Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS17470 Length = 362 Score = 297 bits (761), Expect = 3e-85 Identities = 173/368 (47%), Positives = 230/368 (62%), Gaps = 12/368 (3%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA L L+ V KTY G L I++ + DGEF+++VGPSGCGKSTL+ +AGLE IS G Sbjct: 1 MAALTLQGVKKTYD-GKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEG 59 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 +I + ++ + PKDR+IAMVFQ+YALYP MSV +N+ + LKI + A+I + V + Sbjct: 60 SISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAA 119 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L++E LL RKP +LSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDA+LRV+MR E++ Sbjct: 120 QILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQR 179 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H RL TT++YVTHDQIEAMTL +V VM G +Q G P ++Y PA +FVASFIGSP Sbjct: 180 LHARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPG 239 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPL-GMQDAGLE---DREVILGIRPEQIILANG 296 MN + R+ DG + +G +LPL + G E RE LGIRPE ++ G Sbjct: 240 MNLLEGRVS-DDGAFFEVAGNGP---KLPLTDVASIGREVARGREWTLGIRPEH--MSPG 293 Query: 297 EANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLL 356 +A+ P V E G D L V RL PA GE L + + Sbjct: 294 QADA-PHATLTVDSCELLGADNLAHGRWGKHDVTVRLPHAHRPAAGEALQVALPARHLHF 352 Query: 357 FDAKTGER 364 FD +G R Sbjct: 353 FDPASGRR 360 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: 412 Number of extensions: 13 Number of successful extensions: 2 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: 362 Length adjustment: 30 Effective length of query: 356 Effective length of database: 332 Effective search space: 118192 Effective search space used: 118192 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