Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate PP_0114 PP_0114 methionine ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Putida:PP_0114 Length = 335 Score = 181 bits (459), Expect = 3e-50 Identities = 96/245 (39%), Positives = 154/245 (62%), Gaps = 2/245 (0%) Query: 48 SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKK 107 SL IE+G++F ++G SG+GKSTM+RL+NRL EP+ G +++DG D+ + ++LR R++ Sbjct: 25 SLTIEDGQVFGLIGHSGAGKSTMLRLINRLEEPSGGTIIVDGEDVTAFNASQLRGFRQQ- 83 Query: 108 IAMVFQSFALMPHMTVLDNTAFGMELAG-INAEERREKALDALRQVGLENYAHSYPDELS 166 + M+FQ F L+ TV DN A + LAG ++ E ++ + L +VGL ++A YP +LS Sbjct: 84 VGMIFQHFNLLASKTVADNVALPLALAGELSRSEIDKRVTELLARVGLSDHAKKYPAQLS 143 Query: 167 GGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLD 226 GG +QRVG+ARAL+ NP ILL DEA SALDP + L ++ + + TIV I+H++D Sbjct: 144 GGQKQRVGIARALSTNPKILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMD 203 Query: 227 EAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPNG 286 R+ DR+A+M G++V+ G+ E+ +P + + F + + +D P Sbjct: 204 VIRRVCDRVAVMDAGQIVEQGSVAEVFLHPQHPTTKRFVQEDEQVDEGEQRDDFAHVPGR 263 Query: 287 LIRKT 291 ++R T Sbjct: 264 IVRLT 268 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: 280 Number of extensions: 16 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: 400 Length of database: 335 Length adjustment: 30 Effective length of query: 370 Effective length of database: 305 Effective search space: 112850 Effective search space used: 112850 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