Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Miya:8502037 Length = 375 Score = 205 bits (522), Expect = 1e-57 Identities = 126/367 (34%), Positives = 201/367 (54%), Gaps = 15/367 (4%) Query: 8 LSRLFAAMAIAGFASYSMAADT----IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKA 63 + + A+ +A AS MAA +KI L P+TG A G R + +++NKA Sbjct: 1 MKHVVKALTLALAASLLMAATAFAAPVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKA 60 Query: 64 GGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLM 123 GG+NG ++E V+ DD DP+ A A K+ GV +G S+ T+ + IY++ GV+ Sbjct: 61 GGINGNKVELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAGVVQ 120 Query: 124 ITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFI-AERYKDKTIAVLHDKQQYGEGIA 182 I +TA +T +G K RT D+ QG VA K I A+ Y K +A+LHD Y +G+A Sbjct: 121 IATGSTAVRLTEKGLKRFLRTAPRDDEQGMVAAKLIKAKGY--KAVALLHDNSSYAKGLA 178 Query: 183 TEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQ 242 E K ++ AG K+ ++ L G++D+ A+++KLK A ++ GY+PE+G+LLRQ + Sbjct: 179 DETKALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQKME 238 Query: 243 AGLDARFMGPEGVGNSEITAIAG-DASEGMLATLPRAFEQD---PKNKALIDAFKAK-NQ 297 + MG + ++++ I+G +A++G P QD P K+++ A+KAK N Sbjct: 239 MKWNVPMMGGDAANHADLVKISGKEAAKGYFFLSPPG-PQDLDAPAAKSMLTAYKAKYNG 297 Query: 298 DPSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETP--TGNLGFDEKGDLKN 355 P ++ + A A VI + ++ G+AD +AE L+ P TG + F+EKGD Sbjct: 298 VPGSVWSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDRVG 357 Query: 356 FDFTVYE 362 + VYE Sbjct: 358 DLYRVYE 364 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: 338 Number of extensions: 19 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: 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