Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_068166810.1 HTA01S_RS01610 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_001592305.1:WP_068166810.1 Length = 333 Score = 362 bits (928), Expect = e-104 Identities = 197/355 (55%), Positives = 243/355 (68%), Gaps = 25/355 (7%) Query: 2 SELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLT 61 S L+L +++KSYG + VI GVDLDI+ GEFVVFVGPSGCGK+TLLRMIAGLE+I++G LT Sbjct: 4 SNLRLRNIQKSYGKVHVIHGVDLDIEPGEFVVFVGPSGCGKTTLLRMIAGLEDITAGTLT 63 Query: 62 IDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHIL 121 I D +ND+ PS+RG+AMVFQSYALYPH TV +NM F L+ A VP+AEI++RV EA+ IL Sbjct: 64 IADQTVNDLPPSERGVAMVFQSYALYPHKTVYDNMAFGLKIAKVPKAEIDRRVREASEIL 123 Query: 122 ELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHK 181 ++ L+R PK LSGGQRQRVAIGRAIVR PK+FLFDEPLSNLDA LR MR+E+A LH+ Sbjct: 124 QITEYLERLPKALSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRTKMRVELATLHR 183 Query: 182 QLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNF 241 +L T+VYVTHDQVEAMTLADKIVV+ G +EQVG+PL+LY PA FVA FIGSP+MNF Sbjct: 184 RLGATMVYVTHDQVEAMTLADKIVVLNKGRIEQVGAPLELYHRPATRFVASFIGSPQMNF 243 Query: 242 LKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDLAIDML 301 ++G YA+ D A +GIRPEH L+ + Sbjct: 244 IEG--------GYAQQFD----------------AHAVGIRPEHLRIDAAGQLEGTLRHA 279 Query: 302 EHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRL 356 E LG ETFAY G+L ++ G+RL P + FD G R+ Sbjct: 280 EQLGNETFAYVDAGPLGDL-TARIDGSISVEPGERLRLGHQPEHLYRFDAAGLRI 333 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: 403 Number of extensions: 16 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: 333 Length adjustment: 29 Effective length of query: 329 Effective length of database: 304 Effective search space: 100016 Effective search space used: 100016 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