Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate RR42_RS12250 RR42_RS12250 sulfate ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS12250 Length = 374 Score = 170 bits (430), Expect = 7e-47 Identities = 90/236 (38%), Positives = 143/236 (60%), Gaps = 10/236 (4%) Query: 39 GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDA 98 G + + D +L +EG++ ++G SG GK+T++R++ L GQ+L++G DA Sbjct: 13 GNFVALDDVTLDFDEGQLTALLGPSGCGKTTLLRIIAGLERADAGQILLEG------RDA 66 Query: 99 ELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQ----ERREKALDALRQVGL 154 + VR++++ VFQ +AL HMTV +N AFG+ + A + + R+K L V L Sbjct: 67 SHQHVRQRQVGFVFQHYALFKHMTVFENVAFGLRVKPRAERPGEAQIRDKVRALLELVQL 126 Query: 155 ENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKH 214 + A YP +LSGG RQR+ LARALA+ P +LL+DE F ALD +R E++ L +L + Sbjct: 127 DWLADRYPPQLSGGQRQRIALARALAVEPRVLLLDEPFGALDAKVRKELRRWLRRLHDEL 186 Query: 215 QRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDI 270 T VF++HD +EA+ + D++ +M G V Q GTP+ + N+PA +V F V++ Sbjct: 187 HVTSVFVTHDQEEALEVADQVVLMNRGHVEQAGTPEAVYNHPATPFVFGFLGNVNL 242 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: 349 Number of extensions: 21 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: 374 Length adjustment: 30 Effective length of query: 370 Effective length of database: 344 Effective search space: 127280 Effective search space used: 127280 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