Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 226 bits (575), Expect = 1e-63 Identities = 128/310 (41%), Positives = 183/310 (59%), Gaps = 10/310 (3%) Query: 4 LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63 L + + K++G + G+D+ + G F LLG+SGCGK+T L +I+GL P+ G I +G Sbjct: 19 LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78 Query: 64 ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123 ++ V P R + VFQ+YAL+P+L + N+ FGL R + + K V D L+++ Sbjct: 79 DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRSVK--KPVEDMLDLVEL 136 Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 +L RKP+QLSGGQ+QR+A+ RAL+ PQV L DEPL LD KLR +M+ ELKR+ + Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196 Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243 T V+VTHDQ EAMT+A IAVM GRIEQL +P E+Y+ P T +VA F+G + Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGT 256 Query: 244 AE-MTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLA-----AGSEAQRLT 297 E ++ + +++ L LPAA V +G+RPE +R+A S A LT Sbjct: 257 VESVSGDVVQVAAHGRSLALPAA--RCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLT 314 Query: 298 ASVEVVELTG 307 V G Sbjct: 315 GKVTDASFIG 324 Lambda K H 0.320 0.136 0.385 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: 316 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: 360 Length of database: 386 Length adjustment: 30 Effective length of query: 330 Effective length of database: 356 Effective search space: 117480 Effective search space used: 117480 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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