Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 154 bits (389), Expect = 2e-42 Identities = 87/231 (37%), Positives = 133/231 (57%), Gaps = 3/231 (1%) Query: 11 KSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDD--VRMN 68 K YG L+ ++ V L +G +G SG GKST+LR++ GLE G + +D ++ + Sbjct: 19 KRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRS 78 Query: 69 DVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGA-LL 127 DV P +R + V Q L+PH+T N+ R G R I +R + A + L +L Sbjct: 79 DVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPTGVL 138 Query: 128 DRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTI 187 +R P +LSGGQRQRVA+ RA++ P L DEPL LD +R ++ E+ ++ QL T+ Sbjct: 139 ERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLGKTV 198 Query: 188 VYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPK 238 + VTHD EA A+++V++R G V Q G+ DL + PA+ FV F+ + + Sbjct: 199 IVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAAQR 249 Lambda K H 0.321 0.139 0.396 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: 218 Number of extensions: 9 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: 358 Length of database: 255 Length adjustment: 27 Effective length of query: 331 Effective length of database: 228 Effective search space: 75468 Effective search space used: 75468 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 (21.8 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