Align Inositol transport system sugar-binding protein (characterized)
to candidate WP_028312700.1 H566_RS0119115 ABC transporter
Query= reanno::WCS417:GFF2331 (309 letters) >NCBI__GCF_000482785.1:WP_028312700.1 Length = 312 Score = 146 bits (369), Expect = 5e-40 Identities = 108/316 (34%), Positives = 166/316 (52%), Gaps = 16/316 (5%) Query: 1 MKTPIRFTALALSMLLAS-GVASAADLK-IGVSMSAFDDTFLTYLREDMDKQAKSYPKGD 58 MK+ ALAL++ A+ G A +LK IG+++ + + + + + + +AK+ Sbjct: 1 MKSTRIVAALALALATAAAGSVQARELKSIGITVGSLGNPYFVTMAKGAEARAKAI--NP 58 Query: 59 GVQLQFEDARADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNR 118 GV++ A D+ KQ +Q++NFIS VD I++N D + +K A A I +V V+ Sbjct: 59 GVKVTAVSADYDLNKQFTQIDNFISAGVDLILLNAADPKAIEPAVKKAQKAGIAVVAVD- 117 Query: 119 RPDSQTLAPGV-AAVTSDDVEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVK 177 +A G A V +D+V AGKL +YI +KLG KG VI+ ++ +R G K Sbjct: 118 -----VVAAGADATVQTDNVAAGKLACKYIVDKLGAKGGNVIIQNGPQVSAVIDRVNGCK 172 Query: 178 EVLTKYPGIKI-EQEQTGIWLRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSA 236 L K P +K+ +Q G R+ GM + LT+ A+ + ND AIG +A K Sbjct: 173 AELAKAPSLKVLSDDQDGKGSREGGMNVAQGHLTRFPKVDAIFTINDPQAIGTDLAAKQL 232 Query: 237 GKKGVLIAGVDGTPDGLNAITKGDMTV--SAFQDAKGQADKSVETARKMAK-NEPIEQNV 293 G+KG++I VDG PD + KG+ V SA QD QA ++VE + +P E + Sbjct: 233 GRKGIVITSVDGAPD-IEVALKGNTQVEASASQDPWAQAQRAVEIGADLLNGKKPPETVI 291 Query: 294 VIPFQLITPDNVKDFK 309 + QLIT DNV +K Sbjct: 292 QLAPQLITRDNVAGYK 307 Lambda K H 0.314 0.131 0.357 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: 214 Number of extensions: 17 Number of successful extensions: 5 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: 309 Length of database: 312 Length adjustment: 27 Effective length of query: 282 Effective length of database: 285 Effective search space: 80370 Effective search space used: 80370 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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