Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 244 bits (623), Expect = 3e-69 Identities = 142/331 (42%), Positives = 196/331 (59%), Gaps = 14/331 (4%) Query: 4 LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63 + I + YG LK I + ++ GEF LG SGCGK+TLL +IAG G + IG Sbjct: 19 VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78 Query: 64 ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123 R + G+ RD+ MVFQSYAL+P+++V RN+ FGLE RRVP+AE ++ V L+ + Sbjct: 79 GRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGL 138 Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 ++L DR+PSQLSGGQ+QRVA+ R +V P+V L DEPLSNLDAKLR++MR EL L + L Sbjct: 139 KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKL 198 Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243 T ++VTHDQ EA T+ RIAVM DG ++Q+ P E+YD PA L+VAGF+G+ N+L+ Sbjct: 199 GLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANVLE 256 Query: 244 AEMTA---NGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQ-----R 295 ++ A + G +PLP A AG K+ RP+ L + R Sbjct: 257 GQVRAVDGGTAFVMGGGVPIPLPHGVEPGA-AG---KLMFRPQNLFIRQDGGPPRAGHVR 312 Query: 296 LTASVEVVELTGPELVTTATVGSQRITACLP 326 L V E G + +G Q++ P Sbjct: 313 LMGVVRHREFLGASIRYAVDIGGQQVQVDAP 343 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: 338 Number of extensions: 18 Number of successful extensions: 1 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: 371 Length adjustment: 30 Effective length of query: 330 Effective length of database: 341 Effective search space: 112530 Effective search space used: 112530 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