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 Pf6N2E2_3337 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
Query= TCDB::P71012 (635 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337 Length = 575 Score = 429 bits (1102), Expect = e-124 Identities = 227/517 (43%), Positives = 339/517 (65%), Gaps = 27/517 (5%) Query: 125 MREEIRKQLLEAESEDAIIDIINQHDKDDDEEE-----EEEEAAPAPAGKG--KILAVTA 177 M + K+L + A+ D+ + + +E E + E APA + +++A+TA Sbjct: 64 MSRFVGKRLFRSTPALALQDVDSVLRRGAEEAEVFLASDVVEQAPAVSTDRAPRLVAITA 123 Query: 178 CPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQVE 237 CPTG+AHTFMAA+AL++ A +LG +++VET GS G ++ L+A+ I +A +++A D +V Sbjct: 124 CPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLLATDIEVA 183 Query: 238 MERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGSGI 297 ERF GK++ + +++ + + KA+ + SG + A ++ K+G Sbjct: 184 TERFAGKKIYRCSTGIALKQAEATLNKALVEGRQESASSGASAPAKSE------KTG--- 234 Query: 298 GNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDNAL 357 YKHL++GVS MLP VV GG+++A+SF +GI + +P T AAAL IGGD A Sbjct: 235 ---VYKHLLTGVSFMLPMVVAGGLMIALSFVFGIEAF--KEPG--TLAAALMQIGGDTAF 287 Query: 358 KLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKVFT 417 KL+V +LAG+IA SIADRPG APGM+GG +A+ AGF+GG+IAGFLAGY + + + Sbjct: 288 KLMVPLLAGYIAYSIADRPGLAPGMIGGMLASTLGAGFIGGIIAGFLAGYAAKAISR-YA 346 Query: 418 FIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMGII 477 +PQSL+ LKP+LI PL TG++M ++V PVA + LT++L+S+GT N +L+G++ Sbjct: 347 RLPQSLEALKPILIIPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTNAILLGVL 406 Query: 478 LGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKFTQ 537 LG MM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ +AT I R KF Q Sbjct: 407 LGAMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQ 466 Query: 538 RDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPHGG 597 +REAG +G F++EGAIPFAA DPLRVIPA++ G A+ G L+ +F L APHGG Sbjct: 467 TEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGG 526 Query: 598 VFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKKP 631 +FV I NH +LYLL+IV G+++ + ++K+P Sbjct: 527 LFVMLIPNAINHALLYLLAIVAGSLLTGVAYALLKRP 563 Score = 46.2 bits (108), Expect = 4e-09 Identities = 24/74 (32%), Positives = 41/74 (55%) Query: 175 VTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADK 234 VTACP G+ + + A L A+ G VE + ++ + +L+A +E A +++ A Sbjct: 1 VTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLLVASG 60 Query: 235 QVEMERFKGKRVLQ 248 V+M RF GKR+ + Sbjct: 61 PVDMSRFVGKRLFR 74 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: 780 Number of extensions: 34 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: 575 Length adjustment: 37 Effective length of query: 598 Effective length of database: 538 Effective search space: 321724 Effective search space used: 321724 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