Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_068171287.1 HTA01S_RS11660 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_001592305.1:WP_068171287.1 Length = 364 Score = 293 bits (750), Expect = 5e-84 Identities = 157/316 (49%), Positives = 211/316 (66%), Gaps = 9/316 (2%) Query: 2 SELQLSDVRKSYG----GLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISS 57 S L ++ +RK +G +EV+K +D+D+ GEF++ VGPSGCGKSTLL +IAGLEE S Sbjct: 3 SSLHIAGIRKVFGKGDKAVEVLKRIDIDVAPGEFLILVGPSGCGKSTLLNIIAGLEEPSE 62 Query: 58 GDLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEA 117 G+L I + + P++R IAMVFQSYALYP MTV +N+GFAL VP +KR+ E Sbjct: 63 GELLIAGKNVIGMAPAQRDIAMVFQSYALYPTMTVADNIGFALEMRKVPVEVRKKRIQEV 122 Query: 118 AHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIA 177 A +L++ LLDR+P QLSGGQRQRVA+GRA+ R P++FLFDEPLSNLDA+LRV MR EI Sbjct: 123 AVLLQIEHLLDRRPSQLSGGQRQRVAMGRALARDPQLFLFDEPLSNLDAKLRVEMRAEIK 182 Query: 178 RLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSP 237 RLH T VYVTHDQ+EAMTL +I VM+ G+++Q+ +P ++Y PAN +VAGFIGSP Sbjct: 183 RLHHVSGITTVYVTHDQIEAMTLGSRIAVMKDGILQQIDTPDEIYRRPANTYVAGFIGSP 242 Query: 238 KMNFLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDLA 297 MNF+ G +E D + + G +P VT+G RPEH + A Sbjct: 243 TMNFIPGKVERSGDNG-KFVFEGGSLDLP----CPDVQQVTLGQRPEHIHLSNDAPWRGE 297 Query: 298 IDMLEHLGGETFAYAR 313 + ++E G +T+ + Sbjct: 298 VVLVEPTGADTYVVVK 313 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: 414 Number of extensions: 21 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: 364 Length adjustment: 29 Effective length of query: 329 Effective length of database: 335 Effective search space: 110215 Effective search space used: 110215 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