Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 282 bits (722), Expect = 8e-81 Identities = 156/357 (43%), Positives = 226/357 (63%), Gaps = 8/357 (2%) Query: 3 ALEIRNIRKRYG-EVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDIL 61 ALE+R +RK Y V + + + L+ GEFL LLG SGCGKST L +IAGL +P+ G I Sbjct: 5 ALELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64 Query: 62 IGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLL 121 +G+R + + P DRD+AMVFQSYALYP+L+V +N+ GL++RR AE ++ ++ A L Sbjct: 65 LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124 Query: 122 QIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQ 181 ++++LLDR+P+QLSGGQRQRVA+GRALVR P VFL DEPLSNLDA LR ++R ++K L Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184 Query: 182 MLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNI 241 + VVYVTHDQ EA++L+ RIA++ G ++QL +PD +Y PA +VAGF+GSP MN+ Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244 Query: 242 LDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASVE 301 L + + + LP+P+ A +V G+RPE L+LA + + + Sbjct: 245 LPLPIHSGQAWLG--SRALPIPSHLA----ARSQVLWGLRPEHLKLATPEVERAIPVQLH 298 Query: 302 VVELTGPE-LVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRSL 357 + E G + L+T A + + L + + + TF+ + H F P +G L Sbjct: 299 LTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEPESQHWFCPSTGDRL 355 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: 345 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: 355 Length adjustment: 29 Effective length of query: 331 Effective length of database: 326 Effective search space: 107906 Effective search space used: 107906 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