Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate BPHYT_RS29175 BPHYT_RS29175 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS29175 Length = 390 Score = 311 bits (796), Expect = 3e-89 Identities = 165/356 (46%), Positives = 227/356 (63%), Gaps = 6/356 (1%) Query: 10 NKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADI 69 N T G ++N++L + GEF++L+GPSGCGKSTL++ IAGL ++ G+I + D+ Sbjct: 41 NLTIQLGANTVIENLDLDVQAGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIAGEDM 100 Query: 70 SGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLL 129 + PKDR IA+VFQSYALYPTMSV N++F L+I P AEI VAR S++LQ+ LL Sbjct: 101 TWADPKDRRIALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARASEMLQLGPLL 160 Query: 130 SRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTT 189 RKP QLSGGQ+QRVA+GRA+ R ++LFDEPLSNLDAKLR E+R E+K +HQRL T Sbjct: 161 KRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQRLGATM 220 Query: 190 VYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQ 249 +YVTHDQ+EAMTL ++AVM+ G+IQQFGTP ++Y P NLFVA+F+G+P MN I RL+ Sbjct: 221 IYVTHDQVEAMTLATRMAVMRGGVIQQFGTPAEVYARPDNLFVATFLGTPAMNLIKGRLE 280 Query: 250 RKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGLPTIRAEVQ 309 +DG L + + + +LG+R E + LA G + A+V Sbjct: 281 TRDGALHFCTEHWRLDVS-RYPFRTTPANGLPCVLGVRAEDVRLAEGASE-----HAKVS 334 Query: 310 VTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAKTGERL 365 + EP G +++++ + +V A+G+ FD V LFD G RL Sbjct: 335 LVEPMGNHRVIWLDYHGVQVASIDQTKTPLAIGDAAAFSFDSTHVSLFDEAGGARL 390 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: 441 Number of extensions: 14 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: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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