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 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Keio:16276 Length = 563 Score = 404 bits (1039), Expect = e-117 Identities = 211/473 (44%), Positives = 308/473 (65%), Gaps = 17/473 (3%) Query: 162 AAPAPAGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQE 221 A A +G +++AVTACPTG+AHTFMAA+A++ +AK+ G +KVET GS G + +T +E Sbjct: 96 APVAASGPKRVVAVTACPTGVAHTFMAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEE 155 Query: 222 IEDAPAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSA 281 + A +IVAAD +V++ +F GK + + +++ + ++KA+ + P Y+ +G Sbjct: 156 VAAADLVIVAADIEVDLAKFAGKPMYRTSTGLALKKTAQELDKAVAEATP-YEPAGKAQT 214 Query: 282 ASNDDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSY 341 A+ E K +G+ Y+HL++GVS MLP VV GG+ +A+SF +GI + +P Sbjct: 215 ATT--ESKKESAGA------YRHLLTGVSYMLPMVVAGGLCIALSFAFGIEAF--KEPG- 263 Query: 342 NTFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIA 401 T AAAL IGG +A L+V VLAG+IA SIADRPG PG++GG +A +GF+GG+IA Sbjct: 264 -TLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLTPGLIGGMLAVSTGSGFIGGIIA 322 Query: 402 GFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTN 461 GFLAGY+ L+ +PQS++ LKP+LI PL + G+ M +++ PVA + LT+ Sbjct: 323 GFLAGYIAKLISTQLK-LPQSMEALKPILIIPLISSLVVGLAMIYLIGKPVAGILEGLTH 381 Query: 462 WLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPP 521 WL+++GT N VL+G ILGGMM DMGGP+NKAA+ FG+ ++ Y P AAIMA GMVPP Sbjct: 382 WLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYGPMAAIMAAGMVPP 441 Query: 522 LGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAG 581 L + LAT + R KF + +E G +G F++EGAIPFAA DP+RV+P +VG A+ G Sbjct: 442 LAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIPFAARDPMRVLPCCIVGGALTG 501 Query: 582 GLTEFFRVTLPAPHGGVFVAFITN--HPML-YLLSIVIGAVVMAIILGIVKKP 631 ++ L APHGG+FV I P+L YL++I+ G +V + +K+P Sbjct: 502 AISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAGTLVAGLAYAFLKRP 554 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: 831 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 635 Length of database: 563 Length adjustment: 37 Effective length of query: 598 Effective length of database: 526 Effective search space: 314548 Effective search space used: 314548 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