Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= CharProtDB::CH_001555 (400 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 452 bits (1164), Expect = e-132 Identities = 238/395 (60%), Positives = 296/395 (74%), Gaps = 4/395 (1%) Query: 3 IKLEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGL 62 +K+E+KNLYKIFG P++A ++QGL KE I EKT ++GV+DAS I +GEIFVIMGL Sbjct: 5 VKIEVKNLYKIFGPQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVIMGL 64 Query: 63 SGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMT 122 SGSGKSTMVR+LNRLIEPT GQVLIDG DI ++D +L +VRR K++MVFQSFALMPHMT Sbjct: 65 SGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVFQSFALMPHMT 124 Query: 123 VLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAIN 182 VL N AFG+E+ G++ + R ++AL AL QVGLE +A S PDELSGGM+QRVGLAR LA++ Sbjct: 125 VLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQRVGLARGLAVD 184 Query: 183 PDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGE 242 PDILLMDEAFSALDPLIRTEMQDEL+KLQAK +RTIVFISHDLDEAMRIGDRIAIM+ G Sbjct: 185 PDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIGDRIAIMEGGR 244 Query: 243 VVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPNGLIRKTPGFGPRSALKL 302 VVQVGTP+EIL NPA+DYVR FFRGVD + + +A DIA +T I T G PR+ L+ Sbjct: 245 VVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDIATQT-QVTIPITDGKNPRAGLQR 303 Query: 303 LQDEDREYGYVIERGNKFVGAVSIDSLKTALTQQQG---LDAALIDAPLAVDAQTPLSEL 359 L DR+Y YV++ F G VS DSL+ L + A ++ +A L ++ Sbjct: 304 LVKNDRDYAYVLDSEKTFKGVVSTDSLRDMLENDNVPHLIPNAYLEEVVAAHKDDSLQDI 363 Query: 360 LSHVGQAPCAVPVVDEDQQYVGIISKGMLLRALDR 394 L V P +P++D+D +Y+G ISK + L+ L R Sbjct: 364 LPKVAAHPWPLPILDDDGRYLGAISKNLFLKTLHR 398 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: 503 Number of extensions: 20 Number of successful extensions: 3 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: 415 Length adjustment: 31 Effective length of query: 369 Effective length of database: 384 Effective search space: 141696 Effective search space used: 141696 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 Apr 09 2024. 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