Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SMc01626 SMc01626 ABC transporter permease
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__Smeli:SMc01626 Length = 285 Score = 139 bits (349), Expect = 9e-38 Identities = 91/263 (34%), Positives = 136/263 (51%), Gaps = 12/263 (4%) Query: 12 GVGIVLVLVA-VFPLLWALLNSVKTLLDIVTPTPRFLFTPTLENYRQVI--------GSP 62 GV + LV+V +FP++W L S +T I+ P +FTPTLENY +I G+ Sbjct: 13 GVALTLVVVFFMFPIVWIFLMSFQTNETILRIPPSVVFTPTLENYAALITGKLQTASGTL 72 Query: 63 EV--LVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAVA 120 ++ + L NS ++ ++V L +GVPAAY AR+ G DI F LLS RF PP+ V Sbjct: 73 DIAFMRNLGNSVLLSVASVALALVLGVPAAYAFARHKFRGSEDIAFTLLSFRFAPPLLVL 132 Query: 121 IPLIAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYAV 180 +PL + LGL +T F +I Y L L I W+ F+ + ++E A + G+ ++ Sbjct: 133 LPLTQYFQWLGLSNTYFGLIWIYQLICLPLILWIVRGYFEDISADVEYAYRIAGHSWFST 192 Query: 181 FWKIALPNCATTLLGGIIFSFVLVWNELMIALALTSSNSATLPVVASAFTSMGQEVPWGV 240 F KIALP + + +F+ WN + AL L S++ + V A AF + + +G Sbjct: 193 FRKIALPLAGPGIAAAGLLAFIFAWNNFVFALVLASADKQPVTVGALAFVT-ASGIQYGQ 251 Query: 241 INASTVLLALPPLIFVGVLSRLL 263 I A+ VL P L R L Sbjct: 252 IAAAIVLSITPTLALALYAQRYL 274 Lambda K H 0.327 0.142 0.434 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: 198 Number of extensions: 6 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: 270 Length of database: 285 Length adjustment: 25 Effective length of query: 245 Effective length of database: 260 Effective search space: 63700 Effective search space used: 63700 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: 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