Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate H281DRAFT_02613 H281DRAFT_02613 amino acid ABC transporter ATP-binding protein, PAAT family (TC 3.A.1.3.-)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_02613 Length = 249 Score = 244 bits (624), Expect = 9e-70 Identities = 124/239 (51%), Positives = 162/239 (67%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 ++Q +GV K +G+ VL ++LN+ GE +VL GPSGSGKST +RC+N LE+ G +VV Sbjct: 10 MVQFKGVTKRFGKTVVLDRVDLNIGAGEVVVLIGPSGSGKSTLLRCINALEQIDGGDLVV 69 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 DG+ + K++ IR+E GMVFQ FNLFP +T L+N P VR M K +AE +A Sbjct: 70 DGISVLGGAKKMREIRQEAGMVFQQFNLFPQMTALENVAFGPRQVRGMSKSEAESLAREL 129 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L +V + + Y +LSGGQQQRVAIARAL +KPK+MLFDEPTSALDPE+ +EVL M Sbjct: 130 LTKVGLGSRVGHYACELSGGQQQRVAIARALAVKPKLMLFDEPTSALDPELRQEVLRVMQ 189 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQI 252 LAE+GM+M+ VTHEM FAR V R+IFM+ G I P + DNP N R + FL + Sbjct: 190 ALAEEGMSMVVVTHEMAFARKVGTRLIFMEHGHITVDGPPAELLDNPPNQRLRDFLQHV 248 Lambda K H 0.322 0.137 0.407 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: 180 Number of extensions: 3 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: 254 Length of database: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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 (21.9 bits) S2: 46 (22.3 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