Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate YP_425185.1 Rru_A0093 binding-protein dependent transport system inner membrane protein
Query= reanno::WCS417:GFF4323 (302 letters) >NCBI__GCF_000013085.1:YP_425185.1 Length = 289 Score = 382 bits (980), Expect = e-111 Identities = 177/286 (61%), Positives = 225/286 (78%) Query: 16 LQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWW 75 L R +PKLV+APS L+ YG+I WT +SFT S LP Y+ G+ QYARLF N RW Sbjct: 4 LDRLIPKLVIAPSFAAALLFVYGFIGWTVYISFTKSGILPRYELDGVGQYARLFANPRWD 63 Query: 76 VASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWL 135 VA NL VFGG+FI + LVIG+ LAI +DQKIR EG +RTIYLYPMA+S IVTGTAWKW+ Sbjct: 64 VAVSNLFVFGGLFIALCLVIGILLAILIDQKIRAEGVLRTIYLYPMAVSFIVTGTAWKWI 123 Query: 136 LNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQS 195 LNPG+GLDK++ GWEGF DWLI+P+R +Y +VIA VWQ+SGF+MA+FLAGLR DQ Sbjct: 124 LNPGLGLDKVMHGLGWEGFSFDWLINPERAIYTVVIAGVWQSSGFVMALFLAGLRSFDQE 183 Query: 196 IVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDL 255 +++AA IDGA MP +Y+ ++LPSL VF SAV++LAH+A+KSFDLV A+T GGPGY++D+ Sbjct: 184 VIKAATIDGAGMPTVYFRIILPSLHAVFLSAVVVLAHLAVKSFDLVVALTGGGPGYATDM 243 Query: 256 PAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKRN 301 PA FMY+ F R Q+G +ASA++ML ++AIIVPYLYSELR +R+ Sbjct: 244 PATFMYAMAFQRSQLGTAAASAVMMLMTVMAIIVPYLYSELRERRS 289 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: 354 Number of extensions: 9 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: 289 Length adjustment: 26 Effective length of query: 276 Effective length of database: 263 Effective search space: 72588 Effective search space used: 72588 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 24 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