Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Ac3H11_2396 Extracellular ligand-binding receptor precursor
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2396 Length = 375 Score = 184 bits (467), Expect = 3e-51 Identities = 119/369 (32%), Positives = 186/369 (50%), Gaps = 9/369 (2%) Query: 10 RLFAAMAIAGFASYSMAAD-TIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68 +L AIA A + A + +KI PV+G A YG GA MAIE++N G G Sbjct: 6 KLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIG 65 Query: 69 AQ---LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMIT 125 + E V DDA DPKQ A A K+ + V VVGH+ S +T PA+ +Y D G+ +T Sbjct: 66 GKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVT 125 Query: 126 PSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEV 185 +AT P +T GYK FR I DN G + + K KT+A++ D+ YG+G+A Sbjct: 126 GAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVF 185 Query: 186 KKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGL 245 KKT G+KV + DF A+++ +K +++GG P+ G +LRQ +Q G+ Sbjct: 186 KKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGM 245 Query: 246 -DARFMGPEGVGNSEITAIAGDA---SEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSG 301 + ++ G +G+ SEI +A A + A + + P A + AK + Sbjct: 246 GNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQ 305 Query: 302 IFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVY 361 ++ Y A +I +++A DP+ L ++F+ T + F+ G++KN T+Y Sbjct: 306 VYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLY 365 Query: 362 EWHKDATRT 370 +KD +T Sbjct: 366 V-YKDGKKT 373 Lambda K H 0.316 0.133 0.377 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: 355 Number of extensions: 17 Number of successful extensions: 3 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: 373 Length of database: 375 Length adjustment: 30 Effective length of query: 343 Effective length of database: 345 Effective search space: 118335 Effective search space used: 118335 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: 50 (23.9 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