Align Accumulation of dyads protein 2; Ammonia transport outward protein 1 (characterized)
to candidate WP_109939208.1 DLD82_RS00825 hypothetical protein
Query= SwissProt::P25613 (283 letters) >NCBI__GCF_003173335.1:WP_109939208.1 Length = 196 Score = 108 bits (271), Expect = 7e-29 Identities = 65/168 (38%), Positives = 87/168 (51%), Gaps = 9/168 (5%) Query: 88 ANPAPLGLSAFALTTFVLSMFNARAQGITVPNVVVGCAMFYGGLVQLIAGIWEIALENTF 147 ANPAPLGL AF +TT +LS+ NA P + AMFYGG+ Q+IAGI+E NTF Sbjct: 19 ANPAPLGLCAFGMTTILLSLHNAGLTAAGSP--IFSMAMFYGGIAQIIAGIFEWKKNNTF 76 Query: 148 GGTALCSYGGFWLSFAAI-YIPWFGILEAYEDNESDLNNALGFYLLGWAIFTFGLTVCTM 206 G S+G FW+SFA I ++P G+ N L +L W +F GL VCT Sbjct: 77 GMVTFGSFGFFWISFAFIGFLPKLGL------TAPPTNLELAAFLSVWGLFAMGLFVCTF 130 Query: 207 KSTVMFFLLFFLLALTFLLLSIGHFANRLGVTRAGGVLGVVVAFIAWY 254 K + + F + L + L +G + GGV G+V +A Y Sbjct: 131 KMHRVLQVTLFTVVLLVVFLVVGEITEIGLFSNLGGVTGIVAGLLALY 178 Lambda K H 0.323 0.140 0.436 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: 197 Number of extensions: 12 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: 283 Length of database: 196 Length adjustment: 23 Effective length of query: 260 Effective length of database: 173 Effective search space: 44980 Effective search space used: 44980 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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