Align ABC transporter for Lactose, ATPase component (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 225 bits (573), Expect = 2e-63 Identities = 148/343 (43%), Positives = 196/343 (57%), Gaps = 32/343 (9%) Query: 15 GLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDP-- 72 G ++ +DLDI +GE VV +GPSGCGK+T LR+IAGLE +G + + NDV P Sbjct: 19 GTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVM--FGDNDVTPLP 76 Query: 73 -SKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRKP 131 +RG+ MVFQSYAL+P+MTV EN+ + LR + A +RV+E ++ LG +R+ Sbjct: 77 IEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRI 136 Query: 132 KQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYVT 191 QLSGGQRQRVA+ RAI P++ L DEPL+ LDA+LR +R +I +L + L T VYVT Sbjct: 137 DQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSLHITAVYVT 196 Query: 192 HDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLKGVIEIDED 251 HDQ EAM L D+I+VM G + Q G+P +Y PAN FVA FIG+ MN L V+E D Sbjct: 197 HDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNRLPAVLEADAW 254 Query: 252 QAYARL-PDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDLAIDMLE--HLGGET 308 + L P +G A +L AA + RPE D+A+ E HLGG Sbjct: 255 RVPGGLVPRHGTA---ASLAAAPSPRAELLFRPE----------DVALAQAEDAHLGGSV 301 Query: 309 FA------YAR---HHGNGELIVVETKNGRGLKTGDRLTARFD 342 Y R G +VV+T G GDR+ R D Sbjct: 302 VTALFLGNYTRLLVDVGAPAPLVVDTTRRDGWLAGDRVGLRLD 344 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: 342 Number of extensions: 14 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: 357 Length adjustment: 29 Effective length of query: 329 Effective length of database: 328 Effective search space: 107912 Effective search space used: 107912 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