Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 130 bits (326), Expect = 5e-35 Identities = 75/242 (30%), Positives = 129/242 (53%), Gaps = 18/242 (7%) Query: 4 EILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTIL 63 E +K+E +S +F LAV+ V LT+ ++ AL+G +G+GK+T+ L GF P+ G +L Sbjct: 19 EFVKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVL 78 Query: 64 LDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAF 123 LDG+ I LP H ++ + FQ+ LF MT +N+ F Sbjct: 79 LDGQNITALPPH---KRPINMMFQSYALFPHMTVEQNIA---------------FGLKQD 120 Query: 124 RKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183 + S E E L V++ ++A R L+ GQ++R+ +AR + RP++L+LDEP Sbjct: 121 KLSNTEISERVAEMLKLVHMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGA 180 Query: 184 LNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243 L+ K ++ + + E VT +++ HD + M+++ I +++QG + GTP I + Sbjct: 181 LDKKLRSQMQLELVEIIERVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYE 240 Query: 244 NP 245 +P Sbjct: 241 SP 242 Lambda K H 0.321 0.138 0.398 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: 216 Number of extensions: 7 Number of successful extensions: 2 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: 255 Length of database: 378 Length adjustment: 27 Effective length of query: 228 Effective length of database: 351 Effective search space: 80028 Effective search space used: 80028 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: 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