Align ATPase (characterized, see rationale)
to candidate GFF197 PGA1_c02010 glutamate/glutamine/aspartate/asparagine transport ATP-binding protein BztD
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Phaeo:GFF197 Length = 263 Score = 299 bits (765), Expect = 5e-86 Identities = 150/243 (61%), Positives = 185/243 (76%), Gaps = 1/243 (0%) Query: 19 ETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGE 78 E I + KWYG+ F L ++LTV +GE +V+ GPSGSGKST +R LNALE HQ+G Sbjct: 20 EVAIEINNMNKWYGS-FHVLRDINLTVNQGERIVIAGPSGSGKSTLIRCLNALEEHQQGN 78 Query: 79 IWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATA 138 I ++G LS+D ++I IR EVGMVFQ FNLFPHLT+L+N LAP+ VR+ P +AE A Sbjct: 79 IMVDGTELSNDLKNIDKIRSEVGMVFQHFNLFPHLTILENCTLAPIWVRKTPKKEAEERA 138 Query: 139 RQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLD 198 LE+V+I +QA KYPG LSGGQQQRVAIAR+L M PRI+LFDEPTSALDPEM++EVLD Sbjct: 139 MHFLEKVKIPDQAHKYPGMLSGGQQQRVAIARSLCMMPRIMLFDEPTSALDPEMIKEVLD 198 Query: 199 VMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLA 258 M +LA EGMTML THE+GFAR+VA+RV+ M GQIVE+ P+ FF PQS+R K FL+ Sbjct: 199 TMIELAEEGMTMLCVTHEMGFARQVANRVIFMDAGQIVEQNEPEEFFNNPQSERTKLFLS 258 Query: 259 QIL 261 QIL Sbjct: 259 QIL 261 Lambda K H 0.321 0.134 0.387 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: 216 Number of extensions: 5 Number of successful extensions: 1 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: 261 Length of database: 263 Length adjustment: 25 Effective length of query: 236 Effective length of database: 238 Effective search space: 56168 Effective search space used: 56168 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 (21.9 bits) S2: 47 (22.7 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