Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 325 bits (832), Expect = 2e-93 Identities = 174/369 (47%), Positives = 239/369 (64%), Gaps = 8/369 (2%) Query: 1 MATLELRNVNKTYGPGLP--DTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETIS 58 MA + L+ V KTYG G D + I+ +I DGEF+++VGPSGCGKSTL+ +AGLE IS Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 GGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVAR 118 G I++ D ++ + PK+RDIAMVFQ+YALYP M+V N+A+GLKI+ + +EID V R Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 + +L++ LL R P QLSGGQ+QRVAMGRA+ R+P ++LFDEPLSNLDAKLRV+MR E+ Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGS 238 + +H L+TT++YVTHDQ+EAMTLG ++ VM G+ +Q GTP ++Y PA FVASFIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 239 PPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQII-LANGE 297 PPMN + +L DG + G A L L G +E ILG+RPE ++ + +G Sbjct: 241 PPMNLLQGKLS-ADGASFE-VSKGNASDILRLPQPLTGAAGQERILGVRPEHLLPILDGS 298 Query: 298 ANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLF 357 A + EV++ E G + LV + R +V G+ + F V F Sbjct: 299 A---AQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAGDVHWF 355 Query: 358 DAKTGERLG 366 D K+ R+G Sbjct: 356 DVKSTRRIG 364 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: 385 Number of extensions: 22 Number of successful extensions: 4 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: 364 Length adjustment: 30 Effective length of query: 356 Effective length of database: 334 Effective search space: 118904 Effective search space used: 118904 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