Align ABC transporter for Lactose, ATPase component (characterized)
to candidate AO356_28585 AO356_28585 ABC transporter
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 350 bits (898), Expect = e-101 Identities = 183/357 (51%), Positives = 245/357 (68%), Gaps = 3/357 (0%) Query: 3 ELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTI 62 +L+L +V K GG +++ V L+I +GEFVVFVGPSGCGKSTLLR+IAGL+ I GDL I Sbjct: 3 KLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLI 62 Query: 63 DDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILE 122 D R+ND++P +RG+ MVFQSYALYPHM+V +N+ F L+ A + + +RV + A IL+ Sbjct: 63 DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQ 122 Query: 123 LGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQ 182 L LL RKP++LSGGQRQRVA+GRA+ R P I LFDEPLSNLDA LRV MR EIARLH + Sbjct: 123 LDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGR 182 Query: 183 LATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFL 242 L +T++YVTHDQVEAMTLADKIVV+ G +EQVGSP +LY+ PA+ FVAGF+GSP+MNFL Sbjct: 183 LGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFL 242 Query: 243 KGVIEIDEDQAYARLPDYGDAKIPVTLQA-AAGTAVTIGIRPEHFD-EAGPAALDLAIDM 300 + + + G +P AA T +++GIRPEH +A +A+ Sbjct: 243 AAFLHTPGETSQVESLVLGMTSLPFDSSGLAANTQLSLGIRPEHIALKAAQGTAGIAVSG 302 Query: 301 LEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLR 357 +E+LG ET+ + G + +V + G + GDR+ + D ++ VFD G L+ Sbjct: 303 VEYLGSETYVHL-DTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVFDTHGTALQ 358 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: 395 Number of extensions: 19 Number of successful extensions: 4 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: 379 Length adjustment: 30 Effective length of query: 328 Effective length of database: 349 Effective search space: 114472 Effective search space used: 114472 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