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 PP_0795 PP_0795 fructose PTS permease - IIBC component
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Putida:PP_0795 Length = 580 Score = 432 bits (1111), Expect = e-125 Identities = 222/471 (47%), Positives = 320/471 (67%), Gaps = 18/471 (3%) Query: 163 APAPAGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEI 222 A A + +I+AVTACPTG+AHTFMAA+AL++ A++LG ++ VET GS G ++ L+A+ I Sbjct: 111 AAASSAGARIVAVTACPTGVAHTFMAAEALQQAAQQLGYQLTVETQGSVGARNPLSAEAI 170 Query: 223 EDAPAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAA 282 A +++AAD +V RF GKR+ + +++ + ++KA+ Q A + G+ +A Sbjct: 171 AAADVVLLAADIEVPTARFAGKRIYRCGTGIALKQARATLDKALAQ-ATVENGADAAAAT 229 Query: 283 SNDDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYN 342 + E G YKHL++GVS MLP VV GG+L+A+SF +GI + Sbjct: 230 TPTKSEKTG---------VYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAYK----EAG 276 Query: 343 TFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAG 402 T AAL IGG+ A KL+V +LAG+IA SIADRPG APGM+GG +A+ AGF+GG++AG Sbjct: 277 TLPAALMQIGGEAAFKLMVPLLAGYIAWSIADRPGLAPGMIGGLLASTLGAGFIGGIVAG 336 Query: 403 FLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNW 462 FLAGY + + + +P SL+ LKP+LI PL TG++M +VV PVAA + LT++ Sbjct: 337 FLAGYSAKAIAR-WARLPSSLEALKPILIIPLLASLFTGLVMIYVVGQPVAAMLEGLTHF 395 Query: 463 LESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPL 522 L+S+GT N +L+G++LGGMM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+ Sbjct: 396 LDSMGTTNAILLGLLLGGMMCVDLGGPINKAAYAFSVGLLASSSYAPMAATMAAGMVPPI 455 Query: 523 GIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGG 582 G+ +AT + R KF Q +REAG +G F++EGAIPFAA DPLRVIPA++ G A+ G Sbjct: 456 GLGIATFLARRKFAQSEREAGKAALALGLCFISEGAIPFAAKDPLRVIPASIAGGALTGA 515 Query: 583 LTEFFRVTLPAPHGGVFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKK 630 L+ +F L APHGG+FV I NH +LYLL+IV G++V A++ ++KK Sbjct: 516 LSMYFGCKLMAPHGGLFVLLIPNAINHALLYLLAIVAGSLVTAVVYAVIKK 566 Score = 49.7 bits (117), Expect = 4e-10 Identities = 34/132 (25%), Positives = 63/132 (47%), Gaps = 2/132 (1%) Query: 172 ILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVA 231 I VTACP G + ++A L A+ G VE + + +L+A +I +A ++V Sbjct: 3 IAIVTACPNGQVSSVLSARLLSAAAQRRGWSTSVEVQNTEHPERQLSAAQIAEADWVLVV 62 Query: 232 ADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEE--A 289 + V++ RF GKR+ Q + + + +++A + +G +AAS+ A Sbjct: 63 STGPVDLARFVGKRLYQSTPSQALADREGFLDEAAANAELLAAVTGAPAAASSAGARIVA 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: 761 Number of extensions: 33 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: 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