Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 162 bits (410), Expect = 1e-44 Identities = 94/222 (42%), Positives = 133/222 (59%), Gaps = 11/222 (4%) Query: 36 LDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDI------THVPAENR 89 + LTI+ GEF+TL GPSG GKT+ LR+I+GL T D G + ++ E +V R Sbjct: 21 IKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDASFGKNVSPGRR 80 Query: 90 YVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPHQLS 149 + +FQ Y+LFP+MTV EN+AF L+ K A +ME L + L P LS Sbjct: 81 KLGYLFQDYSLFPNMTVKENIAFALKNAKDKAY-----LMELLESMGLLHLQDTLPKHLS 135 Query: 150 GGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTHDQE 209 GGQQQRVA+ARA+ KP +LLLDE LSALD +R+++Q + A+ RK +T + V+HD Sbjct: 136 GGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYALTTILVSHDAG 195 Query: 210 EALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEI 251 E + +SDRI+ + G++ + TP+E + F GEI Sbjct: 196 EIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQFQGEI 237 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: 256 Number of extensions: 13 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: 290 Length adjustment: 28 Effective length of query: 350 Effective length of database: 262 Effective search space: 91700 Effective search space used: 91700 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: 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