Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 332 bits (852), Expect = 7e-96 Identities = 176/365 (48%), Positives = 243/365 (66%), Gaps = 10/365 (2%) Query: 1 MSALEIRNIRKRYGE----VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPS 56 M+A+ ++ +RK YG V+ + GID + GEF+V++G SGCGKSTLL ++AGL E S Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 GGDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRD 116 G I+IG+R V + PK+RDIAMVFQ+YALYP+++V +N+ +GL+++ + ++E D V+ Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 117 TARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTEL 176 A +L++ LL+R P QLSGGQRQRVA+GRA+VR P VFLFDEPLSNLDAKLR++MR E+ Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 177 KRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGS 236 ++LH LRTT +YVTHDQ+EAMTL R+ VM G EQ+ P EVY RPAT +VA F+GS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 237 PPMNILDAEMTANGLKIE----GCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSE 292 PPMN+L +++A+G E ++L LP GA AG+ +G+RPE L Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGA--AGQERILGVRPEHLLPILDGS 298 Query: 293 AQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPE 352 A +L+ VE+VE G EL+ A G Q + P V G +F +H FD + Sbjct: 299 AAQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAGDVHWFDVK 358 Query: 353 SGRSL 357 S R + Sbjct: 359 STRRI 363 Lambda K H 0.320 0.136 0.385 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: 362 Number of extensions: 14 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: 360 Length of database: 364 Length adjustment: 29 Effective length of query: 331 Effective length of database: 335 Effective search space: 110885 Effective search space used: 110885 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 (21.8 bits) S2: 49 (23.5 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