Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 311 bits (798), Expect = 1e-89 Identities = 171/356 (48%), Positives = 235/356 (66%), Gaps = 11/356 (3%) Query: 1 MSALEIRNIRKRYGE-VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 M+ + + ++RK Y VE + +E GEF+VL+G SGCGKSTLL +IAGL + + G Sbjct: 1 MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60 Query: 60 ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119 + IG+R V V P DRDIAMVFQ+YALYP+++V +NI +GL+ R+ P+AE + V + A+ Sbjct: 61 LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAK 120 Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179 +L +E LDRKPSQLSGGQRQRVA+GRA+VR+P +FLFDEPLSNLDAKLR +MR E+K L Sbjct: 121 MLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKAL 180 Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239 + L T +YVTHDQ+EAMT+A RI V+ GRIEQ+ P E+Y PA+++VA F+G+PPM Sbjct: 181 QRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPM 240 Query: 240 NILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTAS 299 N+LDA + + + + L + GA VK+GIRPE ++L A L Sbjct: 241 NLLDATIANGQVTLPDGVSMGALDTSAQGA------VKLGIRPEDVQLVAEG---GLAID 291 Query: 300 VEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGR 355 VE++E G + +G Q T + V G+ H + D A+ LFD ESG+ Sbjct: 292 VELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPGT-HQISVDPAAICLFDAESGQ 346 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: 343 Number of extensions: 15 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: 348 Length adjustment: 29 Effective length of query: 331 Effective length of database: 319 Effective search space: 105589 Effective search space used: 105589 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