Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05475 Length = 579 Score = 334 bits (856), Expect = 8e-96 Identities = 209/544 (38%), Positives = 310/544 (56%), Gaps = 54/544 (9%) Query: 119 ELSQYLLKDGFADKLRQVTNPDDVINLFNATEEEKKEATPA----APVADSHDFLVAVTA 174 ++S+++ K F Q D + A E + A A A V+ + LVAVTA Sbjct: 68 DMSRFVGKRVFQSTPSQALQDVDAVLRRGAEEAQIYVAPQAVVEPATVSKTAPRLVAVTA 127 Query: 175 CTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAVE 234 C TG+AHT+MA EAL++ A +G ++VET G+ G N L+A I A V++AAD V Sbjct: 128 CPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAQAIADADVVLLAADIEVA 187 Query: 235 MDRFNGKPLISRPVAEGIKKPEELINIIL-DGKAEAYVADNSDLSSEASSSEKAGLGSAF 293 +RF GK + +K+ E +N L +GK E +S + A EK G+ Sbjct: 188 TERFAGKKIYRCGTGIALKQAEATLNKALAEGKQETA---SSGVQGPAKK-EKTGV---- 239 Query: 294 YKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAF 353 YKHL++GVS MLP V+ GG+MIALSF+ +L+ AA+ G+ AF Sbjct: 240 YKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEPGTLA--------AALMQIGGDTAF 291 Query: 354 GFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSG 413 M+P+ A YIAYSIA++PGL G + G +A+T + +G Sbjct: 292 KLMVPLLAGYIAYSIADRPGLAPGMIGGLLAST-----------------------LGAG 328 Query: 414 FLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-NIPMAA 472 F+G + GF+AG + + A +P+SLE +K IL+ PLL L TG +M++V P+A Sbjct: 329 FIGGIIAGFIAGYAAQAINR-YARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAG 387 Query: 473 INTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVV 532 + +L +FL ++ +A+LLG+++GGMM +D+GGP NKAAY F L + + A Sbjct: 388 LLESLTHFLDSMGTTNAILLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAP----- 442 Query: 533 MASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARA 592 MA+ MA GMVPP+ + +AT + + KF Q E +AG +V+GL FI+EGAIPF A DP R Sbjct: 443 MAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRV 502 Query: 593 IPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIAGILFG 649 IP+ I G A+ GAL G KLMAPHGG+FV+ + ++ LLYLL I G+++ +++ Sbjct: 503 IPASIAGGALAGALSMYFGCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYA 562 Query: 650 SLRK 653 ++++ Sbjct: 563 AVKR 566 Score = 41.2 bits (95), Expect = 1e-07 Identities = 26/104 (25%), Positives = 51/104 (49%), Gaps = 1/104 (0%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 L VTAC G+ + + L A G VE + A+ +L+A ++ A+ V++ Sbjct: 3 LAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEDAEWVLLV 62 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVA 272 + V+M RF GK + ++ ++ + ++ + +A+ YVA Sbjct: 63 STGTVDMSRFVGKRVFQSTPSQALQDVDAVLRRGAE-EAQIYVA 105 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: 825 Number of extensions: 37 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: 579 Length adjustment: 37 Effective length of query: 618 Effective length of database: 542 Effective search space: 334956 Effective search space used: 334956 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