Align ATPase (characterized, see rationale)
to candidate 17341 b3271 predicted amino-acid transporter subunit (NCBI)
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Keio:17341 Length = 252 Score = 301 bits (772), Expect = 7e-87 Identities = 153/241 (63%), Positives = 185/241 (76%), Gaps = 1/241 (0%) Query: 21 MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80 MI E V KWYG QF L ++LTVQ GE +V+ GPSGSGKST +R +N LE HQ+G I Sbjct: 12 MITLENVNKWYG-QFHVLKNINLTVQPGERIVLCGPSGSGKSTTIRCINHLEEHQQGRIV 70 Query: 81 IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140 ++G L+ D R+I +RQEVGMVFQ FNLFPHLTVLQN LAP+ VR+ P +AE A Sbjct: 71 VDGIELNEDIRNIERVRQEVGMVFQHFNLFPHLTVLQNCTLAPIWVRKMPKKEAEDLAVH 130 Query: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200 LERVRIAE A K+PGQ+SGGQQQRVAIAR+L M+P+I+LFDEPTSALDPEMV+EVLD M Sbjct: 131 YLERVRIAEHAHKFPGQISGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMVKEVLDTM 190 Query: 201 RDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 LA GMTML THE+GFAR VADRV+ M G+IVE+A PD FF P+S+R + FL+Q+ Sbjct: 191 IGLAQSGMTMLCVTHEMGFARTVADRVIFMDRGEIVEQAAPDEFFAHPKSERTRAFLSQV 250 Query: 261 L 261 + Sbjct: 251 I 251 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: 233 Number of extensions: 7 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: 252 Length adjustment: 24 Effective length of query: 237 Effective length of database: 228 Effective search space: 54036 Effective search space used: 54036 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