Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate HSERO_RS15485 HSERO_RS15485 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__HerbieS:HSERO_RS15485 Length = 349 Score = 303 bits (777), Expect = 3e-87 Identities = 160/354 (45%), Positives = 234/354 (66%), Gaps = 9/354 (2%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+A+ ++ + K +GE + ++ ID +++G+F VLLG SGCGKST L +IAGL +PS G I Sbjct: 1 MAAISLQGVCKHWGEAQAVRNIDFEVKAGQFTVLLGPSGCGKSTTLRLIAGLDKPSSGSI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 IG R V + P R I+MVFQSYAL+P+LSV NI FG+ +R+ P+A ++ ++ A + Sbjct: 61 HIGGRDVTQLPPAQRKISMVFQSYALFPHLSVRDNILFGVRVRKEPRAGYETRLKRVADI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L + +LL+R+P+QLSGGQ+QRVA+GRA++ + V L DEPLSNLDA+LR EMR E++ L Sbjct: 121 LGLAHLLERRPAQLSGGQQQRVALGRAIIADAPVCLMDEPLSNLDAQLRQEMRREIRALQ 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 Q L T+VYVTHDQ EAM++A ++ ++R+GRIEQ AAP ++Y +PAT + A F+G+PPMN Sbjct: 181 QQLNMTMVYVTHDQTEAMSMADQVILLREGRIEQDAAPADLYAQPATAFAARFIGTPPMN 240 Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 +L E A GL I G + +L W ++G+RPE +RLA S++ + A V Sbjct: 241 LLPLEPHAEGLVISGSDVIL---RDLGQTPW-----QLGLRPEHIRLADASDSS-VPAVV 291 Query: 301 EVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESG 354 E VE G + + A +G+ + P + +G G +D + FDP SG Sbjct: 292 ETVEYFGADTIIGARIGAASLLVRAPGQHRLGAGDPVRLAWDARDQYFFDPASG 345 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: 311 Number of extensions: 9 Number of successful extensions: 3 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: 349 Length adjustment: 29 Effective length of query: 331 Effective length of database: 320 Effective search space: 105920 Effective search space used: 105920 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