Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate H281DRAFT_01451 H281DRAFT_01451 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Burk376:H281DRAFT_01451 Length = 415 Score = 304 bits (778), Expect = 3e-87 Identities = 165/370 (44%), Positives = 233/370 (62%), Gaps = 20/370 (5%) Query: 10 NKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADI 69 N T G ++N++L + GEF++L+GPSGCGKSTL++ IAGL ++ G+I + D+ Sbjct: 52 NLTIRLGGNTVIENLDLDVQPGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIAGEDM 111 Query: 70 SGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLL 129 + PKDR IA+VFQSYALYPTMSV N++F L+I P AEI VAR +++LQ+ LL Sbjct: 112 TWADPKDRRIALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARAAEMLQLGPLL 171 Query: 130 SRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTT 189 RKP QLSGGQ+QRVA+GRA+ R ++LFDEPLSNLDAKLR E+R E+K +HQRL T Sbjct: 172 KRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQRLGATM 231 Query: 190 VYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQ 249 +YVTHDQ+EAM L ++AVM+ G IQQFGTP ++Y PANLFVA+F+G+P MN + L+ Sbjct: 232 IYVTHDQVEAMMLATRMAVMRGGAIQQFGTPAEVYARPANLFVATFLGTPAMNLVNGTLE 291 Query: 250 RKDGRL-------------LALLD-SGQARCELPLGMQDAGLEDREVILGIRPEQIILAN 295 ++DG L A +D SG+++ + R +LG+R E + + Sbjct: 292 QRDGALHFCTEQWRLDVSNYAFVDRSGESQPQ-----SQPQSPPRPCVLGVRAEDVRIGP 346 Query: 296 GEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVL 355 + G A++ + EP G +V+++ + ++ G+TL D V Sbjct: 347 TQGEGAGE-HAKISLVEPMGNHRVVWLDYHGVQIASIDQSKTPVMPGDTLAFSLDSTHVS 405 Query: 356 LFDAKTGERL 365 LFDA +G RL Sbjct: 406 LFDAASGARL 415 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: 437 Number of extensions: 15 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: 415 Length adjustment: 31 Effective length of query: 355 Effective length of database: 384 Effective search space: 136320 Effective search space used: 136320 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