Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Koxy:BWI76_RS06690 Length = 369 Score = 323 bits (827), Expect = 5e-93 Identities = 176/361 (48%), Positives = 224/361 (62%), Gaps = 32/361 (8%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M+ ++L NV K FG L +NL +EDGEF VFVGPSGCGKSTLLR+I+GLE+ + GE+ Sbjct: 1 MSNIRLRNVTKRFGSTVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEV 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 IG + + PA RG+AMVFQSYALYPH++V ENM LK + PK+EI +V ++ Sbjct: 61 LIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKT 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L L LDR+P +LSGGQRQRVAIGRA+VR P++F+FDEPLSNLDA LR+ RL IA+LH Sbjct: 121 LQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 +L +M+YVTHDQ+EAMTLADKIVV+ G++EQ+G+PM LY NP N+FVA FIG+P MN Sbjct: 181 HELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMN 240 Query: 241 FVPAQRLGGNPGQF--------------------------IGIRPEY----ARISPVGPL 270 F+PA PGQ +GIRPE+ I V Sbjct: 241 FLPATVTAWQPGQLSVKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHLSTDVNIGTVVEF 300 Query: 271 AGEVIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQR 330 EV VE+LG +T + L G + + FD C+ FDE R Sbjct: 301 QCEV--VERLGNNTYLFGQCYGHDNVKILLPGDVHFRPWQKISVAFDDRYCMVFDENDLR 358 Query: 331 I 331 I Sbjct: 359 I 359 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: 363 Number of extensions: 16 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: 331 Length of database: 369 Length adjustment: 29 Effective length of query: 302 Effective length of database: 340 Effective search space: 102680 Effective search space used: 102680 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: 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