Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Koxy:BWI76_RS01840 Length = 369 Score = 281 bits (718), Expect = 3e-80 Identities = 167/372 (44%), Positives = 224/372 (60%), Gaps = 22/372 (5%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+++++RN+ K +G+V K I++ ++ GEF+V +G SGCGKSTLL +IAGL + GD+ Sbjct: 1 MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSGDL 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 LIG+ + V P +R I MVFQSYALYP+LSVA N+ FGL++ + ++ V A + Sbjct: 61 LIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVAEV 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 LQ+ +LL+RKP LSGGQRQRVAIGR LV P+VFL DEPLSNLDA LR++MR E+ RLH Sbjct: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L T++YVTHDQ+EAMTLA +I V+ GR+ Q+ P E+Y PA +VAGF+GSP MN Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 Query: 241 ILDAEMTANGLKIEGCEEVLP------LPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQ 294 L ++TA IE + LP LP + G + +GIRPE L L + Sbjct: 241 FLPVKVTATA--IEQVQVELPNRQQVWLPVD-SARVQVGANMSLGIRPEHL-LPSDIADV 296 Query: 295 RLTASVEVVELTGPELVTTATVGSQRITACLPPRT----------AVGM--GSAHAFTFD 342 L V+VVE G E + S R A+G+ H F D Sbjct: 297 TLEGEVQVVEQLGHETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFRED 356 Query: 343 GTALHLFDPESG 354 GTA E G Sbjct: 357 GTACRRLHKEPG 368 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: 14 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: 369 Length adjustment: 29 Effective length of query: 331 Effective length of database: 340 Effective search space: 112540 Effective search space used: 112540 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