Align ABC transporter for Lactose, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 147 bits (371), Expect = 4e-40 Identities = 86/231 (37%), Positives = 131/231 (56%), Gaps = 7/231 (3%) Query: 4 LQLSDVRKSY--GGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLT 61 + DV K+Y GG + GV L +K+GE +G SG GKSTL+R+I GLE S+G + Sbjct: 2 ITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVI 61 Query: 62 IDD-----VRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNE 116 +D + + + +R + M+FQ + L TV +N+ F L+ AG P AE++ R E Sbjct: 62 VDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAE 121 Query: 117 AAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEI 176 + L A + P QLSGGQ+QRV I RA+ +PK+ L DE S LD E + I Sbjct: 122 LLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLI 181 Query: 177 ARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPAN 227 A L+++L TIV +TH+ + D++ V+ AG V + G+ +++ PA+ Sbjct: 182 AGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPAS 232 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: 288 Number of extensions: 13 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: 332 Length adjustment: 29 Effective length of query: 329 Effective length of database: 303 Effective search space: 99687 Effective search space used: 99687 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