Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_086511549.1 BZY95_RS19345 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_002151265.1:WP_086511549.1 Length = 248 Score = 172 bits (436), Expect = 6e-48 Identities = 87/241 (36%), Positives = 148/241 (61%), Gaps = 3/241 (1%) Query: 2 AEKSNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSM 61 A ++ L+ +GL YG + GVD + GE +SL+G NG GKTTT+K+I G + Sbjct: 8 ASGASAPLIDARGLHTYYGESHVLHGVDLRLMPGETLSLMGRNGMGKTTTLKSILGFVPP 67 Query: 62 NDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILA- 120 +G + GKS + W L+++G+ VPEGRG+F +++ E+L M A R ++ G Sbjct: 68 REGEVSIKGKSTARRRPWQLIRQGIGYVPEGRGIFPGISVREHLIMAA--RPNERGESPW 125 Query: 121 DIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDK 180 +E++ FPRL +R + +SGGEQQML++GRAL + P +++LDE + GL+P++ D+ Sbjct: 126 TLERVLDTFPRLGQRINHDGSFLSGGEQQMLSIGRALTTNPDMVILDEATEGLAPLIRDE 185 Query: 181 IFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 I++++R++ A G+ ++V++N L +AD+ ++ G + +G Q L DP + +L Sbjct: 186 IWKIIREIKASGIASIIVDKNIDNLLEVADKHLLLVKGEVVYSGDSQGLREDPSILDTHL 245 Query: 241 G 241 G Sbjct: 246 G 246 Lambda K H 0.317 0.136 0.373 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: 170 Number of extensions: 13 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: 242 Length of database: 248 Length adjustment: 24 Effective length of query: 218 Effective length of database: 224 Effective search space: 48832 Effective search space used: 48832 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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