Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 152 bits (383), Expect = 1e-41 Identities = 86/253 (33%), Positives = 144/253 (56%), Gaps = 9/253 (3%) Query: 4 AIKQPVS---PEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCL 60 A+KQ ++ P ++++ V+K + + D+ L + +GE L G SGSGKST +R L Sbjct: 7 AMKQAMAKAEPVEFVKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRIL 66 Query: 61 NRLEEHQQGRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRK 120 E +GR+++DG +T + +R + M+FQ + LFPH+T+ QN + K Sbjct: 67 AGFETPSEGRVLLDGQNIT----ALPPHKRPINMMFQSYALFPHMTVEQNIAFG-LKQDK 121 Query: 121 MPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSAL 180 + + E L+ V + + A + P QLSGGQ+QRVA+AR+L +PK++L DEP AL Sbjct: 122 LSNTEISERVAEMLKLVHMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 181 Query: 181 DPEMVKEVLDTMIGLAED-GMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDN 239 D ++ ++ ++ + E G+T + VTH+ A T+A R+ MD+G IV+ P D +++ Sbjct: 182 DKKLRSQMQLELVEIIERVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYES 241 Query: 240 PQNDRTKLFLSQI 252 P N F+ + Sbjct: 242 PVNRHVAEFVGSV 254 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: 218 Number of extensions: 13 Number of successful extensions: 4 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: 378 Length adjustment: 27 Effective length of query: 227 Effective length of database: 351 Effective search space: 79677 Effective search space used: 79677 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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