Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1 (characterized)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3040 (276 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 119 bits (297), Expect = 9e-32 Identities = 77/270 (28%), Positives = 142/270 (52%), Gaps = 14/270 (5%) Query: 19 WAIAILIFF-----PIFWMVLTSFKTEIDAFATPPQFIFMP---TLENYLHINERSDYFS 70 WAIA L PI W +LTS K D A P I+ P T+E+Y + +++ F Sbjct: 7 WAIAALALSLFSLAPILWQLLTSIKVNADIAAIPT--IYWPRQWTVEHYQALWQQTPAFG 64 Query: 71 -FAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTRGTLLWMLSTKMLPPVGVLMPIYL 129 + NS V+S AT LLI P AY++A + ++ + +L + P V + + Sbjct: 65 RYLLNSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLFQGLLE 124 Query: 130 LAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPRDILEAARLDGATLAQEMLRVL 189 + + + AL+V YT +NLP+V+ ++ ++F+ +P ++ EAA++DG +L Q + +L Sbjct: 125 VVRWLQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLWLIL 184 Query: 190 LPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLF---WAKLSA 246 +P+ L + +L+ I WNE +L+ S +A + + +F + ++A Sbjct: 185 VPLTAPALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGDIAA 244 Query: 247 VSTLACAPILIFGWISQKQLVRGLSFGAVK 276 + +A P++ ++Q++++ GL+ GAVK Sbjct: 245 ATVVATLPLIGLVLVAQRRILEGLTAGAVK 274 Lambda K H 0.328 0.138 0.427 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: 251 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 276 Length of database: 275 Length adjustment: 25 Effective length of query: 251 Effective length of database: 250 Effective search space: 62750 Effective search space used: 62750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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