Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 176 bits (445), Expect = 1e-48 Identities = 95/231 (41%), Positives = 143/231 (61%), Gaps = 8/231 (3%) Query: 35 QLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSG------RIMLDNEDITHVPAEN 88 + D + GEFL ++GPSG GKTT+LR+IAGL ++G RI D+++ H +N Sbjct: 20 EADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQN 79 Query: 89 RYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPHQL 148 R++ V Q + LFP ++ N+ L P+ E PR + AL V L R P QL Sbjct: 80 RHIGFVPQHFGLFPKLSALGNIMAAL--DHLPSQERRPRALAALEKVNLHGLTDRLPSQL 137 Query: 149 SGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTHDQ 208 SGGQ+QRVA+ARA+ +PR+LLLDE SA+D + R+++ EL L+ +L I + VTHD Sbjct: 138 SGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDL 197 Query: 209 EEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVI 259 EAL ++D ++++ G + Q GTP++++ P+N VA +G N+FNA V+ Sbjct: 198 NEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMGLRNIFNAHVV 248 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: 290 Number of extensions: 12 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: 378 Length of database: 370 Length adjustment: 30 Effective length of query: 348 Effective length of database: 340 Effective search space: 118320 Effective search space used: 118320 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