Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= TCDB::Q88NY4 (223 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 128 bits (321), Expect = 2e-34 Identities = 73/210 (34%), Positives = 121/210 (57%), Gaps = 7/210 (3%) Query: 16 WEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVITWFY 75 W G+++TL ++ ++ + LG +LAL R SS + L+ Y+ FR +PL+ ++ + Sbjct: 188 WSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQ 247 Query: 76 LAVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQALGMN 135 + VP +L + + +V +F +AY E VR G+Q+I +GQ AA ALG+N Sbjct: 248 VMVPLML----DSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLN 303 Query: 136 YAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARS---NGDIIGRS 192 QT R I+LPQA R P ++ + L QDT+L+ VGL++ L +RS N +GR Sbjct: 304 LFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRY 363 Query: 193 HEFLIFAGVVYFLISFSASWLVKRLQKRIS 222 E +F GV+Y+L + + L +RL++R++ Sbjct: 364 AEVYLFLGVLYWLCCYGLAQLSRRLEQRLT 393 Lambda K H 0.330 0.141 0.417 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: 296 Number of extensions: 10 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: 223 Length of database: 396 Length adjustment: 26 Effective length of query: 197 Effective length of database: 370 Effective search space: 72890 Effective search space used: 72890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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