Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 414 bits (1063), Expect = e-120 Identities = 222/468 (47%), Positives = 308/468 (65%), Gaps = 21/468 (4%) Query: 167 AGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAP 226 AGK +I+AVTACPTG+AHTFMAA+AL A+ G +I+VET GS G + LT +EI A Sbjct: 125 AGK-RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAAD 183 Query: 227 AIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDD 286 +I+A D +V+ RF GKRV + A +++P + I A+ Q + G Sbjct: 184 VVILACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQ---------- 233 Query: 287 EEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAA 346 ++ G SGSG YKHL++GVS MLP VV GG+L+A+SF +GI + T AA Sbjct: 234 KKTSGASGSGEKKGPYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQEE----GTLAA 289 Query: 347 ALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAG 406 AL IGG A KL++ +LAG+IA SIADRPG APGM+GGF+A + AGFLGG++AGFLAG Sbjct: 290 ALMQIGGGTAFKLMIPLLAGYIAWSIADRPGLAPGMIGGFLAGELGAGFLGGIVAGFLAG 349 Query: 407 YVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESL 466 YV + + +P+S++ LKP+LI PL +TG+ M +V+ P+AA M LT +LE + Sbjct: 350 YVARFISQKLP-MPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGM 408 Query: 467 GTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMID--AGNYAPHAAIMAGGMVPPLGI 524 GT N +L+G ILG MM D+GGP+NKAA+TFG+ ++ +G AP AAIMA GMVP +G+ Sbjct: 409 GTTNAILLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGM 468 Query: 525 ALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLT 584 +A+ I R KF + +R+AG + +G F++EGAIPF A DPLRVIP ++G A+ G L+ Sbjct: 469 GVASFIARRKFAEAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALS 528 Query: 585 EFFRVTLPAPHGGVFVAFITN---HPMLYLLSIVIGAVVMAIILGIVK 629 F V L APHGG+FV I N + YL++I +G++V+ ++K Sbjct: 529 MLFTVKLMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLK 576 Score = 67.4 bits (163), Expect = 2e-15 Identities = 35/101 (34%), Positives = 56/101 (55%), Gaps = 1/101 (0%) Query: 172 ILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSG-IKHKLTAQEIEDAPAIIV 230 ++ VTACP G+A F+AA AL+ A G + +T G G +K + I+ A +I Sbjct: 3 LIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLVIA 62 Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAP 271 A V ++ + GKR+LQ+PVTA + P ++ +A + P Sbjct: 63 AVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRAQAEATP 103 Lambda K H 0.320 0.137 0.390 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: 885 Number of extensions: 34 Number of successful extensions: 7 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: 635 Length of database: 587 Length adjustment: 37 Effective length of query: 598 Effective length of database: 550 Effective search space: 328900 Effective search space used: 328900 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