Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Koxy:BWI76_RS01840 Length = 369 Score = 323 bits (828), Expect = 4e-93 Identities = 183/359 (50%), Positives = 230/359 (64%), Gaps = 33/359 (9%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M ++QL NV K++G V V KDINL ++DGEFVVFVGPSGCGKSTLLR+I+GLE T+G++ Sbjct: 1 MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSGDL 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 IG + PPA+RGI MVFQSYALYPHLSV ENM+ LK KE I RV + + + Sbjct: 61 LIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVAEV 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L L L+R+P LSGGQRQRVAIGR +V EP++FL DEPLSNLDAALR+ R+EI+RLH Sbjct: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 ++L +MIYVTHDQ+EAMTLADKIVVL GR+ QVG P+ELY+ PA+RFVA FIG+P MN Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 Query: 241 FVPAQ--------------------------RLGGNPGQFIGIRPEYARISPVGP--LAG 272 F+P + R+ +GIRPE+ S + L G Sbjct: 241 FLPVKVTATAIEQVQVELPNRQQVWLPVDSARVQVGANMSLGIRPEHLLPSDIADVTLEG 300 Query: 273 EVIHVEKLGGDTNILVDMGEDLTFTARLFGQHD---TNVGETLQFDFDPANCLSFDEAG 328 EV VE+LG +T I + + ++ Q+D G T P C F E G Sbjct: 301 EVQVVEQLGHETQIHIQIPS--IRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDG 357 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: 358 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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