Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 266 bits (681), Expect = 5e-76 Identities = 155/364 (42%), Positives = 215/364 (59%), Gaps = 27/364 (7%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ LE++N+ K YG++ +K + + ++SGEF+V +G SGCGKSTLL +IAGL +GG + Sbjct: 1 MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 ++ R + V P RD+AMVFQSYALYP+++V N+ F L + +V A + V+ A Sbjct: 61 ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L + L R P LSGGQRQRVAIGR++VR+P+VFLFDEPLSNLDA LR R E+ LH Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L T VYVTHDQ+EAMTLA R+ V+RDG IEQ+ P E+YD+P +VA F+G P MN Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240 Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 + PA+ G + + +VGIRPE L++ + E L V Sbjct: 241 V--------------------APASLFG-QFPAQVAEVGIRPEHLQMVS-PEDGLLAGKV 278 Query: 301 EVVELTGPELVTTATVG----SQRITACLPPRTAVGMGSAHAFTFDGTA-LHLFDPESGR 355 +VE G E + + + L RT V +G +D + +H FD + R Sbjct: 279 VLVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFDTKGMR 338 Query: 356 SLRM 359 M Sbjct: 339 LTHM 342 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: 336 Number of extensions: 8 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: 348 Length adjustment: 29 Effective length of query: 331 Effective length of database: 319 Effective search space: 105589 Effective search space used: 105589 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 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