Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 187 bits (475), Expect = 4e-52 Identities = 119/328 (36%), Positives = 180/328 (54%), Gaps = 12/328 (3%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 MS L++ D+ G E +KG+DL + G++V +GPSG GKS LL I G G + Sbjct: 1 MSFLEVRDIYLDVGSFE-LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSV 59 Query: 61 TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120 ++ + P KR I++V+Q L+PHM + EN+ +ALR + +IE V + A + Sbjct: 60 FLEGRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGV 119 Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 L + LL RKP LSGG++QR ++ R++V PK+ L DEP S LDA R +R + + Sbjct: 120 LGIRELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAI 179 Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240 +TT+++VTHD + LA+++VV+R G V QVG P ++ P+ FVA F+G+ N Sbjct: 180 ADYSTTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT---N 236 Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDLAIDM 300 LKG ++ E + + D +I A G VT+ IRPE AG A + Sbjct: 237 VLKGTVKALEGK--LTVIDAEGMEIYSADPAEPGENVTVSIRPEEIILAGGTVESSARNT 294 Query: 301 LEHLGGETFAYARHHGNGELIVVETKNG 328 L+ G + + + H L+VVE K G Sbjct: 295 LK--GRVSGIFKKEH----LVVVEVKMG 316 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: 322 Number of extensions: 12 Number of successful extensions: 2 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: 353 Length adjustment: 29 Effective length of query: 329 Effective length of database: 324 Effective search space: 106596 Effective search space used: 106596 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 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