Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 342 bits (877), Expect = 8e-99 Identities = 185/358 (51%), Positives = 232/358 (64%), Gaps = 27/358 (7%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M + L V KSFG +EV+ ++L V DGEFV FVGPSGCGKSTLLR+I+GLE+ + G++ Sbjct: 1 MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 SIGGQ V PPA RGIAMVFQSYALYPH++ +NMA L R K IA RV A+R+ Sbjct: 61 SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L +ED LDR+P +LSGGQRQRVAIGRA+VREP++FLFDEPLSNLDA LR+ RLEIA+L Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 L A+MIYVTHDQ+EAMTLAD+IVVL GR+EQ GTP+ELY+ P NRFVA FIG+PAMN Sbjct: 181 ADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMN 240 Query: 241 FVPAQRLGGNPGQF--------------------------IGIRPEYARISPVGP-LAGE 273 F+ G G +G+RPE+ ++ G L Sbjct: 241 FLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLADGGAGLLAT 300 Query: 274 VIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI 331 ++ VE+LGG+T+ + + RL G GE L+ + F GQR+ Sbjct: 301 ILAVERLGGETHCHAALEDGQRLLVRLDGDRPVAAGERLRLNLRGETAHLFGPDGQRL 358 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: 409 Number of extensions: 12 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: 358 Length adjustment: 29 Effective length of query: 302 Effective length of database: 329 Effective search space: 99358 Effective search space used: 99358 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