Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 205 bits (521), Expect = 2e-57 Identities = 129/360 (35%), Positives = 198/360 (55%), Gaps = 21/360 (5%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 M+ L+L+DV + YG V+ G+ I++G +GPSGCGK+TLLR IAG E+I++G + Sbjct: 1 MAHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSI 60 Query: 61 TIDDVRMN----DVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNE 116 +D ++ + P +R I MVFQ YAL+PH+TV +N+ F L+ G E ++RV Sbjct: 61 ALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG---GERQQRVAA 117 Query: 117 AAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEI 176 ++ L ++ P +LSGGQ+QRVA+ RA+ P++ L DEP SNLD +LR + +E+ Sbjct: 118 MLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEV 177 Query: 177 ARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGS 236 + K+ TT + VTHDQ EA +AD+I VM G ++Q +P +LY PAN FVA F+G Sbjct: 178 REILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVGQ 237 Query: 237 PKMNFLKG-VIEIDEDQAYARLPDYGDAKIPVTLQAAAGT-----AVTIGIRPEHFDEAG 290 F+ G V+ + Q + + G +PV A G V I +RP+ Sbjct: 238 GV--FVPGTVLAGNRVQMELGILESG---VPVECSAGCGVCGKGCGVDILLRPDDVVHDD 292 Query: 291 PAALDLAIDMLEHLGGETFAYAR-HHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVF 349 + L A++ G + R G L +V + + L G+++ R D V+ F Sbjct: 293 KSPLQAAVEHKAFRGADILYTLRLESGARVLSLVPSHHNHAL--GEKIGIRLDVDHVVAF 350 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: 349 Number of extensions: 21 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: 356 Length adjustment: 29 Effective length of query: 329 Effective length of database: 327 Effective search space: 107583 Effective search space used: 107583 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