Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 170 bits (430), Expect = 6e-47 Identities = 92/253 (36%), Positives = 144/253 (56%), Gaps = 10/253 (3%) Query: 34 ILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIA 93 I ++ G + +L I+ GE+ ++G SG GK++++R++ L P G ++ G D++ Sbjct: 8 INKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVFHGEDVS 67 Query: 94 KISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERR----EKALDAL 149 R+VR + + VFQ +AL HMTV +N AFG+ + EK + L Sbjct: 68 S------RDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELL 121 Query: 150 RQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVK 209 V L+ A YP++LSGG RQR+ LARALA+ P +LL+DE F ALD +R E++ L + Sbjct: 122 GLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLAR 181 Query: 210 LQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVD 269 L T VF++HD +EAM + DRI +M G + Q+GTP E+ NPA+++V F + Sbjct: 182 LHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGDAN 241 Query: 270 ISQVFSAKDIARR 282 Q+ + + R Sbjct: 242 RLQLDDQRSVLFR 254 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: 289 Number of extensions: 16 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: 334 Length adjustment: 30 Effective length of query: 370 Effective length of database: 304 Effective search space: 112480 Effective search space used: 112480 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: 49 (23.5 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