Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012335361.1 M446_RS27465 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000019365.1:WP_012335361.1 Length = 234 Score = 244 bits (624), Expect = 8e-70 Identities = 114/233 (48%), Positives = 171/233 (73%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L+++ L YG + A+KG+ VREG+LV+L+G+NGAGK+TT++AI+G + G I + Sbjct: 1 MLEIRDLVCGYGHVTALKGLSIAVREGQLVALVGANGAGKSTTLRAISGLVPPRSGAISF 60 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128 G+ I G ++ G+ PEGR VF +M++ ENL MGAY+R+D+AG+ AD+++++ Sbjct: 61 NGRDITGSEPRRILAHGIAHCPEGRRVFPQMSVAENLAMGAYLRRDRAGVAADLDRIYGE 120 Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188 FPRL ER+ Q AGT+SGGEQQMLA+GRALM++PK++L DEPS+GL+P +V+++F V+R + Sbjct: 121 FPRLAERRHQAAGTLSGGEQQMLAIGRALMARPKLVLFDEPSLGLAPNIVERMFAVIRAI 180 Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 G T++LVEQNA AL + D Y++E+G I +G G L+ DP +R AYLG Sbjct: 181 CTAGTTVLLVEQNAFAALELCDHAYLLETGRIVRSGTGSALIADPHIREAYLG 233 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: 186 Number of extensions: 7 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: 242 Length of database: 234 Length adjustment: 23 Effective length of query: 219 Effective length of database: 211 Effective search space: 46209 Effective search space used: 46209 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