Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 295 bits (754), Expect = 2e-84 Identities = 161/357 (45%), Positives = 232/357 (64%), Gaps = 25/357 (7%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ + + K+YG+V+ + +D++++ GEF V +G SGCGKSTLL +IAGL E S G+I Sbjct: 1 MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 IG+R V + DR +AMVFQSYALYP+++V N+GFGL+M P+ + + V + +R+ Sbjct: 61 HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L++++ L RKP LSGGQRQRVAIGRA+VR P+VFLFDEPLSNLDA+LR++MR E+ RLH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + + T++YVTHDQ+EAMTLA +I V+R GR+EQ+ +P E+Y P +VAGF+GSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSMN 240 Query: 241 ILDAEMTANGLKIEGCEE-----VLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEA-- 293 L+ + +G+ + E + LPA G +V +G+RP+ L + A + Sbjct: 241 FLEGTVQGDGVVVPALENRRVATSVALPA-------DGSKVLLGLRPQHLSVTAADSSLV 293 Query: 294 ----QRL-TASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMG--SAHAFTFDG 343 +RL S + + E + T G + LP TAV +G A A+ FDG Sbjct: 294 LDLRERLGGVSYDYLSTPTGEKLIVETRGDE----ALPEGTAVALGFDDADAYIFDG 346 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: 340 Number of extensions: 15 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: 353 Length adjustment: 29 Effective length of query: 331 Effective length of database: 324 Effective search space: 107244 Effective search space used: 107244 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