Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_028583721.1 G494_RS0105480 proline/glycine betaine ABC transporter ATP-binding protein ProV
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000429965.1:WP_028583721.1 Length = 409 Score = 442 bits (1138), Expect = e-129 Identities = 229/399 (57%), Positives = 293/399 (73%), Gaps = 3/399 (0%) Query: 5 LEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64 + VKNLYK+FG P + ++ G SKE+I E+TGL++GV+DAS + +GEIFV+MGLSG Sbjct: 4 ITVKNLYKVFGADPAKGLALVKAGNSKEEIYEQTGLTVGVQDASFTVAKGEIFVVMGLSG 63 Query: 65 SGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVL 124 SGKST+VR+LNRLIEPT G+V +DG ++ ++ +L + RR K +MVFQSFALMPH+ VL Sbjct: 64 SGKSTLVRMLNRLIEPTAGEVWVDGDNVLTMNRDQLVKFRRSKTSMVFQSFALMPHLNVL 123 Query: 125 DNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPD 184 DN FG+EL G+ +R E+ +DAL+QVGLE + A P ELSGGM+QRVGLAR LA++PD Sbjct: 124 DNVCFGLELDGMPRPQREERGMDALKQVGLEGWEKAAPGELSGGMQQRVGLARGLAMDPD 183 Query: 185 ILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVV 244 ILLMDEAFSALDPLIR+EMQDEL+KLQ +H+RTIVFISHDLDEA+RIGDRIAIM+ G VV Sbjct: 184 ILLMDEAFSALDPLIRSEMQDELLKLQDRHERTIVFISHDLDEALRIGDRIAIMEGGRVV 243 Query: 245 QVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLLQ 304 QVG+P+EIL NPA+DYVR FFRGVD + V SA DI R + +I TP PR+ L+LL Sbjct: 244 QVGSPEEILQNPADDYVRAFFRGVDPTGVISAGDIVRDNQPKVIWHTPEGSPRATLELLN 303 Query: 305 DEDREYGYVIERGNKFVGVVSIDSLKAALSQAQG---IEAALIDDPLVVDAQTPLSELLS 361 ++DRE+GYV+ KF GVVS DSL+ L G IE A ++ V L ++L Sbjct: 304 NQDREFGYVVGSDRKFYGVVSTDSLRDLLEAKNGKGNIEQAFLEAATPVQEGECLQDILP 363 Query: 362 HVGQAPCAVPVVDEEHQYVGIISKRMLLQALDREGGNNG 400 V +PVVDE + Y G++SK L+ L R G +NG Sbjct: 364 QVASHLWPIPVVDENNLYQGVVSKNRFLRTLYRAGNDNG 402 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: 555 Number of extensions: 26 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: 409 Length adjustment: 31 Effective length of query: 369 Effective length of database: 378 Effective search space: 139482 Effective search space used: 139482 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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