Align PTS system cellobiose-specific EIIC component (characterized)
to candidate 8499436 DvMF_0208 EAL domain protein (RefSeq)
Query= SwissProt::Q9CJ32 (494 letters) >FitnessBrowser__Miya:8499436 Length = 762 Score = 132 bits (333), Expect = 3e-35 Identities = 75/213 (35%), Positives = 112/213 (52%), Gaps = 22/213 (10%) Query: 278 LIVTLFVSVFWFFGLHGPNVLAPVLDGIWGPLGLNNQALYFQVHSQGIRDLIAKGAVDKA 337 L+ T V WFFG HGPN+L P+ D I+ P G N A +A G V Sbjct: 265 LLYTGLSQVLWFFGAHGPNLLFPIEDAIFAPAGAANAAA------------LATGQVPPF 312 Query: 338 HAINGDYVNLWVRGSWDAFAWFGGSGGTITLVIAIILFSKRKDYKIVGRLGLAPGIFNIN 397 + + +D F GGSG T+ L+ AI+ S+ + + + L P + N+N Sbjct: 313 ---------VLTKTFFDVFTRMGGSGSTLCLIAAILYASRDSGTRRLALVALLPALCNVN 363 Query: 398 EPVLFGLPVVLNAIFFIPFAVAPLISVIIAYTATALHLVDPVVNAVPWVTPPIMNAFMAT 457 EP+LFGLP+V+N ++ IPF + PL A+ AT LHLV + V W TPP++N + AT Sbjct: 364 EPLLFGLPLVMNPVYLIPFLLVPLAQTAAAHAATLLHLVPYTLPDVVWTTPPLLNGYAAT 423 Query: 458 GFDWRAIVLTIINLIITFVIWVPFVIAANKLEE 490 G ++ +NL + +++PFV A++ L E Sbjct: 424 G-SVAGSLMQALNLGLGVALYLPFVRASDALRE 455 Lambda K H 0.326 0.141 0.430 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: 897 Number of extensions: 42 Number of successful extensions: 3 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: 494 Length of database: 762 Length adjustment: 37 Effective length of query: 457 Effective length of database: 725 Effective search space: 331325 Effective search space used: 331325 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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