Align ATPase (characterized, see rationale)
to candidate CA265_RS04175 CA265_RS04175 phosphonate ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Pedo557:CA265_RS04175 Length = 232 Score = 141 bits (356), Expect = 1e-38 Identities = 83/223 (37%), Positives = 132/223 (59%), Gaps = 7/223 (3%) Query: 21 MIYAEGVEKWYGNQ---FQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG 77 MI E +EK Y + AL G++L V GE V +MGPSG GKST L + L+ + G Sbjct: 1 MIKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENG 60 Query: 78 EI-WIEGHRLSHDRRDIATIRQE-VGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135 +I+ L+ + R+ + R+ +G VFQ FNL LTV +N+ L P+ + P + + Sbjct: 61 SYKFIDTELLTLNDRERSNFRKRNMGFVFQNFNLIDELTVFENIEL-PLIYNKIPAGERK 119 Query: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195 +++ER+ I ++ +P QLSGGQQQRVA+ARAL +P+++L DEPT LD E Sbjct: 120 KLVNEIIERMNIVNRSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNE 179 Query: 196 VLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEE 238 V++++ +L G T+++ TH A ++R++ + DG ++ E Sbjct: 180 VMELLCELNETGTTIVMVTHSSHDA-SFSNRIINLKDGHVISE 221 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: 118 Number of extensions: 5 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: 261 Length of database: 232 Length adjustment: 24 Effective length of query: 237 Effective length of database: 208 Effective search space: 49296 Effective search space used: 49296 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: 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