Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 187 bits (474), Expect = 6e-52 Identities = 104/240 (43%), Positives = 140/240 (58%), Gaps = 10/240 (4%) Query: 29 LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88 LS Q+ + G + D SL I EGE ++G SGSGKS+++R+L L +P RG VL D Sbjct: 3 LSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD 62 Query: 89 GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERRE----K 144 G D+ + +R+ I +VFQ +AL PHMTV DN AFG+ + A + R + Sbjct: 63 GTDLLALP------AQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAAR 116 Query: 145 ALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQ 204 D LR+V LE YP +LSGG RQRV LARALA+ P +LL+DE F ALD +R ++ Sbjct: 117 VEDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLR 176 Query: 205 DELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 L LQ T V ++HD DEA+ + DR+ +M G + QVG P EI PA +V F Sbjct: 177 VWLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGF 236 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: 363 Number of extensions: 20 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: 384 Length adjustment: 31 Effective length of query: 369 Effective length of database: 353 Effective search space: 130257 Effective search space used: 130257 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