Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 277 bits (708), Expect = 4e-79 Identities = 156/361 (43%), Positives = 228/361 (63%), Gaps = 10/361 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA+++L+NV K +G + K+I L I +GEF++ VGPSGCGKSTL+ IAGLETI+ G Sbjct: 1 MASVQLQNVTKAWGEVVVS--KDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + + + ++ P +R + MVFQSYALYP +SV +N++FGLK+ I++ V +V+ Sbjct: 59 DLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++LQ+ HLL RKP LSGGQ+QRVA+GR L P ++L DEPLSNLDA LRV+MR E+ Sbjct: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H+RL T +YVTHDQ+EAMTL DK+ V+ G + Q G P ++Y+ PA+ FVA FIGSP Sbjct: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238 Query: 241 MNFIPLRLQRK--DGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEA 298 MNF+P+++ D + L + + LP+ +D + + LGIRPE +L + A Sbjct: 239 MNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQV-GANMSLGIRPEH-LLPSDIA 296 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTK--VCCRLAPDVAPAVGETLTLQFDPAKVLL 356 + + + EVQV E G +T + + + + + R V G T + P + L Sbjct: 297 DVI--LEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHL 354 Query: 357 F 357 F Sbjct: 355 F 355 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: 371 Number of extensions: 15 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: 371 Length adjustment: 30 Effective length of query: 356 Effective length of database: 341 Effective search space: 121396 Effective search space used: 121396 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