Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate AO356_14385 AO356_14385 spermidine/putrescine ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_14385 Length = 374 Score = 270 bits (689), Expect = 6e-77 Identities = 140/291 (48%), Positives = 194/291 (66%), Gaps = 1/291 (0%) Query: 17 LVQLAGIRKCFDGKE-VIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75 LV G++K +DG+ ++ L+L I GEFLTLLGPSG GKTT L ++AG ET +G I+ Sbjct: 14 LVSFRGVQKSYDGENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIL 73 Query: 76 LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMV 135 L I +VP R + VFQ+YALFPHMTV EN+AF L ++ ++++ RV L MV Sbjct: 74 LAGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKSDVSDRVKRVLSMV 133 Query: 136 QLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQR 195 QL++FAQR P QLSGGQQQRVA+ARA+V +P+L+L+DE L ALD +LR+ MQ E+K L + Sbjct: 134 QLDSFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQ 193 Query: 196 KLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFN 255 +LG+T V+VTHDQ EALTMSDR+ V G I+Q PR +YEEPKN FVA FIGE N N Sbjct: 194 RLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRTLYEEPKNTFVANFIGENNRLN 253 Query: 256 ATVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEIND 306 + ++ + G + +PG+ + + +RPE + + +++ Sbjct: 254 GRLHSHTGDRCLVELARGEKVEALAVNVGQPGEPVTLSIRPERVSLNGVSE 304 Lambda K H 0.319 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: 353 Number of extensions: 14 Number of successful extensions: 1 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: 378 Length of database: 374 Length adjustment: 30 Effective length of query: 348 Effective length of database: 344 Effective search space: 119712 Effective search space used: 119712 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 (21.7 bits) S2: 50 (23.9 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