 AAIGTGAICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMIS 175 Query: 177 -DSYTAIGHGAMPV----IIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKR 231 DS ++PV +I +AV+ I L T G+YT+A+G N +A R SG+NV R Sbjct: 176 QDSLIGDLLPSLPVPNAVLILFFLAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDR 235 Query: 232 HLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGT 291 + +Y ++G + G+AG++ ++R + Q +G YEL+AIAA VIGGTSL+GG G I GT Sbjct: 236 WKIAIYGLSGAICGIAGLLIASRLNSAQPALGQGYELEAIAAVVIGGTSLSGGAGTILGT 295 Query: 292 VIGALILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYRNKR 336 +IGA I+ V+ +G + V Q ++ GLII++AV D R K+ Sbjct: 296 IIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYGDILRRKK 340 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: 239 Number of extensions: 11 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: 341 Length adjustment: 28 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 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