Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 335 bits (858), Expect = 5e-96 Identities = 209/488 (42%), Positives = 284/488 (58%), Gaps = 44/488 (9%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 +VAVTAC TG+AHT+MA EAL A G I+VET G+ G + LT ++I A VI+A Sbjct: 129 IVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVILA 188 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAG 288 D V+ RF+GK + +KKP + I L+ +A A S + S EK G Sbjct: 189 CDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALE-QAVVLNAGQKKTSGASGSGEKKG 247 Query: 289 LGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQV 348 YKHL++GVS MLP V+ GG++IALSF+ + +L+ AA+ Sbjct: 248 P----YKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQEEGTLA--------AALMQIG 295 Query: 349 GNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLT 408 G AF MIP+ A YIA+SIA++PGL G + G +A GE Sbjct: 296 GGTAFKLMIPLLAGYIAWSIADRPGLAPGMIGGFLA--------------GE-------- 333 Query: 409 GIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-N 467 + +GFLG + GFLAG V + + L +P S+E +K IL+ PLL LVTG M++V Sbjct: 334 -LGAGFLGGIVAGFLAGYVARFISQKLP-MPESIESLKPILIIPLLASLVTGLGMIYVIG 391 Query: 468 IPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAK 527 PMAAI AL FL + +A+LLG I+G MM D+GGP NKAAY FG L+ + Sbjct: 392 EPMAAIMGALTGFLEGMGTTNAILLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGS--- 448 Query: 528 GGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAG 587 GGS MA++MA GMVP + + VA+ + + KF + E AG + V+GL FI+EGAIPF A Sbjct: 449 GGSAPMAAIMAAGMVPAIGMGVASFIARRKFAEAERQAGRASFVLGLCFISEGAIPFMAK 508 Query: 588 DPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIA 644 DP R IP ++G A+TGAL L +KLMAPHGG+FV+A+ S L YL+ IAVG+++ Sbjct: 509 DPLRVIPVCMIGGAITGALSMLFTVKLMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVI 568 Query: 645 GILFGSLR 652 G + L+ Sbjct: 569 GFGYALLK 576 Score = 54.7 bits (130), Expect = 1e-11 Identities = 38/120 (31%), Positives = 60/120 (50%), Gaps = 4/120 (3%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASG-VGNKLTADDIKRAKGVII 227 L+ VTAC G+A ++A AL++ A G + +T G G NK + I++A VI Sbjct: 3 LIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLVIA 62 Query: 228 AADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKA 287 A V +D + GK L+ PV + P+ I+ +AEA D + S E+ ++ A Sbjct: 63 AVGIPVNLDVYAGKRLLQIPVTAALPDPDA---ILTRAQAEATPWDPAMASQESIATSTA 119 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: 949 Number of extensions: 54 Number of successful extensions: 11 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: 587 Length adjustment: 37 Effective length of query: 618 Effective length of database: 550 Effective search space: 339900 Effective search space used: 339900 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 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