Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 229 bits (583), Expect = 1e-64 Identities = 113/235 (48%), Positives = 161/235 (68%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ L++ + KRYG V+ + D+A+E GEF+ LLG SGCGK+T L +IAG + SGG I Sbjct: 1 MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 L+ R + P R + +VFQSYAL+P++SV N+ FGL+MR+VP AE V+ L Sbjct: 61 LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 +++ DR P +LSGGQRQRVA+ RALV P V L DEPLSNLDA LR EM+ E++R+ Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVG 235 + T + VTHDQ EA++++ R+ VM+ GR+ Q+ AP ++Y+ P T +++ FVG Sbjct: 181 CAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVG 235 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: 322 Number of extensions: 11 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: 342 Length adjustment: 29 Effective length of query: 331 Effective length of database: 313 Effective search space: 103603 Effective search space used: 103603 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