Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate BPHYT_RS25065 BPHYT_RS25065 glycine/betaine ABC transporter ATPase
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS25065 Length = 392 Score = 364 bits (935), Expect = e-105 Identities = 189/391 (48%), Positives = 267/391 (68%), Gaps = 9/391 (2%) Query: 4 KLEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLS 63 K+ V+ L K+FG +P++A + G +KE++ +TG +GV + S ++EGEIFV+MGLS Sbjct: 5 KVVVEGLCKVFGTNPKQAIGMLAGGATKEEVFARTGQIVGVHNVSFEVKEGEIFVLMGLS 64 Query: 64 GSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTV 123 GSGKST++RL+NRL+EPT G+VLIDG D+A + +EL +RRK ++MVFQSFALMP TV Sbjct: 65 GSGKSTLIRLINRLVEPTAGKVLIDGRDVASVPRSELTALRRKDMSMVFQSFALMPQRTV 124 Query: 124 LDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINP 183 L N AFG+E+AG+ +ER ++A+ L QVGL +A P +LSGGM+QRVGLARALA+NP Sbjct: 125 LSNAAFGLEVAGVGRKEREKRAMTVLEQVGLAPFAQKLPAQLSGGMQQRVGLARALAVNP 184 Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243 +++MDEAFSALDPL R EMQ+ L+ LQ + QRTI+F+SHDL+EAMRIG RIAIM+ G V Sbjct: 185 SLMIMDEAFSALDPLKRKEMQNVLLDLQREQQRTILFVSHDLEEAMRIGTRIAIMEGGRV 244 Query: 244 VQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLL 303 VQVGTP +I+ NPA+DYVR FF G+D S+ +A D+ + V L++ +P S L Sbjct: 245 VQVGTPQQIITNPADDYVRAFFEGIDTSRYLTAGDLMQTDAVPLMQHSPQIDASSVAATL 304 Query: 304 QDEDREYGYVIERGNKFVGVVSIDSLKAALSQAQGIEAALIDDPLVVDAQTPLSELLSHV 363 + +Y +V++ K G V D++ +A Q IE + TPL +++ V Sbjct: 305 -NGSADYAFVLDSERKIRGFVCRDAMGSASPQVNQIEC--------IRRTTPLDDVVELV 355 Query: 364 GQAPCAVPVVDEEHQYVGIISKRMLLQALDR 394 + +PVV+ + Y G ++K +L L R Sbjct: 356 VASRAPLPVVEADGSYCGSVNKTNVLNVLTR 386 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: 406 Number of extensions: 17 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: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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 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