Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__Miya:8500595 Length = 337 Score = 133 bits (335), Expect = 4e-36 Identities = 79/215 (36%), Positives = 128/215 (59%), Gaps = 15/215 (6%) Query: 16 LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPL-VMVLLW 74 LL+GL ITL+++V A++ GI+ G + + R+S + W A Y+ + R PL V + LW Sbjct: 127 LLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFLW 186 Query: 75 FYLIVPGFLQNVL-------GLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQ 127 ++++ G L N L G+SP L ++A ++F AY +EI+RAGIQS+ RGQ Sbjct: 187 YFVV--GTLINALLEHVGLGGISP-----LWYGVMALALFTGAYVAEIVRAGIQSVHRGQ 239 Query: 128 SSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTI 187 AA +LGM + Q+M+ +ILPQAFR ++P L Q I L +D+SL+ V+++ + + + Sbjct: 240 MEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRELTKATREV 299 Query: 188 GERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 E+ + +Y V++ + SL V YL+RR Sbjct: 300 VTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334 Lambda K H 0.330 0.140 0.412 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: 196 Number of extensions: 6 Number of successful extensions: 2 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: 224 Length of database: 337 Length adjustment: 25 Effective length of query: 199 Effective length of database: 312 Effective search space: 62088 Effective search space used: 62088 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: 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