Align ATPase (characterized, see rationale)
to candidate CCNA_01506 CCNA_01506 cystine transport ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Caulo:CCNA_01506 Length = 246 Score = 221 bits (564), Expect = 9e-63 Identities = 119/238 (50%), Positives = 158/238 (66%), Gaps = 1/238 (0%) Query: 22 IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI 81 I A+ ++K +G+ L GV L V GEVV ++GPSGSGKST LR L LE G++ I Sbjct: 4 IDAKSLKKSFGDT-PVLAGVDLAVVPGEVVAIIGPSGSGKSTLLRCLAGLEPLNDGDLTI 62 Query: 82 EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQL 141 G + VG VFQ FNLFPH T L+N++ P+ VRR A+A A L Sbjct: 63 AGVAAGGKTPLAKALNGRVGFVFQSFNLFPHRTALENVIEGPIVVRREDPAKARAKGLAL 122 Query: 142 LERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMR 201 LE+V +A++ D YP LSGGQQQR AIARALAM P ++LFDEPTSALDPE+V EVL V+R Sbjct: 123 LEKVGLADRVDAYPSALSGGQQQRCAIARALAMDPEVILFDEPTSALDPELVGEVLAVIR 182 Query: 202 DLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQ 259 DLA+E TM++ TH++ FAR+VA+R + M G IVE+ P + +P+ +R ++FLA+ Sbjct: 183 DLAAEKRTMVIVTHQMDFARDVAERTIFMDGGVIVEQGPSRQLLASPREERTRRFLAR 240 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: 203 Number of extensions: 13 Number of successful extensions: 2 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: 246 Length adjustment: 24 Effective length of query: 237 Effective length of database: 222 Effective search space: 52614 Effective search space used: 52614 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