Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 214 bits (546), Expect = 3e-60 Identities = 114/270 (42%), Positives = 174/270 (64%), Gaps = 11/270 (4%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 + L+ + K +G + ++ +L I+ GE + L+GPSGCGK+T++ IAGLET + G I Sbjct: 45 VRLQGLMKRFGKTV--AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIY 102 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + I+ R++ M+FQ+YAL+P ++ +N+AFGLK R + E+ E+VA+ +++ Sbjct: 103 IKGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMV 162 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 ++ + R QLSGGQQQR+A+ RA+ P + L DEPLS LD KLR EMR E+ + Q Sbjct: 163 RLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQ 222 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 +L TT++VTHDQ EA+++ +K+ VMKDG QQ GTP+D+Y+ P N FVA F+G NF Sbjct: 223 QLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANF 280 Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQ 273 D R+L +LD+ Q R + G++ Sbjct: 281 F-------DARVLEVLDNDQVRVRIAEGLE 303 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: 379 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: 406 Length adjustment: 31 Effective length of query: 355 Effective length of database: 375 Effective search space: 133125 Effective search space used: 133125 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 Apr 09 2024. 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