Align ATPase (characterized, see rationale)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 225 bits (573), Expect = 9e-64 Identities = 131/274 (47%), Positives = 172/274 (62%), Gaps = 16/274 (5%) Query: 2 TPLGRQPEPVTAI--ASAP-ETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSG 58 TP+ E TA A+AP + M+ V K YG + L G+ L VQ GE V ++GPSG Sbjct: 3 TPMPTTEESNTAAMAAAAPAQPMVRFASVTKRYG-ELTVLEGLDLDVQEGEKVAIIGPSG 61 Query: 59 SGKSTFLRTLNALESHQRGEIWIEGHRLSH-----------DRRDIATIRQEVGMVFQQF 107 SGKST LR L LE G I ++G L+H + R + +R +VGMVFQ F Sbjct: 62 SGKSTLLRVLMTLEGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSF 121 Query: 108 NLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVA 167 NLFPH+ LQN+M APVQV +A A +LL V + ++ + +P QLSGGQQQRVA Sbjct: 122 NLFPHMNALQNVMEAPVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVA 181 Query: 168 IARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA-SEGMTMLVATHEVGFAREVADR 226 IARALAM+P+++LFDE TSALDPE+ EVL V+R L + +TML+ TH++GFARE ADR Sbjct: 182 IARALAMRPKVMLFDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADR 241 Query: 227 VVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 V G+I E+ PD F PQ DR ++FL+ + Sbjct: 242 VCFFHQGRIHEQGSPDALFNNPQEDRTREFLSAV 275 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: 226 Number of extensions: 11 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: 279 Length adjustment: 25 Effective length of query: 236 Effective length of database: 254 Effective search space: 59944 Effective search space used: 59944 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 Apr 09 2024. 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