Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate BPHYT_RS09400 BPHYT_RS09400 spermidine/putrescine ABC transporter ATPase
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS09400 Length = 359 Score = 185 bits (469), Expect = 2e-51 Identities = 100/256 (39%), Positives = 151/256 (58%), Gaps = 10/256 (3%) Query: 29 LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88 L+ + I ++ G ++ LA+E GE+ ++G SG GK+T ++++ I PT G++L+D Sbjct: 4 LTLQGISKRYGDFTAIEQLDLAVERGELLSLLGPSGCGKTTTLQMVAGFITPTTGRILLD 63 Query: 89 GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDA 148 G DI ++ I +VFQS+AL PHMTV N FG+E+ + +ER E+ +A Sbjct: 64 GRDITN------ERPEKRGIGVVFQSYALFPHMTVAGNVGFGLEMRKVRRKERDERVAEA 117 Query: 149 LRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELV 208 L V L+ H YP ELSGG RQRV +ARA+A+ P++LL+DE S LD +R EM EL Sbjct: 118 LSLVRLKGLGHRYPKELSGGQRQRVAIARAIAMQPELLLLDEPMSNLDAKLREEMHIELR 177 Query: 209 KLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268 +Q + T + ++HD EAM + DRIA+M G + Q+ TP + PA + TF + Sbjct: 178 AIQKRLGITTILVTHDQVEAMTMSDRIAVMHRGVIAQLSTPYDAYERPATPFASTF---L 234 Query: 269 DISQVFSAKDIARRTP 284 + FS ++ RR P Sbjct: 235 GRTNAFSG-EVLRRNP 249 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: 338 Number of extensions: 11 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: 359 Length adjustment: 30 Effective length of query: 370 Effective length of database: 329 Effective search space: 121730 Effective search space used: 121730 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