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 WP_013431305.1 CALKRO_RS12210 PTS transporter subunit EIIC
Query= TCDB::P71012 (635 letters) >NCBI__GCF_000166775.1:WP_013431305.1 Length = 454 Score = 443 bits (1139), Expect = e-129 Identities = 238/463 (51%), Positives = 328/463 (70%), Gaps = 19/463 (4%) Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230 KI+AVT+CPTGIAHT+MAA+AL+ AKELGVEIKVET GS G ++++T +++++A A+I+ Sbjct: 3 KIVAVTSCPTGIAHTYMAAEALQMAAKELGVEIKVETRGSVGAENEITPEDLKEAHAVIL 62 Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAK 290 A D +++ +RF+G +++ V I+ P+ LI KAMN + Y +EAK Sbjct: 63 ACDTKIDEDRFQGLPIVRASVKDAIKDPKGLITKAMNMEKKDYVDK-----VFEAKKEAK 117 Query: 291 GKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNF 350 K+ +G+ YKHLM+GVS M+PFVV GGIL+AISF +GI + + T AAAL Sbjct: 118 EKA-TGV----YKHLMTGVSYMIPFVVAGGILIAISFAFGIKAFEKK----GTLAAALMD 168 Query: 351 IGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVI 410 IGG +A L+V +LAGFIA SIADRPG PGM+GG +A + AGFLGG++AGF AGY+V Sbjct: 169 IGGGSAFYLMVPILAGFIAFSIADRPGLVPGMIGGLLANKLGAGFLGGIVAGFAAGYLVA 228 Query: 411 LLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGN 470 LKK +P++++GL PVLI P+ I G+ M +VV PVAA +T WL+S+ +G+ Sbjct: 229 WLKKTIK-LPKTMEGLMPVLILPVLSTLIIGLGMIYVVGEPVAALNKAMTEWLKSMSSGS 287 Query: 471 LVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAP-HAAIMAGGMVPPLGIALATT 529 VL+GIILG MMA DMGGP+NKAA+TF ++ + AG + AA+MA GM PPLG+ALAT Sbjct: 288 AVLLGIILGLMMAFDMGGPVNKAAYTFAVSTLAAGQPSTIMAAVMAAGMTPPLGLALATL 347 Query: 530 IFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRV 589 I ++KFT +REAG +F+G +F+TEGAIPFAAADPLRVIP+ ++G+AV L+ F+ Sbjct: 348 IAKDKFTTEEREAGKAAFFLGISFITEGAIPFAAADPLRVIPSIMIGSAVTSALSILFKC 407 Query: 590 TLPAPHGGVFVAFITN---HPMLYLLSIVIGAVVMAIILGIVK 629 TL PHGG+FV I N + +LY ++I IG VV A+I+ ++K Sbjct: 408 TLAVPHGGIFVLPIPNAVGNLLLYAVAIAIGTVVTALIVSVLK 450 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: 719 Number of extensions: 29 Number of successful extensions: 5 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: 454 Length adjustment: 35 Effective length of query: 600 Effective length of database: 419 Effective search space: 251400 Effective search space used: 251400 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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