Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate AO353_25130 AO353_25130 ABC transporter
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 285 bits (729), Expect = 1e-81 Identities = 162/360 (45%), Positives = 222/360 (61%), Gaps = 17/360 (4%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M L++ N+ K+ G V L+ + + + +GEF+V +G SGCGKSTLL +IAGL GD+ Sbjct: 1 MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 LI ER V + P++R + MVFQSYALYP++SV NI FGL++ + ++ + V TA++ Sbjct: 61 LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 LQ++ LL RKP +LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA LR++MR E+ RLH Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 L +T++YVTHDQ+EAMTLA +I V+ GR+EQ+ +P E+Y+RPA+ +VAGF+GSP MN Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 241 ILDAEMTANGLKIEGCEEVL---PLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLT 297 L A + A G VL LP + A A + +G+RPE + L A + Sbjct: 241 FLAARLHAPGETSLVDTPVLGMTSLPFDSSNLA-ADTPLSLGVRPEHVSLKAADGT--VG 297 Query: 298 ASVEVVELTGPELVTTATVGSQRITACLPPRTA-----------VGMGSAHAFTFDGTAL 346 V VE G E G C A + +G+ H F DGTAL Sbjct: 298 VIVTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFDADGTAL 357 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: 377 Number of extensions: 10 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: 381 Length adjustment: 30 Effective length of query: 330 Effective length of database: 351 Effective search space: 115830 Effective search space used: 115830 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