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 AZOBR_RS32335 AZOBR_RS32335 PTS fructose transporter subunit IIBC
Query= TCDB::P71012 (635 letters) >FitnessBrowser__azobra:AZOBR_RS32335 Length = 580 Score = 416 bits (1068), Expect = e-120 Identities = 228/481 (47%), Positives = 310/481 (64%), Gaps = 20/481 (4%) Query: 163 APAPAGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEI 222 APA G KI+A+T+CPTGIAHTFMAA+ +++ A+ LG ++VET GS G + LT QEI Sbjct: 105 APAQTGTKKIVAITSCPTGIAHTFMAAEGIQQAAQALGHAVRVETQGSVGARDTLTEQEI 164 Query: 223 EDAPAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAP------IYQGS 276 +A +++AAD QV++ RF GKRV + I + L+E+A+ + P + G Sbjct: 165 READVVLIAADTQVDLARFAGKRVFKSGTKPAINDGRALVERALAEAQPHGTAPALADGV 224 Query: 277 GGGSAASNDDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISF-FWGIHSAD 335 G AA + A+ +SG YKHLM+GVS MLPFVV GG+L+AI+F GI+ + Sbjct: 225 AAGKAAKAEHAAAQ-RSGP------YKHLMTGVSFMLPFVVTGGLLIAIAFALGGIYVFE 277 Query: 336 PNDPSYNTFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGF 395 D T AL IG A L+V LAG+IA SIADRPG PGMVGG +A AGF Sbjct: 278 --DSQQGTLGNALFQIGAKGAFALMVPALAGYIAFSIADRPGITPGMVGGILAANLGAGF 335 Query: 396 LGGLIAGFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAF 455 LGG++AGF+AGY L + + ++L+GLKPVLI PL G +TG+ M +VV PVA Sbjct: 336 LGGIVAGFIAGYATSFLNRNIR-LHKNLEGLKPVLILPLLGSLVTGLAMIYVVGAPVAEA 394 Query: 456 MNFLTNWLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMA 515 + L+ WL+ + + +L+G+++G MMA DMGGP+NKAA+ F +I + Y P AA MA Sbjct: 395 LATLSAWLKGMQGSSAILLGLLIGAMMAFDMGGPVNKAAYAFSTGLIASQVYTPMAAAMA 454 Query: 516 GGMVPPLGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVV 575 GMVPPLG+ALAT +F ++FT+ +REAG +G AF+TEGAIPFAA DPLRVIPA V+ Sbjct: 455 AGMVPPLGLALATKLFADRFTREEREAGNAAGILGIAFITEGAIPFAARDPLRVIPALVL 514 Query: 576 GAAVAGGLTEFFRVTLPAPHGGVFVAFITN---HPMLYLLSIVIGAVVMAIILGIVKKPV 632 GAA+ G ++ L PHGG+FV I N H Y++++V G V A+ L +K+PV Sbjct: 515 GAALTGAISMGIGAELKVPHGGIFVLPIPNAVTHLAGYVVALVAGTVTTAVALRFLKRPV 574 Query: 633 T 633 + Sbjct: 575 S 575 Score = 44.3 bits (103), Expect = 2e-08 Identities = 27/95 (28%), Positives = 48/95 (50%) Query: 172 ILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVA 231 +LAV A +AA+AL++ A LG I+VE S G+++ L + A +I+ Sbjct: 4 MLAVIAAGDLSTQAVLAAEALRKAAAALGHTIQVEVRSSLGVRNTLPTGAAQGAQGVILV 63 Query: 232 ADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAM 266 + ERF G + + A +R + ++E+A+ Sbjct: 64 GSGDLGEERFAGLKRSAAALDAVLRDARAVLEQAL 98 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: 864 Number of extensions: 41 Number of successful extensions: 5 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: 580 Length adjustment: 37 Effective length of query: 598 Effective length of database: 543 Effective search space: 324714 Effective search space used: 324714 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