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 AO356_07325 AO356_07325 PTS fructose transporter subunit IIBC
Query= TCDB::P71012 (635 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07325 Length = 580 Score = 430 bits (1106), Expect = e-125 Identities = 220/481 (45%), Positives = 326/481 (67%), Gaps = 24/481 (4%) Query: 158 EEEEAAPAPAGKG----KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGI 213 E + +A PA +++A+TACPTG+AHTFMAA+AL++ A +LG +++VET GS G Sbjct: 105 EADASAQVPAASAERAPRLVAITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGA 164 Query: 214 KHKLTAQEIEDAPAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIY 273 ++ L+A+ I +A +++A D +V ERF GK++ + +++ + + KA+ + Sbjct: 165 RNPLSAEAIAEADVVLLATDIEVATERFAGKKIYRCGTGIALKQAEATLNKALVEARQES 224 Query: 274 QGSGGGSAASNDDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHS 333 SG + A ++ K+G+ YKHL++GVS MLP VV GG+++A+SF +GI + Sbjct: 225 ASSGASAPAKSE------KTGA------YKHLLTGVSFMLPMVVAGGLMIALSFVFGIEA 272 Query: 334 ADPNDPSYNTFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANA 393 +P T AAAL IGG+ A KL+V +LAG+IA SIADRPG APGM+GG +A+ A Sbjct: 273 F--KEPG--TLAAALMQIGGETAFKLMVPLLAGYIAYSIADRPGLAPGMIGGMLASTLGA 328 Query: 394 GFLGGLIAGFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVA 453 GF+GG+IAGFLAGY + + + +PQSL+ LKP+LI PL TG++M ++V PVA Sbjct: 329 GFIGGIIAGFLAGYAAKAISR-YARLPQSLEALKPILIIPLLASLFTGLVMIYIVGKPVA 387 Query: 454 AFMNFLTNWLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAI 513 + LT++L+S+GT N +L+G++LG MM +D+GGP+NKAA+ F + ++ + +YAP AA Sbjct: 388 GMLEALTHFLDSMGTTNAILLGVLLGAMMCVDLGGPINKAAYAFSVGLLASQSYAPMAAA 447 Query: 514 MAGGMVPPLGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAA 573 MA GMVPP+G+ +AT I R KF Q +REAG +G F++EGAIPFAA DPLRVIPA+ Sbjct: 448 MAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPAS 507 Query: 574 VVGAAVAGGLTEFFRVTLPAPHGGVFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKK 630 + G A+ G L+ +F L APHGG+FV I NH +LYLL+IV G+++ A+ ++K+ Sbjct: 508 IAGGALTGALSMYFGCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVAYALLKR 567 Query: 631 P 631 P Sbjct: 568 P 568 Score = 48.1 bits (113), Expect = 1e-09 Identities = 25/78 (32%), Positives = 43/78 (55%) Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230 K+ VTACP G+ + + A L A+ G VE + ++ + +L+A +E A +++ Sbjct: 2 KLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLL 61 Query: 231 AADKQVEMERFKGKRVLQ 248 A V++ RF GKRV + Sbjct: 62 VASGPVDLSRFVGKRVFR 79 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: 765 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