Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 124 bits (310), Expect = 5e-33 Identities = 81/259 (31%), Positives = 136/259 (52%), Gaps = 15/259 (5%) Query: 32 AVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKP 91 A+D S++I EGE + L+G SG GKS+L R + L PD G + +G D+ L + Sbjct: 17 ALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGTDLLALPAQ---- 72 Query: 92 YRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRK---RVEELLDMVGIGRE 148 R+ + ++FQ +L P MTV I L + + RR RVE+LL V + E Sbjct: 73 -RRDIGLVFQHY--ALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQL-EE 128 Query: 149 FINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGI 208 +P + SGGQ+QR+ +ARALA+ P ++ DEP ALD ++ + L ++Q+ +G+ Sbjct: 129 LGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSLGL 188 Query: 209 SYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQ 268 + + + H+ ++ +V VM G+I + G +I+ P P+ + +I + Sbjct: 189 TTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRANRIRGHVE 248 Query: 269 KQRF----YSLKGELPSPI 283 + R +S +GELP + Sbjct: 249 RDRLHLGGHSFQGELPGDL 267 Lambda K H 0.321 0.142 0.417 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: 275 Number of extensions: 16 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: 328 Length of database: 384 Length adjustment: 29 Effective length of query: 299 Effective length of database: 355 Effective search space: 106145 Effective search space used: 106145 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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