Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate CCNA_00294 CCNA_00294 phosphate transport ATP-binding protein pstB
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__Caulo:CCNA_00294 Length = 274 Score = 137 bits (346), Expect = 2e-37 Identities = 97/259 (37%), Positives = 138/259 (53%), Gaps = 19/259 (7%) Query: 5 APAKKDLRMISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEP 64 APA D + I + V +YGD Q L D ++ V GPSG GKST ++C+N + Sbjct: 19 APATADPK-IKARGVKVFYGDKQALFDVDLDIPAKSVTAFIGPSGCGKSTFLRCINRMND 77 Query: 65 F-----QKGDIVVDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQR---K 116 +G I++DG + + LRSRVGMVFQ FP TI EN+ R Sbjct: 78 TIPSARVEGSILIDGADVNAKSVDPVVLRSRVGMVFQKPNPFPK-TIFENVAYGPRIHGL 136 Query: 117 VLGRSEAEATKKGLALLDRVGL---SAHAKKHPGQ-LSGGQQQRVAIARALAMDPIVMLF 172 G++E EA + + L + GL A PG LSGGQQQR+ IARA+A+ P V+L Sbjct: 137 ATGKAELEAIVE--SSLKKAGLWNEVADRLHQPGTGLSGGQQQRLVIARAIAVSPEVILM 194 Query: 173 DEPTSALDPEMVSEVLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTK 232 DEP SALDP +++ +++ +L + ++ VTH M A +V+ R F G ++E Sbjct: 195 DEPCSALDPIATAKIEELIDELRSQ-FCIVIVTHSMAQAARVSQRTAFFHLGKLVESGPT 253 Query: 233 EEFFGDQSARDQRTQHLLS 251 EE F + RD RTQ ++ Sbjct: 254 EEMF--TNPRDSRTQDYIT 270 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: 158 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: 256 Length of database: 274 Length adjustment: 25 Effective length of query: 231 Effective length of database: 249 Effective search space: 57519 Effective search space used: 57519 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 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