Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::Smeli:SMc03065 (362 letters) >lcl|FitnessBrowser__Cola:Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components Length = 345 Score = 149 bits (377), Expect = 8e-41 Identities = 106/340 (31%), Positives = 171/340 (50%), Gaps = 27/340 (7%) Query: 19 IHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERV----NDVPPSK 74 + I ++I+EG VG +G GK+TLL++IAGLE G++ G+ + + +P ++ Sbjct: 21 VKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQTIVNGKSALPANQ 80 Query: 75 RGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA-DMLQLTPYLDRL--- 130 R + ++FQ YAL+P MT+ +N+ RE+ + R R A D L L D Sbjct: 81 REVGVIFQEYALFPQMTLLENV-------REALHQESRNARQIAMDSLALAGLEDSFSAY 133 Query: 131 PKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIY 190 P LS GQRQR A+ RA+ PK+ L D+P +LD + +I + + + T I Sbjct: 134 PHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIV-KATGITAIV 192 Query: 191 VTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITAT 250 +H +A++LAD I +L G ++QVG P+E+Y++PAN +VA F G N + AT T Sbjct: 193 ASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFFGK--RNELLATPTED 250 Query: 251 GQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIVEALGE 310 G + P +AS K R ED ++ ++ + G V+ V G+ Sbjct: 251 GFYAGFGF-------IPHPDSASYTDKVKIL-FRSEDAKIKKSTEQPLSGIVTRVLFYGD 302 Query: 311 VTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKL 350 ++ +E + I PG G ++ FT DK ++ Sbjct: 303 HQIVKLEDDEGKQISIKAAPG-RNFEMGARMFFTIDKFEI 341 Lambda K H 0.320 0.137 0.387 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: 266 Number of extensions: 14 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: 362 Length of database: 345 Length adjustment: 29 Effective length of query: 333 Effective length of database: 316 Effective search space: 105228 Effective search space used: 105228 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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