Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 330 bits (846), Expect = 4e-95 Identities = 177/365 (48%), Positives = 243/365 (66%), Gaps = 9/365 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA L+L+ V K++ G +K + L + DGEF+++VGPSGCGKSTL+ +AGLE ++ G Sbjct: 1 MAGLKLQAVTKSWD-GKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEG 59 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 I ++D ++ M PKDR IAMVFQ+YALYP MSV +N+A+GLKIR M +I E V + Sbjct: 60 DIWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAA 119 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L+++ LL R+P +LSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDAKLRV+MR E++ Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQ 179 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H+RLKTT++YVTHDQ+EAMTL +V VM G+ +Q GTP ++Y PA+LFVASFIGSP Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPA 239 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 MN + R+ + LD G ELPL R++ LGIRPE I L++ G Sbjct: 240 MNLLTGRVNNEGTHF--ELDGG---IELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEGG 294 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAK 360 +P + + E G D L + K+ RLA P G TL L ++ LFD + Sbjct: 295 VPMV---MDTLEILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDGE 351 Query: 361 TGERL 365 TG+R+ Sbjct: 352 TGQRV 356 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: 399 Number of extensions: 15 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 ( 7.4 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