Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate Dsui_0635 Dsui_0635 periplasmic component of amino acid ABC-type transporter/signal transduction system
Query= reanno::pseudo1_N1B4:Pf1N1B4_771 (304 letters) >FitnessBrowser__PS:Dsui_0635 Length = 299 Score = 370 bits (949), Expect = e-107 Identities = 188/289 (65%), Positives = 224/289 (77%), Gaps = 2/289 (0%) Query: 10 AAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQL 69 A I +AL + PV A E + TLKKIK++G+ITLGHR++SIPFSY D + +GYSH++ L Sbjct: 11 AVIGSALCAAPVLAQE-SPTLKKIKDTGSITLGHRESSIPFSYYDDKQ-QVIGYSHEMML 68 Query: 70 KIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVGIF 129 K V+AIK +L + L VK VTS RI L+QNGTVD+ECGSTTNN+ERQ+QV FS IF Sbjct: 69 KAVDAIKAELKLAKLDVKLMPVTSANRITLLQNGTVDMECGSTTNNLERQKQVGFSTSIF 128 Query: 130 EIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESF 189 IGT+L++KKD+ KDF DL GKNVVTTAGTTSER+++ MN +KQM MN+ISAKDHGESF Sbjct: 129 VIGTRLMAKKDAGVKDFPDLAGKNVVTTAGTTSERLIRKMNEEKQMKMNIISAKDHGESF 188 Query: 190 QMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAVDD 249 LE+GRAVAFMMDDALL GEMAKAK+P DW V GTAQS E YGCM+RK DA FKK VD Sbjct: 189 LTLESGRAVAFMMDDALLYGEMAKAKRPGDWVVVGTAQSKEAYGCMLRKDDAGFKKVVDA 248 Query: 250 AIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKA 298 A+ SGE KIY KWFM PIPPKGLNL P+S+++KAL P DKA Sbjct: 249 ALTKAMTSGEAEKIYNKWFMNPIPPKGLNLNMPLSDDMKALYKAPNDKA 297 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: 317 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 304 Length of database: 299 Length adjustment: 27 Effective length of query: 277 Effective length of database: 272 Effective search space: 75344 Effective search space used: 75344 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 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