Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 338 bits (868), Expect = 1e-97 Identities = 184/366 (50%), Positives = 249/366 (68%), Gaps = 13/366 (3%) Query: 1 MSALEIRNIRKRYGE-VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 M++L IR++ K Y V LKG++I +E G+FL+L+G SGCGKSTLLN+IAGL + G+ Sbjct: 1 MASLSIRDVYKTYPNGVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKGE 60 Query: 60 ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119 I I ++V + PKDRDIAMVFQSYALYP+++V NI FGL +R+VP+ E + V + Sbjct: 61 IQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVSN 120 Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179 LQI +LLDRKP QLSGGQRQRVA+GRAL R+P +FLFDEPLSNLDAKLR+EMR+E+K L Sbjct: 121 TLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKLL 180 Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239 HQ L TT+VYVTHDQIEAMTL RIAVM+DG ++Q AP E+YD P+ L+VAGF+G+PPM Sbjct: 181 HQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPPM 240 Query: 240 NILDAEMTANG----LKIEGCEEVLPLPAAFNGA---AWAGRRVKVGIRPEALRLAAG-- 290 N + ++ G L+++ L F+ A + GR V +G+RPE + A G Sbjct: 241 NFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGREVILGLRPERITDARGAH 300 Query: 291 ---SEAQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALH 347 ++ Q + V+V+E TGP+ + A V +RI + + P + + FD + Sbjct: 301 GDNAKLQPIEVKVDVIEPTGPDTLVFAQVNGKRIVSRVHPASNPQPLANTTLLFDTSKAV 360 Query: 348 LFDPES 353 LFDP + Sbjct: 361 LFDPSN 366 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: 388 Number of extensions: 14 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: 371 Length adjustment: 30 Effective length of query: 330 Effective length of database: 341 Effective search space: 112530 Effective search space used: 112530 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