Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 123 bits (308), Expect = 6e-33 Identities = 78/273 (28%), Positives = 139/273 (50%), Gaps = 3/273 (1%) Query: 18 RWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSF--MPSYKWVGLQQYMRLMDNDRWW 75 R P L LAP++ I+ + + + F SFT + S +WVGL+ + RL+++ +W Sbjct: 7 RLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFW 66 Query: 76 VASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWL 135 N ++ + + + L + LA+L+++ +R R Y P+ +S++V G AW+WL Sbjct: 67 KTLGNTFIYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAGIAWRWL 126 Query: 136 LNPGLGLDKMLRDWGWEGFR-LDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQ 194 L+++ + EGF+ + WL ++ ++ VW+ G+ M ++LAGL+G+ Sbjct: 127 YAETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAGLQGIPL 186 Query: 195 SIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSD 254 + AA +DG+ +L I LP +RP +I A A K F+ V MT GGP SS Sbjct: 187 ELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIMTQGGPLNSSK 246 Query: 255 LPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTI 287 ++Y F + ++ + + VLT+ Sbjct: 247 TVVYYVYQQAFQKLEVSYACTVGLALFLVVLTL 279 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: 284 Number of extensions: 25 Number of successful extensions: 4 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: 293 Length adjustment: 26 Effective length of query: 276 Effective length of database: 267 Effective search space: 73692 Effective search space used: 73692 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