Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate GFF1858 Psest_1897 ABC-type sugar transport systems, permease components
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__psRCH2:GFF1858 Length = 305 Score = 533 bits (1374), Expect = e-156 Identities = 260/304 (85%), Positives = 284/304 (93%), Gaps = 3/304 (0%) Query: 1 MSSVAVFS---KASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSY 57 MSS+A+ + KASP DALQRWLPKLVLAPSMLIVLVGFY YI WTF+LSFTNS FMPSY Sbjct: 1 MSSIALQARPAKASPLDALQRWLPKLVLAPSMLIVLVGFYAYIGWTFLLSFTNSRFMPSY 60 Query: 58 KWVGLQQYMRLMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVY 117 KWVGLQQY RL DNDRWWVAS+NL +FGG+FI++SL++GV LAVLLDQRIR+EG IRT+Y Sbjct: 61 KWVGLQQYERLWDNDRWWVASQNLLVFGGLFIAVSLIIGVVLAVLLDQRIRREGLIRTIY 120 Query: 118 LYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQA 177 LYPMALSMIVTGTAW+WLLNPGLGLDK+LRDWGWEGFR DWLVD DRV+YCLVIAAVWQA Sbjct: 121 LYPMALSMIVTGTAWQWLLNPGLGLDKLLRDWGWEGFRFDWLVDPDRVIYCLVIAAVWQA 180 Query: 178 SGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKS 237 SGFVMA+FLAGLR VDQSIIRAAQVDGASLPTIYL+IVLPSLRPVFFSA MILAHIAIKS Sbjct: 181 SGFVMALFLAGLRSVDQSIIRAAQVDGASLPTIYLRIVLPSLRPVFFSALMILAHIAIKS 240 Query: 238 FDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELR 297 FDLVAAMTAGGPGYSSDLPAMFMY+ TF+RGQMG+G+ASAMLMLGAV+ I+VPYLYSELR Sbjct: 241 FDLVAAMTAGGPGYSSDLPAMFMYAHTFTRGQMGLGAASAMLMLGAVMAIIVPYLYSELR 300 Query: 298 GKRH 301 KRH Sbjct: 301 NKRH 304 Lambda K H 0.329 0.141 0.448 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: 476 Number of extensions: 6 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: 302 Length of database: 305 Length adjustment: 27 Effective length of query: 275 Effective length of database: 278 Effective search space: 76450 Effective search space used: 76450 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: 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