Align ABC transporter for Lactose, ATPase component (characterized)
to candidate YP_001312870.1 Smed_4132 ABC transporter-like protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000017145.1:YP_001312870.1 Length = 357 Score = 624 bits (1609), Expect = 0.0 Identities = 320/358 (89%), Positives = 334/358 (93%), Gaps = 2/358 (0%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 MS LQLS VRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEI+SG+L Sbjct: 1 MSNLQLSQVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEITSGEL 60 Query: 61 TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120 +ID+VRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVP+AEIEKRVNEAA I Sbjct: 61 SIDEVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPKAEIEKRVNEAADI 120 Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 LELG LLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH Sbjct: 121 LELGTLLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240 KQLATTIVYVTHDQVEAMTLADKIVVMR GVVEQ+GSPL+LYDDPANLFVAGFIGSPKMN Sbjct: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRGGVVEQIGSPLNLYDDPANLFVAGFIGSPKMN 240 Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQA-AAGTAVTIGIRPEHFDEAGPAALDLAID 299 FLKG EI E + YARLPD+G KIP++L+A A T VTIG+RPEHF+EAGPA LDL ID Sbjct: 241 FLKGTTEIVEGRTYARLPDHGGLKIPISLEAIAPDTPVTIGLRPEHFNEAGPAVLDLTID 300 Query: 300 MLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLR 357 MLEHLGGETFAYAR HGNG LIVVETKNGRGLK GDRL ARFDP S LVFDGEGKRLR Sbjct: 301 MLEHLGGETFAYAR-HGNGALIVVETKNGRGLKAGDRLAARFDPASALVFDGEGKRLR 357 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: 595 Number of extensions: 20 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: 357 Length adjustment: 29 Effective length of query: 329 Effective length of database: 328 Effective search space: 107912 Effective search space used: 107912 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