Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 305 bits (782), Expect = 9e-88 Identities = 178/371 (47%), Positives = 231/371 (62%), Gaps = 43/371 (11%) Query: 1 MTALQLTNVCKSFGP-VEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGE 59 M ++ L V K++G V++D++L + + EF VF+GPSGCGKSTLLR+I+GLED T G+ Sbjct: 1 MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 ISIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASR 119 +SIGG+ + P A+RG+AMVFQSYAL+PH+SV ENMA LK + PK+E+ +V EA+R Sbjct: 61 LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120 Query: 120 MLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARL 179 +L LE L+R+P LSGGQRQRVAIGRA+VREP +FLFDEPLSNLDA LR TR+EIARL Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HRQLS-ASMIYVTHDQIEAMTLADKIVVL-------RDGRIEQVGTPMELYNNPANRFVA 231 H+Q + AS++YVTHDQIEAMTLADKIV+L R G I Q+G P+ELY+ P +RFVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240 Query: 232 EFIGAPAMNFVPAQ---------------------------RLGGNPGQFIGIRPEYARI 264 FIG+P MNF+P + L + +G+RPE+ Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300 Query: 265 ---SPVGP----LAGEVIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFD 317 S V P L V VE+LG + + +D A+ G GE Sbjct: 301 VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPGGAALVAKAPGNTRLAPGERASLRVP 360 Query: 318 PANCLSFDEAG 328 A C F E G Sbjct: 361 RAACHLFTEDG 371 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: 373 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: 384 Length adjustment: 29 Effective length of query: 302 Effective length of database: 355 Effective search space: 107210 Effective search space used: 107210 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