Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate SMc03120 SMc03120 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Smeli:SMc03120 Length = 262 Score = 164 bits (415), Expect = 2e-45 Identities = 96/252 (38%), Positives = 148/252 (58%), Gaps = 10/252 (3%) Query: 8 VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67 VVL G+ + FGG A+ DV + + +V+ LIGPNGAGKTT FN++T P GT Sbjct: 14 VVLSARGLRRDFGGFTAVKDVDLDVHHARVHALIGPNGAGKTTVFNLLTKFLQPTHGTIT 73 Query: 68 LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVG--RHIRTGSGLFGAVFRTK 125 L G+ TA +VA+ G+ R+FQ +F +T L+NV V R R + + ++ Sbjct: 74 LLGEDITRTAPDKVARMGLVRSFQISAVFPHLTVLDNVRVALQRPNRLATQFWKSL---- 129 Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185 + + +A++L+ VG+ K A+ A LSYG +R LEIA LA +P+++ LDEP Sbjct: 130 ---SSLDTLNGKAEQLIRSVGLDKEANAVAADLSYGRKRVLEIATTLALEPKVLLLDEPM 186 Query: 186 AGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245 AGM + + E+I + + R +L++EH++ +V LC VTVL G+ +AEG+ A V Sbjct: 187 AGMGHEDVGMVAEIIREVARE-RAVLMVEHNLSVVATLCHHVTVLQRGEILAEGDYATVS 245 Query: 246 KNEKVIEAYLGT 257 ++ +V AY+GT Sbjct: 246 EDPRVRTAYMGT 257 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: 178 Number of extensions: 8 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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: 47 (22.7 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