Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 218 bits (556), Expect = 2e-61 Identities = 128/301 (42%), Positives = 176/301 (58%), Gaps = 21/301 (6%) Query: 19 SLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQI 78 SL ++ + + +G+ L LD+ +GEFV +GPSG GKS+LLR +AGL+D G V Sbjct: 2 SLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLR 61 Query: 79 DGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLK---QAGVP-KAEIEEKVAKAA 134 DG ++ + +R I +VFQ YAL+PH+TV DN+ GL+ +A P + +I +V Sbjct: 62 DGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLL 121 Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194 + LE R P +LSGGQRQRVA+ RA+ EP L L DEP LDA +R R+ + Sbjct: 122 RRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRD 181 Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQ 254 L RSL T + VTHDQ EA+ LAD++VV+N GRIEQVG+P E+Y PA FV GF+G Sbjct: 182 LQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRAN 241 Query: 255 --MNFIEAAKL------------GD--GEAKTIGIRPEHIGL-SRESGDWKGKVIHVEHL 297 +E +L GD G +RPEH+ L SR G W G++ H++ Sbjct: 242 RIRGHVERDRLHLGGHSFQGELPGDLAGREIEAWLRPEHLALASRGLGGWTGRLQHLDLA 301 Query: 298 G 298 G Sbjct: 302 G 302 Lambda K H 0.320 0.137 0.393 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: 356 Number of extensions: 16 Number of successful extensions: 2 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: 352 Length of database: 384 Length adjustment: 30 Effective length of query: 322 Effective length of database: 354 Effective search space: 113988 Effective search space used: 113988 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