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 AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC
Query= TCDB::P71012 (635 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05475 Length = 579 Score = 441 bits (1135), Expect = e-128 Identities = 234/519 (45%), Positives = 344/519 (66%), Gaps = 26/519 (5%) Query: 122 TLLMREEIRKQLLEAESEDAI--IDIINQHDKDDDEEEEEEEAAPAPAGKGK----ILAV 175 T+ M + K++ ++ A+ +D + + ++ + +A PA K ++AV Sbjct: 66 TVDMSRFVGKRVFQSTPSQALQDVDAVLRRGAEEAQIYVAPQAVVEPATVSKTAPRLVAV 125 Query: 176 TACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQ 235 TACPTG+AHTFMAA+AL++ AK LG +++VET GS G ++ L+AQ I DA +++AAD + Sbjct: 126 TACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAQAIADADVVLLAADIE 185 Query: 236 VEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGS 295 V ERF GK++ + +++ + + KA+ + G AS+ + K + Sbjct: 186 VATERFAGKKIYRCGTGIALKQAEATLNKALAE--------GKQETASSGVQGPAKKEKT 237 Query: 296 GIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDN 355 G+ YKHL++GVS MLP VV GG+++A+SF +GI + +P T AAAL IGGD Sbjct: 238 GV----YKHLLTGVSFMLPMVVAGGLMIALSFVFGITAF--KEPG--TLAAALMQIGGDT 289 Query: 356 ALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKV 415 A KL+V +LAG+IA SIADRPG APGM+GG +A+ AGF+GG+IAGF+AGY + + Sbjct: 290 AFKLMVPLLAGYIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFIAGYAAQAINR- 348 Query: 416 FTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMG 475 + +PQSL+ LKP+LI PL TG++M +VV PVA + LT++L+S+GT N +L+G Sbjct: 349 YARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGLLESLTHFLDSMGTTNAILLG 408 Query: 476 IILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKF 535 ++LGGMM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ +AT I R KF Sbjct: 409 VLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKF 468 Query: 536 TQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPH 595 Q +REAG +G F++EGAIPFAA DPLRVIPA++ G A+AG L+ +F L APH Sbjct: 469 AQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLMAPH 528 Query: 596 GGVFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKKP 631 GG+FV I NH +LYLL+IV G+++ A++ VK+P Sbjct: 529 GGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYAAVKRP 567 Score = 53.5 bits (127), Expect = 2e-11 Identities = 30/103 (29%), Positives = 55/103 (53%), Gaps = 1/103 (0%) Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230 K+ VTACP G+ + + A L A+ G VE + ++ + +L+A +EDA +++ Sbjct: 2 KLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEDAEWVLL 61 Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIY 273 + V+M RF GKRV Q + ++ ++ + ++A IY Sbjct: 62 VSTGTVDMSRFVGKRVFQSTPSQALQDVDAVLRRGA-EEAQIY 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: 789 Number of extensions: 33 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