Align ATPase (characterized, see rationale)
to candidate RR42_RS16445 RR42_RS16445 hypothetical protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Cup4G11:RR42_RS16445 Length = 252 Score = 253 bits (645), Expect = 4e-72 Identities = 136/237 (57%), Positives = 170/237 (71%), Gaps = 11/237 (4%) Query: 36 QALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSH------- 88 +AL GV+L VQRGEVV ++GPSGSGKST LR++N LE RG+I I+G + H Sbjct: 15 KALNGVNLEVQRGEVVCLIGPSGSGKSTLLRSINYLERPTRGDISIDGQTVGHVNQAGKK 74 Query: 89 ----DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLER 144 R++A +R EVGMVFQ F L+PHL+VL+N+ L V+VR +A A RQLL + Sbjct: 75 ARPMSGRELARVRSEVGMVFQMFYLWPHLSVLENVTLGMVEVRGVRLADAAQRGRQLLAK 134 Query: 145 VRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA 204 V ++ + D YP QLSGGQ+QRVAIARALAM P+I+LFDEPTSALDPE V EVL M +A Sbjct: 135 VGLSGKYDAYPEQLSGGQRQRVAIARALAMDPKIILFDEPTSALDPERVGEVLQTMETVA 194 Query: 205 SEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQIL 261 +EGMTM+VATHE+GFAR VADRVV M +G++VE P F PQS R KQFL ++L Sbjct: 195 AEGMTMIVATHEMGFARRVADRVVFMDEGRVVEAGSPGDIFDRPQSARLKQFLDKVL 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: 225 Number of extensions: 10 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