Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 135 bits (339), Expect = 2e-36 Identities = 81/231 (35%), Positives = 130/231 (56%), Gaps = 6/231 (2%) Query: 13 MISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 72 +I+ +NV K +G + + S V +GE + GPSG GK+TL++ + E +G I++ Sbjct: 14 IITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILI 73 Query: 73 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGLAL 132 DG I+ N+P + V MVFQ + +FPH+T+ +N+ KV +AE + Sbjct: 74 DGQDIS----NVPPNKRPVNMVFQSYAVFPHMTVADNVAYGL-KVDNVPKAEREARVAEA 128 Query: 133 LDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMV 192 L+ V L + P QLSGGQ+QRVA+ARAL P V+L DEP SALD ++ ++ + Sbjct: 129 LELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELC 188 Query: 193 QLAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSAR 242 L ++ G+T + VTH+ A +A+R M KG + + T + + ++R Sbjct: 189 TLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSR 239 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: 198 Number of extensions: 13 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: 381 Length adjustment: 27 Effective length of query: 229 Effective length of database: 354 Effective search space: 81066 Effective search space used: 81066 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: 48 (23.1 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