Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 251 bits (640), Expect = 3e-71 Identities = 142/302 (47%), Positives = 191/302 (63%), Gaps = 4/302 (1%) Query: 28 DGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRI-MLDNEDITHVPA 86 DG + LDL I GE + LLGPSGCGKTT LR+IAGLE D+G + M + D+T +P Sbjct: 18 DGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGDNDVTPLPI 77 Query: 87 ENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPH 146 E R V VFQSYALFP+MTV EN+A+GLR+++ AA RV E L M+ L FA+R+ Sbjct: 78 EQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRID 137 Query: 147 QLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTH 206 QLSGGQ+QRVA+ARA+ +PR+LLLDE L+ALD KLR ++ ++ L R L IT V+VTH Sbjct: 138 QLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSLHITAVYVTH 197 Query: 207 DQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVIERLDEQR 266 DQ EA+ + DRI+VM GRI Q GTP++IY P N FVA FIG +N A + D R Sbjct: 198 DQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGTMNRLPAVL--EADAWR 255 Query: 267 VRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIGYVRERNYKGMT 326 V + R + A P + +L RPED+ + + D + ++ + NY + Sbjct: 256 VPGGLVPRH-GTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTALFLGNYTRLL 314 Query: 327 LE 328 ++ Sbjct: 315 VD 316 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: 291 Number of extensions: 9 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: 357 Length adjustment: 30 Effective length of query: 348 Effective length of database: 327 Effective search space: 113796 Effective search space used: 113796 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