Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AZOBR_RS25585 AZOBR_RS25585 ABC transporter permease
Query= uniprot:D8IPH8 (292 letters) >FitnessBrowser__azobra:AZOBR_RS25585 Length = 301 Score = 110 bits (275), Expect = 4e-29 Identities = 88/287 (30%), Positives = 149/287 (51%), Gaps = 14/287 (4%) Query: 4 RGKTSLPYLFLGPSLLVMLVLGLVPTVAAINLALKNRVLRYPDS-DYVWLRNLERLMSDR 62 R + +LFL P L+V+ + P + + + L + V L N LM D Sbjct: 12 RQRRRAAWLFLLPMLIVLAGVAGWPLFRTVFFSFTDATLATLEGFQGVGLDNYLWLMRDP 71 Query: 63 RFLNAIEVSAVWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSAAF 122 + A+ + V+ VV+V +G+ IA+ L N H R + ++ P +P V +A Sbjct: 72 VWWRAVWNTLVFTVVSVGIETALGLGIALIL--NAHLPGRGLLRAAVLIPWAIPTVVSAQ 129 Query: 123 IWKFMYSPLTGILGWLLGLVGI--HDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLL 180 +W +M+ L G++ +L +G+ A+ +DP LAL V VD+W+ F A+++L L Sbjct: 130 MWGWMFHDLYGVVNAILMGLGLIAEPRAWTADPDLALPVVIAVDVWKSTPFMALLILAAL 189 Query: 181 ETLPPEPLEAARLDYARTWQVYAYIALPMLKGPLISLVFIKMVESLRSFDLIYVMTKGGP 240 + LP + EAAR+D +V+ I LP+++ L+ V + +++LR FDL+YV+T Sbjct: 190 QMLPRDLYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDALRVFDLMYVLT---- 245 Query: 241 GVATETLDMYAYAQGIGLS----GKVSYASTMAVLMM-IATTLIFTL 282 G + T+ M YA+ + G S A+T+ VL++ +AT L TL Sbjct: 246 GNSRSTMSMSVYARQYLIDFQDVGYGSAAATLLVLVLAVATVLAVTL 292 Lambda K H 0.328 0.141 0.439 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: 252 Number of extensions: 12 Number of successful extensions: 1 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: 292 Length of database: 301 Length adjustment: 26 Effective length of query: 266 Effective length of database: 275 Effective search space: 73150 Effective search space used: 73150 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 (21.7 bits) S2: 48 (23.1 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