Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 319 bits (818), Expect = 7e-92 Identities = 174/366 (47%), Positives = 235/366 (64%), Gaps = 8/366 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA ++L + K YG + I+L IDDGEF++LVGPSGCGKSTLM +AGLE ISGG Sbjct: 1 MAAVQLSGIFKRYGD--TQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 +++ + ++P+ R+I+MVFQSYALYP +SV +NIAFG +IRK +A + + Sbjct: 59 DLMIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L + L R P LSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDAKLRV+MRTE+K Sbjct: 119 KMLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKA 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQRLK T +YVTHDQIEAMT+ D++ VM G I+Q G P ++Y++PANLFVASF+GSP Sbjct: 179 LHQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPS 238 Query: 241 MNFIP-LRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEAN 299 MNF + R G+ LAL +G L G + + +V LG+RPE I Sbjct: 239 MNFAEGVIASRAQGQGLALNLTGGGEIVLE-GAPASAVVGAKVTLGVRPEHI----ETMT 293 Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359 P EV+V EPTG +T ++ + + C G+ +TL+ + LFD Sbjct: 294 PTPDATMEVEVVEPTGAETHLYGKIGGSTWCVTTRQRSKIEPGQRVTLRLPAEHIHLFDT 353 Query: 360 KTGERL 365 ++G RL Sbjct: 354 ESGRRL 359 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: 394 Number of extensions: 13 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: 360 Length adjustment: 30 Effective length of query: 356 Effective length of database: 330 Effective search space: 117480 Effective search space used: 117480 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