Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 320 bits (820), Expect = 4e-92 Identities = 183/365 (50%), Positives = 237/365 (64%), Gaps = 37/365 (10%) Query: 1 MTALQLTNVCKSFGPVE-VLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGE 59 M ++ L K++G V+++++L + + EF VF+GPSGCGKSTLLR I+GLED T+G+ Sbjct: 1 MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60 Query: 60 ISIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASR 119 + IGG+ V P A+R +AMVFQSYAL+PH++V ENM+ L + PK EI +V EA+R Sbjct: 61 LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120 Query: 120 MLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARL 179 +L LE+ L R+P ELSGGQRQRVAIGRA+VR P +FLFDEPLSNLDA LR TR+EIARL Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180 Query: 180 HRQL-SASMIYVTHDQIEAMTLADKIVVL-------RDGRIEQVGTPMELYNNPANRFVA 231 HRQ AS++YVTHDQ+EAMTLAD+IV+L R G I QVGTPMELY++P NRFVA Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240 Query: 232 EFIGAPAMNFVPAQ-----------RLGGN-------------PGQF--IGIRPEYARIS 265 FIG+P MNF+PAQ RL G+ PGQ +G+RPE+ I Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300 Query: 266 PVGP--LAGEVIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLS 323 G + EV+ VE+LG T + +D A+ G GE ++ PA Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDEPAGQPLVAKAAGDARITRGERVRVAIAPACAYL 360 Query: 324 FDEAG 328 FD+ G Sbjct: 361 FDQDG 365 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: 375 Number of extensions: 14 Number of successful extensions: 4 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: 381 Length adjustment: 29 Effective length of query: 302 Effective length of database: 352 Effective search space: 106304 Effective search space used: 106304 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