Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 160 bits (405), Expect = 3e-44 Identities = 96/271 (35%), Positives = 152/271 (56%), Gaps = 9/271 (3%) Query: 15 SALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFI 74 +AL L++ LAP+ W L+ SI AD++A P +WP + Y+ L AF Sbjct: 10 AALALSLFSLAPILWQLLTSIKVNADIAAIPTIYWPRQWTVEHYQALWQQTP-----AFG 64 Query: 75 ASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWSLY--AVIATYMLPPVALAVPLYM 132 LLNS V+ +ATLAA+++ P A+A++R + + +++ + P V L L Sbjct: 65 RYLLNSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLFQGLLE 124 Query: 133 GLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILT 192 + + N+ L + Y + P LL+S F+ +P E+E AA IDG L Q L ++ Sbjct: 125 VVRWLQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLWLIL 184 Query: 193 LPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSD--YGLIAT 250 +PL AP + T+ + AF+ +W+E+ AL F S Q KT+ +A+A++ G + D YG IA Sbjct: 185 VPLTAPALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGDIAA 244 Query: 251 AGVLAALPPVLIGLIMQRALISGLTSGGVKG 281 A V+A LP + + L+ QR ++ GLT+G VKG Sbjct: 245 ATVVATLPLIGLVLVAQRRILEGLTAGAVKG 275 Lambda K H 0.325 0.136 0.402 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: 210 Number of extensions: 12 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: 281 Length of database: 275 Length adjustment: 25 Effective length of query: 256 Effective length of database: 250 Effective search space: 64000 Effective search space used: 64000 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 (21.7 bits) S2: 47 (22.7 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