Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate HSERO_RS18950 HSERO_RS18950 glycerol-3-phosphate transporter permease
Query= reanno::WCS417:GFF4323 (302 letters) >FitnessBrowser__HerbieS:HSERO_RS18950 Length = 294 Score = 136 bits (342), Expect = 7e-37 Identities = 83/289 (28%), Positives = 148/289 (51%), Gaps = 13/289 (4%) Query: 18 RWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTY-----KWAGLAQYARLFDND 72 +WLP L++AP + I L+ F+ W V + S L ++ + LF + Sbjct: 10 KWLPYLLVAPQIIITLLFFF----WPAVQALYQSMLLQDAFGGYSEFVWFDNFKTLFGDP 65 Query: 73 RWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAW 132 + + + A+F + L + + LA+F D+ R +T ++P A+S +V G W Sbjct: 66 TYLESFRTTAIFSALVAFFGLALSLLLAVFADRVRRGASIYKTFLIWPYAVSPVVVGVLW 125 Query: 133 KWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGV 192 +LL+P +G+ L W G D++I+ + +VIAA+W+ + FLAGL+ + Sbjct: 126 MFLLSPSLGI--LSHVLSWLGLPWDYMINGTHAMILIVIAAIWKQISYNFLFFLAGLQSI 183 Query: 193 DQSIVRAAQIDGASMPRIYWSVVLPSLRP-VFFSAVMILAHIAIKSFDLVAAMTAGGPGY 251 +S++ AA IDGA + ++++V P + P FF V+ + + +F +V A T GGPG Sbjct: 184 PKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGGPGK 243 Query: 252 SSDLPAMFMYSFTFSRGQMGMGSA-SAILMLGAILAIIVPYLYSELRTK 299 +++ ++S F G +G +A S +LM IL +V + Y E + + Sbjct: 244 DTEILVYKVFSDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQ 292 Lambda K H 0.330 0.141 0.455 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: 273 Number of extensions: 13 Number of successful extensions: 5 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: 294 Length adjustment: 26 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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