Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Burk376:H281DRAFT_05701 Length = 362 Score = 318 bits (816), Expect = 1e-91 Identities = 176/360 (48%), Positives = 237/360 (65%), Gaps = 6/360 (1%) Query: 1 MSALEIRNIRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 M+AL ++ ++K Y G+ L GID+ + GEF+V++G SGCGKSTLL ++AGL S G Sbjct: 1 MAALTLQGVKKTYDGKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERISEGT 60 Query: 60 ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119 I I + V + PKDR+IAMVFQ+YALYP++SVA N+G+ L++ V +A+ + V A+ Sbjct: 61 ISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAQRVNAAAQ 120 Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179 +L++E LL RKP +LSGGQRQRVA+GRA+VR P VFLFDEPLSNLDA+LR++MR E++RL Sbjct: 121 ILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180 Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239 H L TT +YVTHDQIEAMTLA R+ VM G EQ+ AP EVY+RPAT++VAGF+GSP M Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFIGSPGM 240 Query: 240 NILDAEMTANG--LKIEGCEEVLPLP--AAFNGAAWAGRRVKVGIRPEALRLAAGSEAQR 295 N+L+ ++ +G + G LPL A+ GR +GIRPE + ++A Sbjct: 241 NLLEGRVSDDGSTFDVAGNGPQLPLAGVASIGREVAKGREWTLGIRPEHMS-PGQADAPH 299 Query: 296 LTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGR 355 T +V+ EL G + + G +TA LP G A LH FDP SGR Sbjct: 300 TTLTVDSCELLGADNLAHGRWGKHDVTARLPHAHRPAAGEALQVALPARHLHFFDPASGR 359 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: 383 Number of extensions: 18 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: 362 Length adjustment: 29 Effective length of query: 331 Effective length of database: 333 Effective search space: 110223 Effective search space used: 110223 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