Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate HSERO_RS08545 HSERO_RS08545 glycine/betaine ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__HerbieS:HSERO_RS08545 Length = 377 Score = 193 bits (491), Expect = 6e-54 Identities = 118/358 (32%), Positives = 201/358 (56%), Gaps = 20/358 (5%) Query: 36 EKTGLSLGVKDA-SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAK 94 +K G + DA SL + EGEI V +G SG GK+T ++++NRLI PT G+VL++G D + Sbjct: 13 QKDGTQVKAVDAVSLKVAEGEICVFLGPSGCGKTTTLKMINRLINPTSGRVLLNGQDTSG 72 Query: 95 ISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGL 154 I + ELR + I V Q L P+MT+ +N L G + + +E+A + + V L Sbjct: 73 IDEVELR----RHIGYVIQQIGLFPNMTIEENITIVPRLLGWDKKRCQERATELMAMVAL 128 Query: 155 E--NYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQA 212 + + YP ELSGG +QR+G+ RALA + +LLMDE F A+DP+ R +Q+E ++Q Sbjct: 129 DPKKFLKRYPRELSGGQQQRIGVIRALAADAPVLLMDEPFGAVDPINRESIQNEFFQMQR 188 Query: 213 KHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDIS- 271 + +T++ +SHD+DEA+++GD++A+ + G++VQ PD +L P +D+V F G D + Sbjct: 189 QLNKTVIMVSHDIDEAIKLGDKVAVFRAGKLVQFDNPDTLLARPKDDFVSAFV-GQDHTL 247 Query: 272 ---QVFSAKDIARRTPNGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFVGAVSIDS 328 + A + A P P AL L+ D+D Y +I+ N+ +G ++ Sbjct: 248 KRLLLVRAGEAATTPPTA----HPDVSCDQALALMDDQDSRYLTIIDADNRALGYLTRRD 303 Query: 329 LKTAL-TQQQGLDAALIDAPLAVDAQTPLSELLSHVGQAPCAVPVVDEDQQYVGIISK 385 ++ + + + ++A + + LS++ H + +PV+ D YVG +++ Sbjct: 304 VRGSTGVAEDKVRPFTMNADPDENLRVVLSKMYKH---STSWMPVIANDGSYVGEVTQ 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: 370 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 377 Length adjustment: 30 Effective length of query: 370 Effective length of database: 347 Effective search space: 128390 Effective search space used: 128390 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