Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF3356 HP15_3298 glycine betaine/L-proline ABC transporter, ATPase subunit
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Marino:GFF3356 Length = 352 Score = 290 bits (742), Expect = 4e-83 Identities = 150/334 (44%), Positives = 220/334 (65%), Gaps = 3/334 (0%) Query: 3 IKLEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGL 62 IK+ I+NLYKIFG P A +Y+ +G+ K +LE+ LG++D ++ I +GEI VIMGL Sbjct: 5 IKISIRNLYKIFGPTPDVALEYVRKGMGKADLLEQQRHVLGLRDINVDIHDGEITVIMGL 64 Query: 63 SGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMT 122 SGSGKST++R LNRLI+PT G++ +DG DI S+ +LR++RR++++MVFQ FAL+PH T Sbjct: 65 SGSGKSTLIRHLNRLIDPTAGEIRVDGEDIMSYSEEQLRKLRRERMSMVFQKFALLPHKT 124 Query: 123 VLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAIN 182 VL+N ++ G + A L +VGLE + YP +LSGGM+QRVG+ARAL + Sbjct: 125 VLENAGMAKDIRGYTTSDFEADARKWLARVGLEGNEYQYPHQLSGGMQQRVGIARALVSD 184 Query: 183 PDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGE 242 I+LMDEAFSALDPLIR++MQD L++LQ + Q+TIVFI+HDLDEA+++ D + I+++GE Sbjct: 185 APIMLMDEAFSALDPLIRSDMQDLLLELQEELQKTIVFITHDLDEALKLADHLVILKDGE 244 Query: 243 VVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPNGLIRKTPGFGPRSALK- 301 VVQ G P EIL NP + Y+ F ++ ++V + + +G + L+ Sbjct: 245 VVQQGDPQEILLNPGDPYIVDFISDINRARVLRVRSVMSPPDDGEATFAGDISEKDNLET 304 Query: 302 --LLQDEDREYGYVIERGNKFVGAVSIDSLKTAL 333 L D D + + R ++ VG + + L AL Sbjct: 305 VLLKSDGDMSLNFRVVRDDQHVGTLHMKDLARAL 338 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: 394 Number of extensions: 17 Number of successful extensions: 1 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: 352 Length adjustment: 30 Effective length of query: 370 Effective length of database: 322 Effective search space: 119140 Effective search space used: 119140 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