Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 223 bits (567), Expect = 7e-63 Identities = 123/314 (39%), Positives = 188/314 (59%), Gaps = 18/314 (5%) Query: 36 KLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGT 95 K + +L+++ L S S F+ + N ++++ +VN +++ T VI+T+GIDLSVG+ Sbjct: 6 KFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGS 65 Query: 96 MMTFCAVMAGVVLTNW----GMPLPLGIAA------AIFFGALSGWISGMVIAKLKVPPF 145 ++ C + ++ N G+ L +G A + G GW +G I + KVPPF Sbjct: 66 ILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPF 125 Query: 146 IATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVA 205 +ATL M+ + +GL+++ +G PI E F+ + +G IP V I ++ Sbjct: 126 VATLAMLTIARGLTMLWTGGFPIN-GLGEDFAFLGTGWFLG-------IPMPVWITAVIV 177 Query: 206 IGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLN 265 A ++ KT FGRY +A+G NE A RLSG+ + K+ VY +G + + G+I+ SRL+ Sbjct: 178 ALAVLLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLD 237 Query: 266 SAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQT 325 SAQP G YELDAIAAVVIGGTSLSGG GTI+G ++G I+ VL NGL +++V+ WQ Sbjct: 238 SAQPNAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQ 297 Query: 326 VVTGVIIILAVYLD 339 VV G +I+LAV +D Sbjct: 298 VVKGAVILLAVVID 311 Lambda K H 0.326 0.139 0.398 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: 250 Number of extensions: 14 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: 347 Length of database: 318 Length adjustment: 28 Effective length of query: 319 Effective length of database: 290 Effective search space: 92510 Effective search space used: 92510 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: 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