Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate CCNA_00457 CCNA_00457 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Caulo:CCNA_00457 Length = 852 Score = 634 bits (1634), Expect = 0.0 Identities = 369/837 (44%), Positives = 506/837 (60%), Gaps = 30/837 (3%) Query: 7 LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66 L L APL G + AL++ PD VF+ R++GDGL IDP TL AP G + ++ + HAV++ Sbjct: 6 LVLTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRARHAVTL 65 Query: 67 TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126 NG ++LMH+GL+TV L G+GF V+EGQ V+AG LI D D +A ARSL+T ++ Sbjct: 66 RATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPVV 125 Query: 127 VVSGEPFSLLA---DGLVETGQPLLQLSP-SGAVEAVDEEEGDALFSKPLTLPNANGLHA 182 + +GE F ++ D + GQ L++LSP +GA A D + ++ + +P A+G+HA Sbjct: 126 ITNGEAFQIVRRDQDRQIGVGQFLMELSPIAGASRAAASGAADQI-TRQIIVPLAHGIHA 184 Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242 RPAA AQ AK F + + L + ANA+S V +M+L GDT+Q+ A+G DA+AA+ A Sbjct: 185 RPAARIAQMAKTFASDLTLATGPRRANARSPVGLMSLAIRHGDTIQLLASGPDAQAAVTA 244 Query: 243 LVALLAEGCGEAVVNVAEPVATQSSAT-----------------LLRGVCASPGSAFGQV 285 L L+ G GE A+ +T+++ T +L+GV A+PG A G+ Sbjct: 245 LAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGVLKGVPAAPGLAIGKA 304 Query: 286 VQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAGS---AQAEIFRAHQEL 342 V+++ E+V+ E G G A E AAL L E ++ KAA + A+ I AHQ Sbjct: 305 VRLSTAEIVVREAGEGVAHEEAALAVAL----ETVRARIGKAAETGDKARKAILAAHQAF 360 Query: 343 LEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKL 402 L+DP L AHRL+ EGKSA FAW A V Q LG+ +AER DL D+ ++VL+ Sbjct: 361 LDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVDDLIDLERQVLRA 420 Query: 403 ILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPA 462 + G +++ L +IL+A++L PSQ D + GF T GG TSHVAILA A+G+PA Sbjct: 421 LSGEEETGAALAPGSILLADELLPSQLMGADPAALAGFATARGGPTSHVAILAAAMGVPA 480 Query: 463 ICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPA 522 + V + + +G ++LDAD G L + P+ +E + A + R A A PA Sbjct: 481 LVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQRKAAAKAAAHEPA 540 Query: 523 TTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIA 582 TRDG +EV AN S+ + + A+ G EG GLLR+EFL+LDR P +EQA Y AIA Sbjct: 541 VTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPDEDEQARQYQAIA 600 Query: 583 RALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILAS 642 AL R L++RTLDVGGDK Y+P+ AE NP LGLRG+R+ L RP LL+ Q RAIL Sbjct: 601 EALDG-RPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHLLKAQLRAILRV 659 Query: 643 AGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPH 702 + IM+PMV+ L EL R +LEE LG+T+ +LG+MIE P+AA+ AD+ A Sbjct: 660 EPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPAAAVTADLLAAE 719 Query: 703 VDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGAL 762 DF SIGTNDLTQY LAMDR +P LA D+ HPAVLR+I T + A H +WVGVCG L Sbjct: 720 ADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAARHHRWVGVCGGL 779 Query: 763 ASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVR 819 AS+ A P+L+GLGV ELS + + P +KA VR L L C+ +A Q L VR Sbjct: 780 ASDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALEQTSPQAVR 836 Lambda K H 0.318 0.133 0.371 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: 1557 Number of extensions: 70 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: 838 Length of database: 852 Length adjustment: 42 Effective length of query: 796 Effective length of database: 810 Effective search space: 644760 Effective search space used: 644760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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