Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_052473371.1 SUTH_RS06770 phosphate ABC transporter ATP-binding protein PstB
Query= TCDB::Q88NY5 (256 letters) >NCBI__GCF_000828635.1:WP_052473371.1 Length = 267 Score = 128 bits (322), Expect = 1e-34 Identities = 82/235 (34%), Positives = 133/235 (56%), Gaps = 18/235 (7%) Query: 16 IKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGD------ 69 +++++ YG F L S + +V + GPSG GKSTL++C N + G+ Sbjct: 20 VRDLDFHYGAFHALKRVSMPIHDHKVTALIGPSGCGKSTLLRCFNRMHDLYPGNRYAGGG 79 Query: 70 --IVVDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENL--TIAQRKVLGRSE--- 122 + D T++ P + ++R R+ MVFQ FP +I EN+ ++ R + ++E Sbjct: 80 IVLYPDNTNLLSPDVDPIEVRMRISMVFQKPNPFPK-SIFENVAYSLRVRGMTNKNELAD 138 Query: 123 -AEATKKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP 181 EA KG AL + V S K+ LSGGQQQR+ IARALA DP ++LFDEPTSALDP Sbjct: 139 RVEAALKGAALWNEV--SNRLKELGANLSGGQQQRLCIARALASDPEIILFDEPTSALDP 196 Query: 182 EMVSEVLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFF 236 + + +++++L +E +T++ VTH M A ++++ +M G ++E ++ F Sbjct: 197 IATASIEELIIEL-KEKVTILIVTHNMQQAARISDYTAYMYLGEMVEFGVTDQIF 250 Lambda K H 0.319 0.134 0.383 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: 133 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: 256 Length of database: 267 Length adjustment: 25 Effective length of query: 231 Effective length of database: 242 Effective search space: 55902 Effective search space used: 55902 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 (21.8 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