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 BWI76_RS19725 BWI76_RS19725 PTS fructose transporter subunit EIIBC
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Koxy:BWI76_RS19725 Length = 558 Score = 421 bits (1081), Expect = e-122 Identities = 219/470 (46%), Positives = 310/470 (65%), Gaps = 18/470 (3%) Query: 165 APAGKGKILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIED 224 A G +I+AVTACPTG+AHTFMAA+A++ +AK+ G +KVET GS G + +T +E+E Sbjct: 99 AANGPKRIVAVTACPTGVAHTFMAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVEQ 158 Query: 225 APAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASN 284 A ++VAAD +V++ +F GK + + +++ + ++KA+ + P YQ +G AA+ Sbjct: 159 ADLVVVAADIEVDLAKFAGKPMYRTTTGLALKKTAQELDKAVVEAKP-YQPAGKSQAAAE 217 Query: 285 DDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTF 344 +E+ G Y+HL++GVS MLP VV GG+ +A+SF +GI + + D T Sbjct: 218 GKKESAGA---------YRHLLTGVSYMLPMVVAGGLCIALSFAFGIKAFEVKD----TL 264 Query: 345 AAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFL 404 AAAL IGG +A L+V VLAGFIA SIADRPG PG++GG +A +GF+GG+IAGFL Sbjct: 265 AAALMQIGGGSAFALMVPVLAGFIAFSIADRPGLTPGLIGGMLAVSTGSGFIGGIIAGFL 324 Query: 405 AGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLE 464 AGYV + +PQS++ LKP+LI PL I G+ M +++ PVA + LT+WL+ Sbjct: 325 AGYVAKAISTKLK-LPQSMEALKPILIIPLVSSLIVGLAMIYLIGKPVAGILEGLTHWLQ 383 Query: 465 SLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGI 524 ++GT N VL+G ILGGMM DMGGP+NKAA+ FG+ ++ YAP AAIMA GMVPPL + Sbjct: 384 TMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYAPMAAIMAAGMVPPLAL 443 Query: 525 ALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLT 584 LAT I R KF + +E G +G F+TEGAIPFAA DP+RV+P +VG AV G ++ Sbjct: 444 GLATLIARKKFDKAQQEGGKAALVLGLCFITEGAIPFAARDPMRVLPCCIVGGAVTGAMS 503 Query: 585 EFFRVTLPAPHGGVFVAFITN--HPML-YLLSIVIGAVVMAIILGIVKKP 631 + L APHGG+FV I P+L YL++IV+G +V + ++K+P Sbjct: 504 MWVGAKLMAPHGGLFVLLIPGAITPVLGYLMAIVVGTLVAGLSYAVLKRP 553 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: 844 Number of extensions: 39 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: 558 Length adjustment: 37 Effective length of query: 598 Effective length of database: 521 Effective search space: 311558 Effective search space used: 311558 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