Align leucine-specific-binding protein LivK (characterized)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)
Query= CharProtDB::CH_107418 (369 letters) >FitnessBrowser__Miya:8502037 Length = 375 Score = 181 bits (458), Expect = 4e-50 Identities = 118/371 (31%), Positives = 196/371 (52%), Gaps = 10/371 (2%) Query: 1 MKRNAKTIIAGMIA-LAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAK 59 MK K + + A L ++ TA A +K+ ++ ++G A G N ++N Sbjct: 1 MKHVVKALTLALAASLLMAATAFAAPVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKA 60 Query: 60 GGIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILM 119 GGI G+K+ V DD DP+ A A K+ G+ IG S+ T+ + IY++ G++ Sbjct: 61 GGINGNKVELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAGVVQ 120 Query: 120 ISPGATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLAR 179 I+ G+T LT++G + +RTA D QG AAK +++ + +A++HD Y +GLA Sbjct: 121 IATGSTAVRLTEKGLKRFLRTAPRDDEQGMVAAK-LIKAKGYKAVALLHDNSSYAKGLAD 179 Query: 180 SVQDGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSV 239 + L A +VF+D +T GE+D++A++ +LK N D ++ GYYPE+G +LRQ + Sbjct: 180 ETKALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQKMEM 239 Query: 240 GLKTQFMGPEGVGNASLSNIAG-DAAEG-MLVTMPKRYDQD-PANQGIVDALKADKKDPS 296 MG + +A L I+G +AA+G ++ P D D PA + ++ A KA Sbjct: 240 KWNVPMMGGDAANHADLVKISGKEAAKGYFFLSPPGPQDLDAPAAKSMLTAYKAKYNGVP 299 Query: 297 GPYVWITYA--AVQSLATALERTGSDEPLALVKDLKANGAN--TVIGPLNWDEKGDLKGF 352 G VW A A + A++ TG + A+ + LK N G ++++EKGD G Sbjct: 300 GS-VWSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDRVGD 358 Query: 353 DFGVFQWHADG 363 + V++ +A+G Sbjct: 359 LYRVYEVNANG 369 Lambda K H 0.315 0.133 0.386 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: 366 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: 369 Length of database: 375 Length adjustment: 30 Effective length of query: 339 Effective length of database: 345 Effective search space: 116955 Effective search space used: 116955 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 (21.5 bits) S2: 49 (23.5 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