Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_011384493.1 AMB_RS10565 ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_000009985.1:WP_011384493.1 Length = 257 Score = 139 bits (350), Expect = 6e-38 Identities = 82/243 (33%), Positives = 140/243 (57%), Gaps = 8/243 (3%) Query: 15 IQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVD 74 I++ GV+K +G VL I+L+V +GE +V+ G SG+GKS ++C+ L + G I +D Sbjct: 7 IELTGVHKAFGPKVVLDGIDLSVARGESVVVIGGSGTGKSVMLKCILGLLRPESGSIRID 66 Query: 75 GVELTN-DLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 G ++ K + I ++ GM+FQ LF L + +N + +KM + KA +IA+ Sbjct: 67 GEDVVGMGPKDRDRIMKKFGMLFQGGALFDSLKVWENVAFGLIQGQKMERAKARDIAIEK 126 Query: 134 LERVRIPEQAHKY-PGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTM 192 L +V + + P +LSGG Q+RV++ARA+ P+I+ FDEPT+ LDP M + D + Sbjct: 127 LAQVGLAASTGELSPSELSGGMQKRVSLARAIATNPEIIFFDEPTTGLDPIMADVINDLI 186 Query: 193 IGLAED-GMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQ 251 + ++ G T L +TH+M AR +++R+ + KG ++ P D+ N+ ++ Q Sbjct: 187 VKCCKEVGATALSITHDMASARKISDRIAMLYKGRLI-WVGPAKDIDHSGNE----YVDQ 241 Query: 252 ILH 254 +H Sbjct: 242 FIH 244 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: 167 Number of extensions: 9 Number of successful extensions: 4 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: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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