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 GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component
Query= TCDB::P71012 (635 letters) >FitnessBrowser__psRCH2:GFF3289 Length = 579 Score = 434 bits (1116), Expect = e-126 Identities = 226/527 (42%), Positives = 344/527 (65%), Gaps = 21/527 (3%) Query: 111 NTHLEALSRLSTLLMREEIRKQLLEAESEDAIID----IINQHDKDDDEEEEEEEAAPAP 166 N L + + L ++ + K++ ++ +A++D + + D + ++ +E A Sbjct: 55 NADLVVVVKTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSAADTASELQQADEAEAAHT 114 Query: 167 AGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAP 226 +GK K++AVTACPTG+AHTFMAA+AL++ A G +++VET GS G ++ L A I A Sbjct: 115 SGKPKLVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAAD 174 Query: 227 AIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDD 286 +++AAD +V++ RF GKRV + +++P+ +++A+ + A + SG A S Sbjct: 175 VVLLAADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALEEGAVL---SGNAVATSASG 231 Query: 287 EEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAA 346 E+ K+G YKH+++GVS MLP VV GG+L+A+SF +GI + T AA Sbjct: 232 EKKGEKTG------VYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKEE----GTLAA 281 Query: 347 ALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAG 406 AL IGG+ A +L+V +LAG+IA SIADRPG APGM+GG +A AGF+GG+IAGF+AG Sbjct: 282 ALMKIGGETAFQLMVPLLAGYIAYSIADRPGLAPGMIGGLLAGTLGAGFIGGIIAGFVAG 341 Query: 407 YVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESL 466 Y + + +P S++ LKP+LI PL +TG++M ++V TPVA + LT +L+++ Sbjct: 342 YAAKAVSRWIP-LPASIESLKPILIIPLLASLVTGLVMIYIVGTPVAKLLAGLTEFLDTM 400 Query: 467 GTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIAL 526 GT N +L+G++LG MM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ + Sbjct: 401 GTSNAILLGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGMGI 460 Query: 527 ATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEF 586 AT I R KF Q +REAG +G F++EGAIPFAA DPLRVIPA++ G A+ G L+ Sbjct: 461 ATLIARRKFAQTEREAGKAALVLGCCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMA 520 Query: 587 FRVTLPAPHGGVFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKK 630 F L APHGG+FV I NH +LYL++I+ G++V +I ++K+ Sbjct: 521 FGAKLLAPHGGLFVLLIPNAINHALLYLVAILAGSLVTGVIYAVIKQ 567 Score = 54.7 bits (130), Expect = 1e-11 Identities = 34/132 (25%), Positives = 62/132 (46%), Gaps = 2/132 (1%) Query: 172 ILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVA 231 +L VTACP G+ + + + L+ A LG VE + I LT +I +A ++V Sbjct: 3 LLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVVVV 62 Query: 232 ADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEE--A 289 + ++RF GKRV Q + + P+ + A + + + Q +A ++ + A Sbjct: 63 KTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSAADTASELQQADEAEAAHTSGKPKLVA 122 Query: 290 KGKSGSGIGNTF 301 +G+ +TF Sbjct: 123 VTACPTGVAHTF 134 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: 791 Number of extensions: 36 Number of successful extensions: 6 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: 579 Length adjustment: 37 Effective length of query: 598 Effective length of database: 542 Effective search space: 324116 Effective search space used: 324116 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