Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Ga0059261_3668 Ga0059261_3668 ABC transporter
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Korea:Ga0059261_3668 Length = 201 Score = 119 bits (299), Expect = 5e-32 Identities = 74/187 (39%), Positives = 105/187 (56%), Gaps = 14/187 (7%) Query: 26 IKSGE-FVVFVGPSGCGKSTLLRMIAGLEEISSGDLTI------DDVRMNDVDPSKRGIA 78 I+ GE +V GPSG GK+++L M+AGL E +G + + D DV P +R Sbjct: 20 IEGGEGIIVLFGPSGVGKTSVLDMVAGLLEPDTGHVRVGGETLFDAAIGEDVPPERRRAG 79 Query: 79 MVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRKPKQLSGGQ 138 VFQ L+PH++VR N+ + G P + + A ++ LLDR P+ LSGG+ Sbjct: 80 YVFQDARLFPHLSVRANLLYGA--GGDPSG-----LGDLAARFDIAHLLDRWPRSLSGGE 132 Query: 139 RQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYVTHDQVEAM 198 +RVAIGRA++ P+ L DEPLS+LD R + I RL + A I+ VTHD VEA Sbjct: 133 ARRVAIGRALLAKPRFLLLDEPLSSLDRARREEVTRVIERLRDEAALPILMVTHDPVEAE 192 Query: 199 TLADKIV 205 L +I+ Sbjct: 193 RLGQRII 199 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: 216 Number of extensions: 13 Number of successful extensions: 3 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: 201 Length adjustment: 25 Effective length of query: 333 Effective length of database: 176 Effective search space: 58608 Effective search space used: 58608 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: 47 (22.7 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