Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >MicrobesOnline__882:206675 Length = 247 Score = 172 bits (435), Expect = 1e-47 Identities = 101/265 (38%), Positives = 154/265 (58%), Gaps = 28/265 (10%) Query: 5 LEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64 + I+N++K FGE + D SL ++ GE VI+G SG Sbjct: 9 ISIRNVWKFFGE------------------------LTALHDVSLDVQAGEKVVIIGPSG 44 Query: 65 SGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVL 124 SGKST++R +NRL +G +++DG DI + D+++ +R+ + MVFQSF L PH TVL Sbjct: 45 SGKSTLLRSINRLENVDKGSIIVDGKDI-RAEDSDINVIRQD-LGMVFQSFNLFPHKTVL 102 Query: 125 DN-TAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINP 183 N T M L + +E +ALD L++VG+ + A+ YP LSGG +QRV +ARALA+NP Sbjct: 103 QNLTMAPMRLRKVPRDEAESRALDLLKKVGISDKANVYPAMLSGGQQQRVAIARALAMNP 162 Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243 I+L DE SALDP + E+ D +V L AK T+V ++H++ A + DRI M +G++ Sbjct: 163 KIMLFDEPTSALDPEMIGEVLDVMVTL-AKEGMTMVCVTHEMGFAREVADRIIFMDHGQI 221 Query: 244 VQVGTPDEILNNPANDYVRTFFRGV 268 ++ GTP P + ++ F + + Sbjct: 222 LEQGTPQHFFEAPEHPRLQKFLQQI 246 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: 231 Number of extensions: 14 Number of successful extensions: 4 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: 247 Length adjustment: 27 Effective length of query: 373 Effective length of database: 220 Effective search space: 82060 Effective search space used: 82060 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: 48 (23.1 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