Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >MicrobesOnline__882:209225 Length = 354 Score = 151 bits (381), Expect = 3e-41 Identities = 117/348 (33%), Positives = 169/348 (48%), Gaps = 30/348 (8%) Query: 4 LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63 L + + + E L +++ +GE + L+G SG GK+TLL IAGL P G I + Sbjct: 3 LAVEGLGRTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRVT 62 Query: 64 ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123 G + +VFQ Y L+P+LSV N+ FG R V A + V R ++ Sbjct: 63 PPQGHG-----GGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRL 117 Query: 124 E-----NLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 + ++ R P+QLS GQRQRVA+ RALV +P V L DEP +NLD LR EM ++ Sbjct: 118 DTDDLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRD 177 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 + + V VTHD EA + R+ VM G + QLA P +VY PA A F+G P Sbjct: 178 VVRRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG--P 235 Query: 239 MNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTA 298 + +LD E T L I+ PAA A + +++ RPEAL + ++ + Sbjct: 236 VTVLD-ETTRRTLGID------TPPAAATACADTMQGLRL-YRPEALAVRPWADGPAVLV 287 Query: 299 SVE--------VVELTGPELV--TTATVGSQRITACLPPRTAVGMGSA 336 S ++++ G EL+ T C+ R GM SA Sbjct: 288 SARFTGQVMQLLLDVEGQELLVHTLDDAPPTGTRLCVSLREIPGMTSA 335 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: 294 Number of extensions: 16 Number of successful extensions: 3 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: 354 Length adjustment: 29 Effective length of query: 331 Effective length of database: 325 Effective search space: 107575 Effective search space used: 107575 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