Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate WP_090447275.1 BLS63_RS18555 glutamate/aspartate ABC transporter substrate-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_771 (304 letters) >NCBI__GCF_900100495.1:WP_090447275.1 Length = 304 Score = 462 bits (1190), Expect = e-135 Identities = 228/294 (77%), Positives = 257/294 (87%) Query: 8 LGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDI 67 + A+AA L+STP A ELTGTLKKIKE+GTI LGHRDASIPFSY D+ +PVG+SHD+ Sbjct: 10 VAVALAATLLSTPALAEELTGTLKKIKETGTIVLGHRDASIPFSYFGDSPQQPVGFSHDL 69 Query: 68 QLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVG 127 QLK+VEAIK+ L MP L+V+YNLVTSQTRIPLVQNGTVD+ECGSTTNNVERQQQVDFSVG Sbjct: 70 QLKVVEAIKQQLAMPELKVRYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQVDFSVG 129 Query: 128 IFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGE 187 IFE+GT+LL+KK S DFADLKGKNVVTTAGTTSER+LK MNA +QMGMN+ISAKDHGE Sbjct: 130 IFEVGTRLLTKKTSGVADFADLKGKNVVTTAGTTSERLLKVMNAKQQMGMNIISAKDHGE 189 Query: 188 SFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAV 247 SF MLE+GRA+AFMMDDALL GEMAKAK+P DWAV GT QS EIYGCM+RKGD FK+ V Sbjct: 190 SFLMLESGRALAFMMDDALLYGEMAKAKQPADWAVVGTPQSFEIYGCMLRKGDPAFKQVV 249 Query: 248 DDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAADE 301 D AI ATY+SGE+ IY+KWFMQPIPPKGLNL FPMS ELK LIA PTDKAA++ Sbjct: 250 DGAIAATYQSGEVTAIYDKWFMQPIPPKGLNLNFPMSAELKKLIAKPTDKAAEQ 303 Lambda K H 0.315 0.131 0.365 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: 362 Number of extensions: 9 Number of successful extensions: 1 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: 304 Length of database: 304 Length adjustment: 27 Effective length of query: 277 Effective length of database: 277 Effective search space: 76729 Effective search space used: 76729 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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