Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >MicrobesOnline__882:209027 Length = 368 Score = 217 bits (553), Expect = 3e-61 Identities = 132/353 (37%), Positives = 199/353 (56%), Gaps = 16/353 (4%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + +R ++ NF LD ++L+I +GEFL LLG SGCGK+T+L I+G G I +K Sbjct: 8 IELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLK 67 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 + + P+ R + VFQ+YAL+P M+V +N+ FGL++ + P EI +RV A ++ + Sbjct: 68 GQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHL 127 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 + R+P +LSGGQ+QRVAI RA+V + V L DEP S LD KLR ++++EIK L + L Sbjct: 128 EAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQL 187 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243 T ++VTHDQ EA ++DR+ VM G I+Q+ P IY P NL+VA F+G +N Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVG--EINILN 245 Query: 244 GEVEPKDGRSFVRA--GGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQ 301 + G A G+ F + + PG KV + LRPE ++V + P Sbjct: 246 AVIAANHGDGLYDAVIEGVTFPIR---SQRTFAPGDKVNVLLRPEDLRVYTLTEDRPAGP 302 Query: 302 AVVD-IEEPM--GA--DNLLWLTFAGQSMSVRIAGQR----RYPPGSTVRLSF 345 + IEE + GA D ++ L+ + M+ + Y PG TV +S+ Sbjct: 303 HLTGRIEESVYKGATVDLIVTLSDGRRLMAAEFFNEDDVDINYNPGETVTVSW 355 Lambda K H 0.320 0.137 0.392 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: 338 Number of extensions: 11 Number of successful extensions: 2 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: 361 Length of database: 368 Length adjustment: 29 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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