Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate PP_3597 PP_3597 Amino-acid ABC transporter, ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Putida:PP_3597 Length = 260 Score = 329 bits (843), Expect = 4e-95 Identities = 157/241 (65%), Positives = 194/241 (80%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +I+++G+NK YG FHVL+DI+L V++GERIVLCGPSGSGKST IRC+NRLE QQG I V Sbjct: 20 LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 DG++L ++ +R ++GMVFQHFNLFPH+++L NC LAP VR + ++ AEE A Y Sbjct: 80 DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L +V I QAHKYP QLSGGQQQRVAIARALCMKP+IMLFDEPTSALDPEMV EVLD ++ Sbjct: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253 LA GMTMLCVTHEMGFAR VA RV+F++ G+I+E + P FF+ P+ +R K FL+QIL Sbjct: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQIL 259 Query: 254 H 254 H Sbjct: 260 H 260 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: 237 Number of extensions: 3 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 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