Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 157 bits (397), Expect = 4e-43 Identities = 109/362 (30%), Positives = 188/362 (51%), Gaps = 49/362 (13%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+ L++ V+K Y AG L++ L +K G + +VG SG GKS+L+ IAGLE + G Sbjct: 1 MSYLKVSEVSKRYDAGSL-ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAG 59 Query: 61 AIMIGDQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEV 116 + +GDQ + + P +I ++ Q Y LYP +V ENI L + +A Sbjct: 60 VVHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLL--YDKAYQKERT 117 Query: 117 ARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 A + +LL + ++KP QLSGGQQQ+VA+GRAL+ P++ L DEP S+LDA + ++ Sbjct: 118 AEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIE 177 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFI 236 E+K + L+ T ++VTHD +A+ + +++ +++ G + Q G +E++ PA+ +VA Sbjct: 178 ELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237 Query: 237 GSPPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAG 296 G +N +P G E+ V RP ++ + Sbjct: 238 GY--LNLIP------------------------------GAEEAYV----RPSEVKIT-- 259 Query: 297 EGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRL-APDVAPQVGETLTLQFDPSKVL 355 S +SI+AEV + L+ V+L D+++ ++ P + VG+ + L + +++ Sbjct: 260 ---SKTSIKAEVVKQQFLIHYNLLTVKLEDSELFWKVDDPSRSVNVGDEVFLDYQKEQLI 316 Query: 356 LF 357 F Sbjct: 317 QF 318 Lambda K H 0.318 0.135 0.382 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: 9 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: 386 Length of database: 318 Length adjustment: 29 Effective length of query: 357 Effective length of database: 289 Effective search space: 103173 Effective search space used: 103173 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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