Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_048081400.1 EJ01_RS05520 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000745485.1:WP_048081400.1 Length = 348 Score = 197 bits (502), Expect = 3e-55 Identities = 104/266 (39%), Positives = 165/266 (62%), Gaps = 6/266 (2%) Query: 19 IKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDPSKRGIA 78 I ++L ++ E+ + +GPSG GK+ LL +IAG+ + SG + +D+ + + P KRGI Sbjct: 16 INNINLQVEDSEYFIILGPSGSGKTMLLELIAGMWPLDSGKIYMDNKDITTLPPEKRGIG 75 Query: 79 MVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRKPKQLSGGQ 138 V+Q+Y L+PH TV EN+ F L+ V EI+ RV E +L++ L DR P+ LSGG+ Sbjct: 76 FVYQNYMLFPHKTVFENIAFGLKVRKVRDEEIKTRVKEMMDLLKISHLADRLPRTLSGGE 135 Query: 139 RQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYVTHDQVEAM 198 +QR A+ RA++ +PKI L DEPLS LD + R + E+ +H++ T+V+VTH+ EA+ Sbjct: 136 QQRTALARALIIYPKILLMDEPLSALDRKTRDELMQELKEIHRKFDVTLVHVTHNFDEAL 195 Query: 199 TLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLKGVIEIDEDQAYARLP 258 LAD+I +MR G + QVG+ +++ PA+ FVA F+G+ N ++G + D ++ + Sbjct: 196 MLADRIAIMRNGEISQVGTSTEIFRHPADKFVADFVGAE--NIIEGTAKKDGER--LTII 251 Query: 259 DYGDAKIPVTLQAAAGTAVTIGIRPE 284 D G+ I T Q +T +RPE Sbjct: 252 DTGNISIYSTEQKQGHVHIT--VRPE 275 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: 300 Number of extensions: 14 Number of successful extensions: 1 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: 348 Length adjustment: 29 Effective length of query: 329 Effective length of database: 319 Effective search space: 104951 Effective search space used: 104951 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: 49 (23.5 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