Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate PP_5179 PP_5179 spermidine/putrescine ABC transporter - ATP binding subunit
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Putida:PP_5179 Length = 380 Score = 179 bits (454), Expect = 1e-49 Identities = 103/255 (40%), Positives = 151/255 (59%), Gaps = 13/255 (5%) Query: 23 KYIEKGLSKEQIL-------EKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLN 75 K +E G +Q+L +K ++ V D SL I +GEIF ++G SGSGKST++R+L Sbjct: 10 KALEGGQQPKQVLVKIDRVTKKFDETVAVDDVSLEIRKGEIFALLGGSGSGKSTLLRMLA 69 Query: 76 RLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAG 135 P+ G++ +DGVDI + E + I M+FQS+AL PHMTV N AFG++ Sbjct: 70 GFERPSEGRIFLDGVDITDMPPYE------RPINMMFQSYALFPHMTVAQNIAFGLQQDK 123 Query: 136 IAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSAL 195 + E + + L+ V + YA P +LSGG RQRV LAR+LA P +LL+DE AL Sbjct: 124 MPKAEIDARVAEMLKLVHMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 183 Query: 196 DPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNN 255 D +R++MQ ELV++ + T V ++HD +EAM + RIAIM G + Q+G+P +I Sbjct: 184 DKKLRSQMQLELVEIIERVGVTCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYET 243 Query: 256 PANDYVRTFFRGVDI 270 P + V F V++ Sbjct: 244 PTSRLVCEFIGNVNL 258 Lambda K H 0.319 0.137 0.378 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: 327 Number of extensions: 15 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: 400 Length of database: 380 Length adjustment: 30 Effective length of query: 370 Effective length of database: 350 Effective search space: 129500 Effective search space used: 129500 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 (21.8 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