Align ABC transporter for Lactose, ATPase component (characterized)
to candidate SM_b20630 SM_b20630 sugar uptake ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Smeli:SM_b20630 Length = 361 Score = 383 bits (984), Expect = e-111 Identities = 207/360 (57%), Positives = 257/360 (71%), Gaps = 18/360 (5%) Query: 6 LSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDV 65 LSD+RKSYGGLEVI G+DL I+ G+FVVFVGPSGCGKSTLLRMIAGLEE+S G++ I Sbjct: 12 LSDIRKSYGGLEVIHGIDLTIEEGDFVVFVGPSGCGKSTLLRMIAGLEEVSEGEIAIKGR 71 Query: 66 RMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGA 125 + D+DPS+RGIAMVFQSYALYPHM+V EN+GF L+ A AEI +RV + + IL++ Sbjct: 72 DVTDLDPSERGIAMVFQSYALYPHMSVSENLGFGLKMARTDPAEIARRVAQVSAILKIDH 131 Query: 126 LLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLAT 185 LLDR+P QLSGGQRQRVAIGRAIVR P +FLFDEPLSNLDAELRV MRIEIARLH++L Sbjct: 132 LLDRRPGQLSGGQRQRVAIGRAIVRKPDVFLFDEPLSNLDAELRVSMRIEIARLHRELGN 191 Query: 186 TIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFL--- 242 T+VYVTHDQ EAMTLAD+IVV+R G +EQ GSP D+Y+DPAN+FVAGFIGSP+MNFL Sbjct: 192 TMVYVTHDQTEAMTLADQIVVLRDGRIEQAGSPRDVYEDPANMFVAGFIGSPRMNFLDAE 251 Query: 243 ---KGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHF--DEAGPAALDLA 297 G I + E A + D G K G + +GIRPEH E GP + Sbjct: 252 WQGDGTIRVGETTLEAAI-DGGSLK--------HGERLLLGIRPEHIAVAEPGPERIAAQ 302 Query: 298 IDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLR 357 ++ E+LGG + Y + +G+ +VVE + G + G++L+ F +G+RLR Sbjct: 303 VEFSEYLGGTRYLYCQLE-DGQSLVVEQREGPNWQAGEKLSFAVPDDRRRFFAEDGRRLR 361 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: 418 Number of extensions: 22 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: 361 Length adjustment: 29 Effective length of query: 329 Effective length of database: 332 Effective search space: 109228 Effective search space used: 109228 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