Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_008538691.1 HMPREF9454_RS06610 PTS transporter subunit EIIC
Query= TCDB::Q1LZ59 (655 letters) >NCBI__GCF_000245775.1:WP_008538691.1 Length = 458 Score = 330 bits (845), Expect = 1e-94 Identities = 199/490 (40%), Positives = 294/490 (60%), Gaps = 45/490 (9%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 +V +TAC TGIAHTYMA EAL K A EMG IK+ET G V N L+ +DI+ A VIIA Sbjct: 3 IVGITACPTGIAHTYMAAEALTKAAQEMGHEIKIETQGVE-VENILSDNDIQSADIVIIA 61 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAG 288 K V++ RF GK + P+ +K P+++I +DGK + +L+ E + +KA Sbjct: 62 CQKTVDLSRFEGKRVTEIPIERAVKNPQKVIQDAIDGKNISIF----ELAKEDKAKKKAQ 117 Query: 289 LGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQV 348 + YKHLMSGV+ MLPFVI GGI+IA SF+ G+ K+S + +++ IA + + Sbjct: 118 Q-TGIYKHLMSGVNFMLPFVISGGILIAFSFMF----GI-KASDPNDPSFNVIAKALSDI 171 Query: 349 GN-AAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASL 407 G AAFG M+P+ AA IAYSIA K G+ +G VAG +A + Sbjct: 172 GGGAAFGMMVPMLAAGIAYSIAGKQGMCSGMVAGVIAKS--------------------- 210 Query: 408 TGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLF-V 466 I +GFLG L G AG + L + + +P++++ +K ++L PL+ V +TG M+F V Sbjct: 211 --IGAGFLGGLIGAIFAGYLTKTLMEKI-HLPKAIQTLKGLILVPLISVFITGMFMIFIV 267 Query: 467 NIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALA 526 P+ + L N+L ++ + V+ GLI+G MMA DMGGP NKA ST + A ++ Sbjct: 268 GEPVKFLLDGLTNYLNSMDSSNGVIFGLIIGAMMASDMGGPINKAI-----STFSIALMS 322 Query: 527 KGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGA 586 G +A+ M GM PPL + +AT+LFK +FT+EE +AG + V+GLS+ITEGAIPF Sbjct: 323 TGVYAPIAACMVAGMTPPLGLALATVLFKKRFTKEEREAGKSCWVLGLSYITEGAIPFAV 382 Query: 587 GDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVI 643 DP R IP+ ++GSAV GA+ +G +APHGGI+++ + +N +Y+L + G+++ Sbjct: 383 ADPIRVIPALMLGSAVAGAISLGAGCASLAPHGGIWILPIPNVITNLPMYVLALVAGSIV 442 Query: 644 AGILFGSLRK 653 + L++ Sbjct: 443 TCLSVALLKR 452 Lambda K H 0.320 0.137 0.381 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: 761 Number of extensions: 51 Number of successful extensions: 7 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: 655 Length of database: 458 Length adjustment: 36 Effective length of query: 619 Effective length of database: 422 Effective search space: 261218 Effective search space used: 261218 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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