Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_086511770.1 BZY95_RS20650 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_002151265.1:WP_086511770.1 Length = 422 Score = 286 bits (732), Expect = 7e-82 Identities = 166/366 (45%), Positives = 225/366 (61%), Gaps = 16/366 (4%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 + L V+K +G + I + GEF+IL+GPSGCGKST + IAGLE + G I Sbjct: 31 IRLEAVSKRWGDTA--AVDAIGFDVAPGEFVILLGPSGCGKSTTLRMIAGLEQATAGRIE 88 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + D++ + P DR I+MVFQSYAL+P +SV DNI FGL+ RK+P AE E +ARV++L+ Sbjct: 89 IGGRDVTHLPPGDRGISMVFQSYALFPHLSVADNIVFGLRSRKVPKAERRERLARVAQLV 148 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 +E L RKP QLSGGQ+QRVA+ RA+ I L DEPLSNLDA+LR EMR E+K + Q Sbjct: 149 DLEAYLERKPAQLSGGQRQRVALARAIISEHPICLMDEPLSNLDARLRGEMRREIKALQQ 208 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 RL T +YVTHDQ+EAM++GD+V +M+DG I Q TP ++Y PA+ F A FIGSP MN Sbjct: 209 RLGMTVIYVTHDQVEAMSMGDRVILMQDGRIVQDATPSELYERPASAFAAGFIGSPAMNL 268 Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGLPT 303 + L DG ++ G+ RC + A E + LG+RPE+I L +A G+P Sbjct: 269 VTLS-AAADGAVI----DGEPRCSV------APHEAKGHWLGLRPEEIRLLPADAPGVP- 316 Query: 304 IRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAKTGE 363 AEV E G D++V + + ++ RL + A G LQ+ FDA G+ Sbjct: 317 --AEVIDAEYLGADSIVRLKVGSQQLRARLDGRPSLAAGSPCRLQWRRETAHFFDASDGQ 374 Query: 364 RLGVAG 369 RL + G Sbjct: 375 RLAITG 380 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: 459 Number of extensions: 22 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: 422 Length adjustment: 31 Effective length of query: 355 Effective length of database: 391 Effective search space: 138805 Effective search space used: 138805 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