Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_086509379.1 BZY95_RS07790 PTS system fructose-like transporter subunit IIB
Query= TCDB::Q1LZ59 (655 letters) >NCBI__GCF_002151265.1:WP_086509379.1 Length = 580 Score = 340 bits (873), Expect = 8e-98 Identities = 212/526 (40%), Positives = 298/526 (56%), Gaps = 54/526 (10%) Query: 139 PDDVINLFNATEEEKKEATPA-APVADSHDF-----LVAVTACTTGIAHTYMAEEALKKQ 192 PD L A E + PA + A+ H +VAVTAC TG+AHT+MA EAL + Sbjct: 87 PDPEAFLQRAQREAESFTPPAQSAAANQHKAPGGSKIVAVTACPTGVAHTFMAAEALSEA 146 Query: 193 AAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGI 252 +G I+VET G+ G NKLT ++I A VI+A D V+ RF GK + + Sbjct: 147 GKSLGHEIRVETQGSVGAQNKLTDEEIAAADVVILACDIEVDPTRFAGKRIYRTSTGNAL 206 Query: 253 KKPEELINIILDGKAEAYVADNSDLS-SEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGG 311 KKP I LD +A V D+ S+AS S K YKHL++GVS MLP V+ G Sbjct: 207 KKPRPTIEAALD---QAEVEDSGTARRSDASRSIKE---KGVYKHLLTGVSFMLPMVVAG 260 Query: 312 GIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEK 371 G++IALSF+ + +L+ AA+ G AF MIPV A YIAYSIA++ Sbjct: 261 GLLIALSFVFGIEAFQEEGTLA--------AALMQIGGGTAFALMIPVLAGYIAYSIADR 312 Query: 372 PGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVL 431 PG+ G + G +A I +GF+G + GFLAG V L + Sbjct: 313 PGIAPGMIGGMLAAN-----------------------IEAGFIGGIIAGFLAGYVALAV 349 Query: 432 KKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-NIPMAAINTALYNFLGNLSGGSAV 490 + + +P S+E +K IL+ PL+ LVTG M+++ P+AAI L FL + +AV Sbjct: 350 TRHVK-LPASVESLKPILIIPLVSSLVTGLTMIYIIGEPVAAILAGLTGFLAGMDATNAV 408 Query: 491 LLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVA 550 LLG+++G MM D+GGP NKAAY FG L + A MA++MA GMVP + + +A Sbjct: 409 LLGILLGAMMCFDLGGPVNKAAYTFGVGLLASQTYAP-----MAAIMAAGMVPAIGMGIA 463 Query: 551 TLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLS 610 + + ++KF++ E +AG + V+GL FI+EGAIPF A DP R IP+ I G AVTGAL L Sbjct: 464 SFVARHKFSEPEREAGKASFVLGLCFISEGAIPFAAKDPLRVIPACIAGGAVTGALSMLV 523 Query: 611 GIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIAGILFGSLRK 653 G +LMAPHGGIFV+ + + LLYL I +G+++ G+ + ++++ Sbjct: 524 GAQLMAPHGGIFVLLIPNAITPVLLYLGAIVIGSLVTGLGYAAIKR 569 Score = 55.1 bits (131), Expect = 9e-12 Identities = 35/123 (28%), Positives = 62/123 (50%), Gaps = 4/123 (3%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 ++ VTAC +G+A T++A L++ A +G +E + ++AD I A+ +++A Sbjct: 3 VIIVTACPSGMATTFLAARRLEQAARRLGWQASIEMHSQLEAVEPVSADAIAAAELIVVA 62 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAG 288 AD+ +RF GK L + E + PE + +AE++ S A++ KA Sbjct: 63 ADQIPAAERFAGKQLFRAAIGEALPDPEAFLQ-RAQREAESF---TPPAQSAAANQHKAP 118 Query: 289 LGS 291 GS Sbjct: 119 GGS 121 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: 917 Number of extensions: 56 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 655 Length of database: 580 Length adjustment: 37 Effective length of query: 618 Effective length of database: 543 Effective search space: 335574 Effective search space used: 335574 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