Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Synpcc7942_1414 Synpcc7942_1414 ATPase
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__SynE:Synpcc7942_1414 Length = 241 Score = 139 bits (351), Expect = 4e-38 Identities = 89/226 (39%), Positives = 132/226 (58%), Gaps = 9/226 (3%) Query: 23 IQISQMNKWYGQ----FHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGK 78 IQ ++K YG+ L ++ V GE I G SGSGKST + I L+ +G+ Sbjct: 9 IQFEHVSKIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGCLDRPTAGR 68 Query: 79 IIVDGIELTS-DLKNIDKVRS-EVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEE 136 +DG ++ D + VR+ ++G VFQ F+L P L+ +EN+ L I+ + ++E + Sbjct: 69 YYLDGTDVADLDDDALAAVRNRKIGFVFQQFHLLPQLSAVENVMLPMIYAG-ISQQERRD 127 Query: 137 TAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEV 196 A+ L +V + ++ P QLSGGQQQRVAIAR++ +P ++L DEPT ALD + +EV Sbjct: 128 RAVAALTQVGLAQRLDNKPNQLSGGQQQRVAIARAIVNQPVLLLADEPTGALDSQTTEEV 187 Query: 197 LDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIV-EQNNP 241 L+ QL + G+T++ VTHE A A RVI+ DGQI E NP Sbjct: 188 LNIFDQLHQRGITIVIVTHEAEVADR-AERVIWFRDGQIQRETQNP 232 Lambda K H 0.320 0.134 0.391 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: 165 Number of extensions: 11 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: 263 Length of database: 241 Length adjustment: 24 Effective length of query: 239 Effective length of database: 217 Effective search space: 51863 Effective search space used: 51863 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: 46 (22.3 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