Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Pf6N2E2_1960 Various polyols ABC transporter, ATP-binding component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1960 Length = 365 Score = 280 bits (717), Expect = 4e-80 Identities = 156/359 (43%), Positives = 224/359 (62%), Gaps = 9/359 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MATL++ N+ K + GL +K I+L++ D EF++ VGPSGCGKSTL+ IAGLE ++ G Sbjct: 1 MATLKIENLKKGF-EGL-SIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 I +D DI+ ++P RD+AMVFQ+YALYP M+VR N++F L + +++ +VA + Sbjct: 59 TIELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L++ LL RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+ R E+ Sbjct: 119 RILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H+ L+ T +YVTHDQ+EAMTL KV V+ G I+Q G+P ++Y++PANLFVA F+G+P Sbjct: 179 LHKELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPK 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 M F+ + + + + +P + + V +GIRPE + L+ A G Sbjct: 239 MGFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSV-GQSVTIGIRPEHLTLS---AEG 294 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLND-TKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358 + VTE G DT VN++ + R+ D L D A LFD Sbjct: 295 --QVPVTTDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFD 351 Lambda K H 0.319 0.138 0.393 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: 388 Number of extensions: 19 Number of successful extensions: 1 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: 365 Length adjustment: 30 Effective length of query: 356 Effective length of database: 335 Effective search space: 119260 Effective search space used: 119260 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 (21.7 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