Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 205 bits (522), Expect = 1e-57 Identities = 116/318 (36%), Positives = 174/318 (54%), Gaps = 33/318 (10%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + +R ++ F LD ++L I +GEFL LLG SGCGK+T+L ++G + G++ I Sbjct: 8 IELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRIN 67 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 + V P+ R + VFQ+YAL+P MTV N++FGLK+ + E +RV A ++ + Sbjct: 68 GQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHL 127 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 + RKP +LSGGQ+QRVAI RA++ + V L DEP S LD KLR ++++EIK L + L Sbjct: 128 ENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQL 187 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI--------- 234 T ++VTHDQ EA ++DR+ VM G I+Q+ P IY P N++VA F+ Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGDINALPGR 247 Query: 235 ---------------------GSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRL 273 G+P +++P + GG F V + RL Sbjct: 248 IDAVRLDWSAAPGTPLAPPAPGTPEHAALPPDLKPGEHLYDATVGGTVFPVR---SRRRL 304 Query: 274 QPGQKVVLGLRPEHVKVD 291 PG V + LRPE +++D Sbjct: 305 APGDGVQVLLRPEDLRID 322 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: 372 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 361 Length of database: 399 Length adjustment: 30 Effective length of query: 331 Effective length of database: 369 Effective search space: 122139 Effective search space used: 122139 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: 50 (23.9 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