Align ABC transporter for Lactose, ATPase component (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 247 bits (630), Expect = 4e-70 Identities = 136/319 (42%), Positives = 189/319 (59%), Gaps = 39/319 (12%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 M+ ++ + K + G + G+DL + EF+V +GPSG GK+TLLR+IAGLE +SGD+ Sbjct: 1 MATVETRSLTKRFDGTNAVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSGDI 60 Query: 61 TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120 + + + P +AMVFQSYALYPH++V N+ F L +PR I ++V+ AA + Sbjct: 61 LVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAAAL 120 Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 +G LL RKP+QLSGG+RQRVA+ RA+VR P FL DEPLSNLDA+LR R E+ +L Sbjct: 121 FGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQLQ 180 Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240 ++LATT +YVTHDQ+EA+ L D++ ++ G V Q+G+P +Y+ PA+ FVA FIGSP MN Sbjct: 181 RRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIGSPPMN 240 Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHF--------DEAGPA 292 +D D A+ G RPEHF DEA Sbjct: 241 L------VDTD------------------------ALVTGFRPEHFLPREVYGSDEA-LE 269 Query: 293 ALDLAIDMLEHLGGETFAY 311 I +E+LG + Y Sbjct: 270 PFPFHITRIENLGSDRLVY 288 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: 327 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 351 Length adjustment: 29 Effective length of query: 329 Effective length of database: 322 Effective search space: 105938 Effective search space used: 105938 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