Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >MicrobesOnline__882:209027 Length = 368 Score = 153 bits (387), Expect = 6e-42 Identities = 83/237 (35%), Positives = 137/237 (57%), Gaps = 8/237 (3%) Query: 23 ALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNI 82 AL + +E +G LLGPSGCGKTT+L ++SG P G + G+ + A P+ R + Sbjct: 22 ALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLKGQRMDDAPPEARQV 81 Query: 83 AQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAAD 142 VFQ ++ M+V EN+ F LR ++ P+ +I +RV M+ + ++R L+ Sbjct: 82 NTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHLEAHADRRPRQLSGG 141 Query: 143 AKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVE 202 +Q++++ R +V + +L DEP + +D L+ Q++ ++K + +L +T ++VTHDQ E Sbjct: 142 QQQRVAIARAVVN-NPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQLGITFVFVTHDQEE 200 Query: 203 ALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPA-----HRDG 254 A +D+VVVM GK Q+GS ++E PA+ +V F+G +N L A H DG Sbjct: 201 AFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGE--INILNAVIAANHGDG 255 Lambda K H 0.320 0.136 0.395 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: 288 Number of extensions: 16 Number of successful extensions: 3 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: 368 Length adjustment: 29 Effective length of query: 329 Effective length of database: 339 Effective search space: 111531 Effective search space used: 111531 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