Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate Synpcc7942_1236 Synpcc7942_1236 nitrate transport ATP-binding subunits C and D
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__SynE:Synpcc7942_1236 Length = 274 Score = 152 bits (384), Expect = 1e-41 Identities = 78/216 (36%), Positives = 133/216 (61%), Gaps = 11/216 (5%) Query: 39 GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDA 98 G + ++D +L++++GE ++G SG GKST++ L++ +PT G V +DG I + Sbjct: 31 GPYVAIEDVNLSVQQGEFICVIGHSGCGKSTLLNLVSGFSQPTSGGVYLDGQPIQEPGPD 90 Query: 99 ELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAG--IAAQERREKALDALRQVGLEN 156 + +VFQ+++L+P + DN A ++ A ++ E+R+ L VGL Sbjct: 91 RM---------VVFQNYSLLPWKSARDNIALAVKAARPHLSTSEQRQVVDHHLELVGLTE 141 Query: 157 YAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQR 216 H PD+LSGGM+QRV +ARAL+I P++L++DE F ALD + + E+Q+EL+ + + + Sbjct: 142 AQHKRPDQLSGGMKQRVAIARALSIRPEVLILDEPFGALDAITKEELQEELLNIWEEARP 201 Query: 217 TIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEI 252 T++ I+HD+DEA+ + DR+ +M NG +G EI Sbjct: 202 TVLMITHDIDEALFLADRVVMMTNGPAATIGEVLEI 237 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: 236 Number of extensions: 13 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: 274 Length adjustment: 28 Effective length of query: 372 Effective length of database: 246 Effective search space: 91512 Effective search space used: 91512 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: 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