Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Pf6N2E2_3333 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3333 Length = 385 Score = 193 bits (491), Expect = 6e-54 Identities = 130/368 (35%), Positives = 207/368 (56%), Gaps = 30/368 (8%) Query: 33 QILEKTGLSLG-----VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLI 87 Q L KT S G V +L + EGEI V +G SG GKST ++++NRLI PT G+VLI Sbjct: 5 QNLSKTFKSNGKDVKAVDSVNLTVNEGEICVFLGPSGCGKSTTLKMINRLIPPTSGKVLI 64 Query: 88 DGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALD 147 +G D + + LR + I V Q L P+MT+ +N L G + ++ ++A + Sbjct: 65 NGEDTTGLDEVTLR----RNIGYVIQQIGLFPNMTIEENITVVPRLLGWDKQKCHDRARE 120 Query: 148 ALRQVGLE--NYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQD 205 + + LE Y H YP ELSGG +QR+G+ RALA + +LLMDE F A+DP+ R +Q+ Sbjct: 121 LMSMIKLEPKQYLHRYPRELSGGQQQRIGVIRALAADAPLLLMDEPFGAVDPINREMIQN 180 Query: 206 ELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF 265 E ++Q +T++ +SHD+DEA+++GD+IAI + G++VQ PD +L +PA+++V +F Sbjct: 181 EFFEMQRALNKTVIMVSHDIDEAIKLGDKIAIFRAGKLVQCDHPDTLLAHPADEFVSSFV 240 Query: 266 RGVDIS----QVFSAKDIARRTPNGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFV 321 G D + + A+D A P+ +P AL+L+ + DR Y V NK + Sbjct: 241 -GQDSTLKRLLLVKAEDAADNAPS----VSPETPVNEALELMDEHDRRYVVVTCAENKAL 295 Query: 322 GAVSIDSLKTALTQQQGLDAALI---DAPLAVDAQTPLSELLSHVGQAPCA-VPVVDEDQ 377 G V + L +Q G + +A A D L LLS + + + +PV+D ++ Sbjct: 296 GYVR----RRDLYRQTGTCGQYLREFNATAAYDEH--LRILLSRMYEFNRSWLPVMDAER 349 Query: 378 QYVGIISK 385 ++G +++ Sbjct: 350 VFLGEVTQ 357 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: 380 Number of extensions: 14 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: 385 Length adjustment: 31 Effective length of query: 369 Effective length of database: 354 Effective search space: 130626 Effective search space used: 130626 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