Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 17939 b3899 PTS system, fructose-like enzyme IIBC component (VIMSS)
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__Keio:17939 Length = 483 Score = 272 bits (695), Expect = 3e-77 Identities = 171/461 (37%), Positives = 245/461 (53%), Gaps = 19/461 (4%) Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180 RIVA+T CP G+AHT+M AEAL+ A LG ++VETQGS G N L +IAAAD V+L Sbjct: 6 RIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVIL 65 Query: 181 AADIDV---DTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKR 237 A + D ARFAGKK+Y ALK Q+ +A + + ++ + Sbjct: 66 ATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSELPTNSQLFAADSGVKLGKQEVQS 125 Query: 238 G-VYKHLLTGVSFMLPMVVAGGLLIALS---LAFGI---DAYKQPGSLAAVLRTVGDTAF 290 G V HL+ GVS LP V+ GG+L+AL+ + FG+ D K S V+ ++G F Sbjct: 126 GSVMSHLMAGVSAALPFVIGGGILVALANMLVQFGLPYTDMSKGAPSFTWVVESIGYLGF 185 Query: 291 VLMVPMLAGYIAYSIADRPGLAPGML-------GGLLAGTLGAGFIGGIVAGFIAGYAAR 343 M+P++ YIA SIAD+P AP L LL GAGF+G +V G GY Sbjct: 186 TFMIPIMGAYIASSIADKPAFAPAFLVCYLANDKALLGTQSGAGFLGAVVLGLAIGYFVF 245 Query: 344 AISHGLRLPASLEALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNA 403 +RL +L+ L ++IP + LV G+L YV+G ++ ++ L FL+ + S Sbjct: 246 WFRK-VRLGKALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDLMGGLLHFLNTIPPSMK 304 Query: 404 ILLGLLLGGMMCVDLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLA 463 L+G M+ D+GGP+NK A+ F LL H Y A V ++PP+ GLAT +A Sbjct: 305 FAAAFLVGAMLAFDMGGPINKTAWFFCFSLLEKHIYDWYAIVGVVALMPPVAAGLATFIA 364 Query: 464 RRKFAESERQAGKAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL 523 + F E++A +A V+G +E AIP+A PL +I A+ G +TG L + FG K Sbjct: 365 PKLFTRQEKEAASSAIVVGATVATEPAIPYALAAPLPMITANTLAGGITGVLVIAFGIKR 424 Query: 524 QAPHGGLFVMLVPNAINHALAYLLAIVAGSLLTGLLYAVLK 564 AP G+F L+ ++ ++ L + G L VLK Sbjct: 425 LAPGLGIFDPLI-GLMSPVGSFYLVLAIGLALNISFIIVLK 464 Score = 53.5 bits (127), Expect = 2e-11 Identities = 57/213 (26%), Positives = 88/213 (41%), Gaps = 30/213 (14%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60 +++ +T CP G + + A L A LG VE S E LS+E+IA AD+V+ Sbjct: 5 LRIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVI 64 Query: 61 LV---GVEPLAAARFVGKPVYRARPAEALADPRAFL-------QRAAALASVEVAGDE-- 108 L G+ ARF GK VY ++AL + Q AA + V++ E Sbjct: 65 LATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSELPTNSQLFAADSGVKLGKQEVQ 124 Query: 109 -----AGLVAPEAGAAPRIV--------AVTACPTGVAHTFMAAEALQL-----AAGQLG 150 + L+A + A P ++ A G+ +T M+ A + G LG Sbjct: 125 SGSVMSHLMAGVSAALPFVIGGGILVALANMLVQFGLPYTDMSKGAPSFTWVVESIGYLG 184 Query: 151 FALQVETQGSVGARNPLDPADIAAADVVLLAAD 183 F + G+ A + D A A +V A+ Sbjct: 185 FTFMIPIMGAYIASSIADKPAFAPAFLVCYLAN 217 Lambda K H 0.321 0.137 0.392 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: 584 Number of extensions: 28 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: 585 Length of database: 483 Length adjustment: 35 Effective length of query: 550 Effective length of database: 448 Effective search space: 246400 Effective search space used: 246400 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 (21.9 bits) S2: 52 (24.6 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