Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate BPHYT_RS22015 BPHYT_RS22015 spermidine/putrescine ABC transporter ATPase
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS22015 Length = 363 Score = 185 bits (469), Expect = 2e-51 Identities = 94/236 (39%), Positives = 143/236 (60%), Gaps = 6/236 (2%) Query: 29 LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88 L+ + + G V D +L++E+GE ++G SG GK+T ++++ +E T G++ +D Sbjct: 4 LTLTDVTKSFGDLQAVADVNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVETTHGRITLD 63 Query: 89 GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDA 148 G DI + ++ + +VFQS+AL PHM+V DN FG+E+ I+ ER+E+ +A Sbjct: 64 GRDITHMKP------NKRGLGIVFQSYALFPHMSVADNVGFGLEMRNIDKAERKERIREA 117 Query: 149 LRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELV 208 L V L+ AH +P ELSGG RQRV LARA+ I P +LL+DE S LD +R +MQ EL Sbjct: 118 LSLVRLDTLAHRFPRELSGGQRQRVALARAIVIAPPVLLLDEPMSNLDAKLREDMQFELR 177 Query: 209 KLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 +Q K T + ++HD EA+ I DR+ +M+ G + Q+ TP E P N +V F Sbjct: 178 GIQRKIGTTTIMVTHDQSEALSISDRVVVMEAGRITQIDTPYEAYERPENRFVSQF 233 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: 275 Number of extensions: 14 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: 363 Length adjustment: 30 Effective length of query: 370 Effective length of database: 333 Effective search space: 123210 Effective search space used: 123210 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