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) >FitnessBrowser__Cola:Echvi_1022 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:
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