Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_085637869.1 MGEO_RS12095 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_002115805.1:WP_085637869.1 Length = 365 Score = 345 bits (884), Expect = 2e-99 Identities = 191/362 (52%), Positives = 242/362 (66%), Gaps = 10/362 (2%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 LE+RN+ K++G D LKNI + ID G+F++LVGPSGCGKSTL+NCIAGLE I+ G I Sbjct: 5 LEIRNLYKSFGS--VDVLKNINVSIDPGDFVVLVGPSGCGKSTLLNCIAGLEPITRGTIE 62 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + D++ + +DRDIAMVFQSYALYPTMSV NI FG+++R + ++++A V++LL Sbjct: 63 IAGEDMTDVPARDRDIAMVFQSYALYPTMSVAQNITFGMRVRGIDRETREKKLAEVARLL 122 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 +IE LL R+P QLSGGQ+QRVAMGRAL R PK++LFDEPLSNLDAKLRVEMR E++ +HQ Sbjct: 123 KIEPLLDRRPKQLSGGQRQRVAMGRALVREPKLFLFDEPLSNLDAKLRVEMRAEIRRLHQ 182 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 RL TT VYVTHDQIEAMTL K+AVMK G + Q G PK+IY P N+FVA FIGSP MN Sbjct: 183 RLSTTIVYVTHDQIEAMTLATKIAVMKAGEVHQIGKPKEIYERPVNMFVADFIGSPSMNL 242 Query: 244 IPLRLQRKDGRL-LALLDSGQARCELPLGMQDAGLED--REVILGIRPEQIILANGEANG 300 P R R DG L + SG A PL ++D D +V++G+RPE I AN + Sbjct: 243 FPARATRVDGHTRLEVSRSGGA----PLVLKDPRQFDLPSQVVVGLRPEDIAEANLRSGP 298 Query: 301 -LPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359 + T + E +G DT V L V R + G + FD AKVL F Sbjct: 299 FVQTGTCRIDFIEQSGSDTYVLTKLGGVDVFGRFHTETHVEEGMEIDFAFDLAKVLFFHP 358 Query: 360 KT 361 +T Sbjct: 359 ET 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: 419 Number of extensions: 23 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: 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 24 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