Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 162 bits (411), Expect = 8e-45 Identities = 105/331 (31%), Positives = 178/331 (53%), Gaps = 20/331 (6%) Query: 1 MTALQLTNVCKSFGPVEV-LKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGE 59 M+ L+++ V K + + L+D +L V+ G V VG SG GKS+LLR+I+GLE +AG Sbjct: 1 MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60 Query: 60 ISIGGQTVTTTP----PAKRGIAMVFQSYALYPHLSVRENMA--LALKQERQPKEEIAAR 113 + +G Q + P I ++ Q Y LYP+ +V EN+A L L + KE R Sbjct: 61 VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQKE----R 116 Query: 114 VAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTR 173 AE +LSL + D++P +LSGGQ+Q+VAIGRA+ EP++ L DEP S+LDA + + Sbjct: 117 TAEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLI 176 Query: 174 LEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEF 233 E+ + L ++I+VTHD +A+ +++++++++ G++ Q G E++ PA+ +VA Sbjct: 177 EELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARL 236 Query: 234 IGAPAMNFVPAQRLGGNPGQFIGIRPEYARISPVGPLAGEVIHVEKLGGDTNILVDMGED 293 G +N +P + +RP +I+ + EV+ + L + V + + Sbjct: 237 FG--YLNLIPG-------AEEAYVRPSEVKITSKTSIKAEVVKQQFLIHYNLLTVKLEDS 287 Query: 294 LTFTARLFGQHDTNVGETLQFDFDPANCLSF 324 F NVG+ + D+ + F Sbjct: 288 ELFWKVDDPSRSVNVGDEVFLDYQKEQLIQF 318 Lambda K H 0.320 0.137 0.391 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: 239 Number of extensions: 13 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: 331 Length of database: 318 Length adjustment: 28 Effective length of query: 303 Effective length of database: 290 Effective search space: 87870 Effective search space used: 87870 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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