Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate Ac3H11_4180 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4180 Length = 367 Score = 257 bits (657), Expect = 3e-73 Identities = 133/244 (54%), Positives = 174/244 (71%), Gaps = 1/244 (0%) Query: 16 PLVQLAGIRKCFDGKE-VIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRI 74 PLV+ G++K +DG++ V+ LDL I GEFL+LLGPSG GKTT L ++AG E+ +G I Sbjct: 7 PLVRFTGVQKTYDGEQLVVRALDLDIQRGEFLSLLGPSGSGKTTTLMMLAGFESPTAGDI 66 Query: 75 MLDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRM 134 +LD + IT P R VFQ+YALFPH+TV ENVA+ L ++K P AE RV +AL M Sbjct: 67 LLDGKQITRTPPHKRNFGMVFQNYALFPHLTVGENVAYPLTVRKVPKAEQAERVKKALDM 126 Query: 135 VQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQ 194 V+L A R P +LSGGQQQRVA+ARA+V P+L+L+DE L ALD +LR+ MQ ELK L Sbjct: 127 VRLTGMADRLPARLSGGQQQRVALARALVFNPQLVLMDEPLGALDKQLREHMQIELKELH 186 Query: 195 RKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMF 254 R+LG+TFV+VTHDQ EALTMSDR+ V +G I+Q +YE P N FVAGF+G+ + Sbjct: 187 RQLGVTFVYVTHDQGEALTMSDRVAVFNEGVIQQLADVESLYETPSNRFVAGFVGDSTVL 246 Query: 255 NATV 258 + T+ Sbjct: 247 SGTL 250 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: 338 Number of extensions: 13 Number of successful extensions: 2 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: 367 Length adjustment: 30 Effective length of query: 348 Effective length of database: 337 Effective search space: 117276 Effective search space used: 117276 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