Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF2246 PGA1_c22780 glycine betaine transport ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Phaeo:GFF2246 Length = 352 Score = 265 bits (677), Expect = 2e-75 Identities = 140/344 (40%), Positives = 215/344 (62%), Gaps = 7/344 (2%) Query: 5 LEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64 + + LYKIFG + +++ G+ KE++L + LG+ + ++ ++ GEI V+MGLSG Sbjct: 6 VRLSGLYKIFGARDKDVLHHVQGGMGKEELLAQHKHVLGLNNINVDMQAGEITVVMGLSG 65 Query: 65 SGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVL 124 SGKST++R LNRLIEPT G++++ G D+ ++S+ LR R++K++MVFQ FAL+PH TVL Sbjct: 66 SGKSTLIRHLNRLIEPTAGEIIVQGEDVMQLSEDGLRHARQEKMSMVFQKFALLPHKTVL 125 Query: 125 DNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPD 184 N + + G + +A L +VGL + + YP +LSGGM+QRVG+ARAL N Sbjct: 126 KNAGMPLSVRGEDEATCDREAAKWLERVGLSGFENHYPAQLSGGMQQRVGIARALTANTP 185 Query: 185 ILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVV 244 I+LMDEAFSALDPLIRT+MQD L++LQ + +TI+FI+HDLDEA+++ D + I+++G VV Sbjct: 186 IMLMDEAFSALDPLIRTDMQDLLLELQKELHKTIIFITHDLDEALKLADHLVILKDGFVV 245 Query: 245 QVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPNGLIRKTPGFGPRSALKLLQ 304 Q G P IL NP + Y+ F ++ ++V + I G + K G L+ Sbjct: 246 QQGEPQHILLNPNDPYIEDFVSDINRARVLRVRSIMTPLVGGKVPK-DAHGEVDVNDTLE 304 Query: 305 D------EDREYGYVIERGNKFVGAVSIDSLKTALTQQQGLDAA 342 D + YV++ G + VG + + L AL + +A+ Sbjct: 305 SMIARSGGDTSHAYVVKDGEQTVGTLDMTELVRALVPRVASEAS 348 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: 385 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