Align ABC transporter for Lactose, ATPase component (characterized)
to candidate SMc04140 SMc04140 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Smeli:SMc04140 Length = 360 Score = 386 bits (991), Expect = e-112 Identities = 208/355 (58%), Positives = 250/355 (70%), Gaps = 4/355 (1%) Query: 6 LSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDV 65 L V K YG L+VI G+DL I GEF VFVGPSGCGKSTLLRMIAGLEEIS G L +D Sbjct: 7 LQKVEKRYGALDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLMLDSD 66 Query: 66 RMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGA 125 RMN+V P++RGIAMVFQSYALYPHM+V +N+ F L AG +AEIE +V AA IL++ Sbjct: 67 RMNEVAPARRGIAMVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEILQIEK 126 Query: 126 LLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLAT 185 LLDRKPK LSGGQRQRVAIGRAIVR P+IFLFDEPLSNLDAELRV MR+EI+RLH+ L Sbjct: 127 LLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHRDLGN 186 Query: 186 TIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLKGV 245 T++YVTHDQVEAMT+ADKIVV+ +G +EQVG+PLDLY++P N FVAGFIGSPKMNFLK Sbjct: 187 TMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKMNFLKAR 246 Query: 246 IEIDEDQAYARLPDYGDAKIPVTLQAAA-GTAVTIGIRPEHFD--EAGPAALDLAIDMLE 302 I A G ++P L A G VT GIRPEH E G + ++++E Sbjct: 247 IADVTGSETAIEVCGGTIRLPRRLNGATQGQDVTFGIRPEHLSAREGGIELATVNVEIVE 306 Query: 303 HLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLR 357 +LGGET Y +L V + + ++ G L FDP VF +G+ +R Sbjct: 307 NLGGETMLYGITPDRQQL-TVALEGQQKVERGSNLAVHFDPSRCHVFGADGRAMR 360 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: 423 Number of extensions: 11 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: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 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 17 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