Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_036260808.1 DL86_RS10065 polyamine ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000746085.1:WP_036260808.1 Length = 376 Score = 111 bits (278), Expect = 2e-29 Identities = 74/255 (29%), Positives = 127/255 (49%), Gaps = 21/255 (8%) Query: 2 TEKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTP 61 T S+ +++ G++KR GG+ A+ + +T++RG+ + L+GP+G GKT+ +I G TP Sbjct: 4 THDSSAPFVQLEGVTKRHGGVAAVDALSLTLRRGEFFALLGPSGCGKTSLLRLIAGFETP 63 Query: 62 DAGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAV 121 D G + G+ T H + + FQ LF M N+ G ++ G Sbjct: 64 DEGRIFIDGEDVTGTPPH---RRPVNMMFQTYALFPHMNVARNIGFGL-VQEG------- 112 Query: 122 FRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIAL 181 A IA+R E+L V + + + LS G ++R+ +ARAL P+L+ L Sbjct: 113 -------IARAEIARRVTEMLRLVQLEGLGERRPDQLSGGQKQRVALARALVKRPKLLLL 165 Query: 182 DEPAAGMNATEKVQLR-ELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGN 240 DEP A ++ + + + EL+ T L++ HD + M + R+ V+ G+ G Sbjct: 166 DEPLAALDRRLREETQFELMHLQERLGATFLVVTHDQREAMVMASRIGVMRAGRIEQIGA 225 Query: 241 PAEVQKNEKVIEAYL 255 PAE+ E+ I +Y+ Sbjct: 226 PAEIY--ERPISSYV 238 Lambda K H 0.319 0.137 0.384 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: 14 Number of successful extensions: 3 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: 260 Length of database: 376 Length adjustment: 27 Effective length of query: 233 Effective length of database: 349 Effective search space: 81317 Effective search space used: 81317 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 (21.7 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