Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 200 bits (509), Expect = 5e-56 Identities = 136/370 (36%), Positives = 197/370 (53%), Gaps = 27/370 (7%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA LEL +V + YGA + I I+ G L+GPSGCGK+TL+ CIAG E I G Sbjct: 1 MAHLELADVMQRYGAHT--VVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAG 58 Query: 61 AIMIGDQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEV 116 +I + + VS ++P+ R I MVFQ YAL+P ++V +NI FGLK + + V Sbjct: 59 SIALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG---GERQQRV 115 Query: 117 ARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 A + L+ + + P +LSGGQQQRVA+ RALA P++ L DEP SNLD LR + Sbjct: 116 AAMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSL 175 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFI 236 E++ + ++ TT + VTHDQ EA + D++ VM +G IQQ+ TP +Y+ PAN+FVA F+ Sbjct: 176 EVREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFV 235 Query: 237 GS----PPMNFVPLRLQRKDGRLVALLDSG-QARCELALNTTEAGLEDRDVILGLRPEQI 291 G P R+Q + G +L+SG C G V + LRP+ + Sbjct: 236 GQGVFVPGTVLAGNRVQMELG----ILESGVPVECSAGCGVCGKGC---GVDILLRPDDV 288 Query: 292 MLAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQ-VGETLTLQFD 350 + D S ++A V+ G D L ++L L P +GE + ++ D Sbjct: 289 V-----HDDKSPLQAAVEHKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIGIRLD 343 Query: 351 PSKVLLFDAN 360 V+ F N Sbjct: 344 VDHVVAFKQN 353 Lambda K H 0.318 0.135 0.382 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: 326 Number of extensions: 14 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: 386 Length of database: 356 Length adjustment: 30 Effective length of query: 356 Effective length of database: 326 Effective search space: 116056 Effective search space used: 116056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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