Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_012676168.1 PERMA_RS09515 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000021565.1:WP_012676168.1 Length = 287 Score = 164 bits (414), Expect = 3e-45 Identities = 103/255 (40%), Positives = 147/255 (57%), Gaps = 21/255 (8%) Query: 22 VDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID------DVRMNDVDPSKR 75 +DL IK GEFV G SG GK+T+LRMI+GLE+ G + ID + D+ P KR Sbjct: 21 LDLHIKKGEFVTLFGRSGSGKTTVLRMISGLEKPDRGKIEIDGKVYFDSEKGIDLPPQKR 80 Query: 76 GIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRKPKQLS 135 I VFQ+YAL+P+MTV EN+ FA+ R + EK + E + L L DR P LS Sbjct: 81 NIGFVFQNYALFPNMTVLENILFAM-----DRPDREKAI-ELLKTVHLEDLKDRYPDTLS 134 Query: 136 GGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYVTHDQV 195 GGQ+QRVA+ RA+ R P I L DEPLS LD +R ++ EI R+H+ T + V+HD+ Sbjct: 135 GGQQQRVAVARALAREPSILLLDEPLSALDFSIREKLQEEIKRIHRVFNLTTILVSHDKT 194 Query: 196 EAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLKGVIEIDE-DQAY 254 E L+D++V + G + + GSP ++ + N+ S K +F+ V++I + D Y Sbjct: 195 EVFKLSDRVVWIEKGRIIKEGSPRKVFIE-KNI-------SGKFSFIGNVLQIKKADTIY 246 Query: 255 ARLPDYGDAKIPVTL 269 + GD + V L Sbjct: 247 IATIEIGDNLVEVVL 261 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: 279 Number of extensions: 12 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: 287 Length adjustment: 28 Effective length of query: 330 Effective length of database: 259 Effective search space: 85470 Effective search space used: 85470 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 Apr 09 2024. 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