Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 226 bits (577), Expect = 3e-64 Identities = 126/261 (48%), Positives = 167/261 (63%), Gaps = 14/261 (5%) Query: 4 AIKQPVSPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRL 63 A P P +++ V K YG+ VL+ ++L+V++GE++ + GPSGSGKST +R L L Sbjct: 17 AAAAPAQP--MVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTL 74 Query: 64 EEHQQGRIVVDGVELTN-----------DLKQIEAIRREVGMVFQHFNLFPHLTILQNCT 112 E G I VDG LT+ + + + +R +VGMVFQ FNLFPH+ LQN Sbjct: 75 EGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVM 134 Query: 113 LAPMWVRKMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIML 172 AP+ V + KR+A E A L V + ++ +P QLSGGQQQRVAIARAL M+PK+ML Sbjct: 135 EAPVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVML 194 Query: 173 FDEPTSALDPEMVKEVLDTMIGLAE-DGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQA 231 FDE TSALDPE+ EVL + L E +TML VTH+MGFAR A+RV F +G I EQ Sbjct: 195 FDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQG 254 Query: 232 APNDFFDNPQNDRTKLFLSQI 252 +P+ F+NPQ DRT+ FLS + Sbjct: 255 SPDALFNNPQEDRTREFLSAV 275 Lambda K H 0.322 0.137 0.407 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: 212 Number of extensions: 6 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: 254 Length of database: 279 Length adjustment: 25 Effective length of query: 229 Effective length of database: 254 Effective search space: 58166 Effective search space used: 58166 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