Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate YP_428809.1 Rru_A3728 extracellular ligand-binding receptor
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000013085.1:YP_428809.1 Length = 392 Score = 141 bits (355), Expect = 3e-38 Identities = 105/338 (31%), Positives = 160/338 (47%), Gaps = 10/338 (2%) Query: 5 TQRLSRLFAAMAIA-GFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKA 63 T R L A A+A GFA + +AD IKI A +TG A + GA +AI+ +N A Sbjct: 6 TTRAGLLAGAFALAIGFAGPAASADPIKIGGAFNLTGGQASLDGPAKNGAQLAIDTLNAA 65 Query: 64 GGVNGAQLEGVIYDDACDPKQAVAVANKVVN-DGVKFVVGHVCSSSTQPATDIYEDEGVL 122 GGVNG LE V+YD DP ++ ++++N D V ++G S + GV Sbjct: 66 GGVNGTPLELVVYDGKTDPAVVASLGSQLINSDKVSAIIGFSDSDPVLALGPNAQKAGVP 125 Query: 123 MITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHD-KQQYGEGI 181 I AT+P++ + +F DN Q V F + K K++ VL D +Y + Sbjct: 126 FIAVGATSPKLPDQIGDTMFLACFGDNTQAAVGASFAIDDLKAKSVYVLEDTANEYATLL 185 Query: 182 ATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQ--FVYFGGYHPEMGLLLRQ 239 + ++T E G KV + GDK F A I+K+K A + +Y +GL++RQ Sbjct: 186 SKYFRETFEHLGGKVIGRDTYRTGDKSFTAQITKIKAAAEKPDILYIAATPDSIGLVVRQ 245 Query: 240 AKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDP---KNKALIDAF-KAK 295 +QAGL +G +G + + G ++ + T +F D K DA+ KA Sbjct: 246 VRQAGLKLPIVGGDGYDTPLLLEVGGASANNVYFT-THSFVSDSAPGPMKTFFDAYGKAY 304 Query: 296 NQDPSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEAL 333 P F Y V ++A I++AG DP + +AL Sbjct: 305 GNAPENAFAALGYDTVMLVADAIKRAGSGDPAAIRKAL 342 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: 377 Number of extensions: 23 Number of successful extensions: 5 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: 373 Length of database: 392 Length adjustment: 30 Effective length of query: 343 Effective length of database: 362 Effective search space: 124166 Effective search space used: 124166 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 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