Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, periplasmic substrate-binding component (characterized)
to candidate 206178 DVU0752 amino acid ABC transporter, amino acid-binding protein
Query= reanno::pseudo3_N2E3:AO353_16290 (304 letters) >MicrobesOnline__882:206178 Length = 275 Score = 112 bits (281), Expect = 7e-30 Identities = 83/267 (31%), Positives = 126/267 (47%), Gaps = 16/267 (5%) Query: 11 AITAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGVPVGYSHDIQLK 70 A+ AA + AA + + I +G SIP + + G G+ +DI + Sbjct: 8 ALAAAFLVFTGSAALAGPAYDNVMKDKKIRVGLMTDSIPGGFYNE-KGEWGGFDYDIATE 66 Query: 71 IVEAIKKDLDMPNLKVKYNLVTSQTRIPLVQNGTVDVECGSTTNNTERQQQVDFSVGIFE 130 I + + D++ V ++TRI VQ G VD+ + T+ ER + VDFS+ F Sbjct: 67 IAKRMGVDIERVQ-------VNNKTRIAYVQQGRVDISVSNMTHTRERDKSVDFSITYFF 119 Query: 131 IGTKLLSKKDSTYKDFADLKGKNVVTTAGTTSE----RILKSMNADKQMGMNVISAKDHG 186 G K+L+KK +K D+ GK + T GTTSE R LK D +VIS + Sbjct: 120 DGQKVLAKK-GQFKSVKDMVGKKIATMQGTTSEVNVKRALKEA-GDPNPDQSVISFQKES 177 Query: 187 ESFQMLESGRAVAFMMDDALLAGEMAKAKSPTDWAVTGTAQSYEIYGCMVRKGDAPFKKA 246 E FQ L+ GR + D ++L G AK P + + G + E YG + + D+ + A Sbjct: 178 ECFQALQMGRVAGWSTDASILVG--YSAKEPGKFELVGNFLAEEPYGIAMPQDDSALRDA 235 Query: 247 VDDAIVATYKSGEINTIYGKWFTQPIP 273 V+ A+ +K G TIY KW+ P Sbjct: 236 VNAALQDMWKDGTYKTIYNKWYGPGTP 262 Lambda K H 0.314 0.130 0.364 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: 189 Number of extensions: 16 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: 304 Length of database: 275 Length adjustment: 26 Effective length of query: 278 Effective length of database: 249 Effective search space: 69222 Effective search space used: 69222 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: 42 (22.0 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