Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_11555 AO353_11555 sulfate ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11555 Length = 329 Score = 139 bits (350), Expect = 8e-38 Identities = 79/239 (33%), Positives = 129/239 (53%), Gaps = 15/239 (6%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 ++V +SK F +AL+ + + I+ G++ L+GP+G GKTT +I GL TPDAG+ Sbjct: 3 IEVRNVSKNFNAFKALNSINLDIQSGELVALLGPSGCGKTTLLRIIAGLETPDAGSIVFH 62 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 G E + H+V + FQ+ LF MT +NV FG + K + Sbjct: 63 G---EDVSGHDVRDRNVGFVFQHYALFRHMTVFDNV-----------AFGLRMKPKNQRP 108 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 E+ IA + ELL+ V + +D LS G ++R+ +ARALA +P+++ LDEP ++ Sbjct: 109 SESQIAVKVHELLNMVQLDWLSDRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALD 168 Query: 190 ATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 A + +LR + R+ D N T + + HD + M + DR+ V++ G G+P +V +N Sbjct: 169 AKVRKELRRWLARLHEDINLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGSPGDVYEN 227 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: 188 Number of extensions: 7 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: 260 Length of database: 329 Length adjustment: 26 Effective length of query: 234 Effective length of database: 303 Effective search space: 70902 Effective search space used: 70902 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 17 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