Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate RR42_RS04825 RR42_RS04825 glycine/betaine ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS04825 Length = 391 Score = 189 bits (479), Expect = 2e-52 Identities = 121/364 (33%), Positives = 198/364 (54%), Gaps = 32/364 (8%) Query: 36 EKTGLSLGVKDA-SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAK 94 +K G + DA SL + +GEI V +G SG GK+T ++++NRLI+P+ G+VLIDG D ++ Sbjct: 13 QKDGAEVRAVDAVSLTVPKGEICVFLGPSGCGKTTTLKMINRLIQPSSGRVLIDGEDTSR 72 Query: 95 ISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGL 154 + + LR +KI V Q L P+MT+ +N L G + + RE+A + + V L Sbjct: 73 VDEVTLR----RKIGYVIQQIGLFPNMTIEENIMVVPRLLGWDKKRSRERARELMSMVQL 128 Query: 155 E--NYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQA 212 + YP ELSGG +QR+G+ RALA + +LLMDE F A+DP+ R +Q+E +Q Sbjct: 129 DPGKMLTRYPRELSGGQQQRIGVIRALAADAPVLLMDEPFGAVDPINRESIQNEFFLMQR 188 Query: 213 KHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF------FR 266 + +T++ +SHD+DEA+++GDR+A+ + G++VQ PD +L PA+D+V+ F + Sbjct: 189 QLGKTVIMVSHDIDEAIKLGDRVAVFRGGKLVQFDHPDALLARPADDFVQAFIGHDNTLK 248 Query: 267 GVDISQVFSAKDIARRTPNGLIRKTPGFGPRSA-----LKLLQDEDREYGYVIERGNKFV 321 + + + A +A+ +G+ F L ++ D R GYV R + Sbjct: 249 RLLLVRAGDAATMAQTCSSGM-PLAQAFAIMDEADVRHLPVVDDAQRALGYVTRRDARAG 307 Query: 322 GAVSIDSLKTALTQQQGLDAALIDAPLAVDAQTPLSELLSHVGQAPCAVPVVDEDQQYVG 381 V D+++ + A D L + LS + H +PVVD D Y+G Sbjct: 308 RGVCADAMRPFMA------TAAFDEHLRI----VLSRMYQH---NTSWLPVVDADGVYLG 354 Query: 382 IISK 385 +++ Sbjct: 355 EVTQ 358 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: 368 Number of extensions: 15 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: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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