Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 281 bits (720), Expect = 1e-80 Identities = 151/325 (46%), Positives = 212/325 (65%), Gaps = 32/325 (9%) Query: 1 MSALEIRNIRKRYGEV----ETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPS 56 M++L +RNI KRYG + + G++ ++ GEF+V++G SGCGKSTLL ++AGL E S Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 GGDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRD 116 GG++ IG+R V + P RDIAMVFQ+YALYP+++ N+ +GL++ +VP+ E V Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 117 TARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTEL 176 A++L++ +LL+RKP +LSGGQRQRVA+GRA+VR PQVFLFDEPLSNLDAKLR + R E+ Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 177 KRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGS 236 ++LH+ L T ++VTHDQ+EAMTLA R+ VM G +EQ P+EVY PAT +VA F+GS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 237 PPMNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRL 296 PPMN+L A A +GIRPE L + ++ Sbjct: 241 PPMNLL------------------------KNAPGAQPGTILGIRPEHLDV----RSEGW 272 Query: 297 TASVEVVELTGPELVTTATVGSQRI 321 +VE VEL G E + + +++ Sbjct: 273 AVTVETVELLGAERLIYGRINGEQV 297 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: 334 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: 360 Length of database: 334 Length adjustment: 29 Effective length of query: 331 Effective length of database: 305 Effective search space: 100955 Effective search space used: 100955 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