Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 154 bits (389), Expect = 2e-42 Identities = 94/242 (38%), Positives = 134/242 (55%), Gaps = 18/242 (7%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 + ++ V K YGG ++ V LD+ GE +V GPSG GKSTL+R I GLE G + I Sbjct: 2 IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIG 61 Query: 64 DVRMNDVDPSKR-------GIAMVFQSYALYPHMTVRENMGFA-LRFAGVPRAEIEKRVN 115 + ++V P +R + MVFQ + L+PH+T+ EN A ++ G+ R E Sbjct: 62 E---DEVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALAR 118 Query: 116 EAAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIE 175 E + + D+ P QLSGGQ+QR AI RA+ P+I LFDEP S LDAE M E Sbjct: 119 ELLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAE----MVKE 174 Query: 176 IARLHKQLAT---TIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAG 232 + + K LAT T++ VTH+ A +AD+I+ M AG + + GSP D + P + Sbjct: 175 VLDIMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRA 234 Query: 233 FI 234 F+ Sbjct: 235 FL 236 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: 206 Number of extensions: 13 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: 358 Length of database: 241 Length adjustment: 26 Effective length of query: 332 Effective length of database: 215 Effective search space: 71380 Effective search space used: 71380 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