Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AZOBR_RS30470 AZOBR_RS30470 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__azobra:AZOBR_RS30470 Length = 590 Score = 324 bits (830), Expect = 1e-92 Identities = 213/588 (36%), Positives = 325/588 (55%), Gaps = 26/588 (4%) Query: 261 PVATQSSATLLRGVCASPGSAFG--QVVQ---VTDPELVITEQGTGGATERAALTRGLLA 315 P A Q + LRG+ SPG A G VV+ + PE +T R A G Sbjct: 6 PAAGQGRS--LRGLGVSPGIAIGPAHVVESGAIRVPEYTLTADQVEAEAARFADACG--K 61 Query: 316 ANEALQVLQDKAA---GSAQAEI---FRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSA 369 A ++ L+ KA GSA EI AH ++ + L R + + A A A Sbjct: 62 ARRQIRKLKAKALVLPGSASEEIGFLLDAHLAMVTNSRLTRGVERRIQQELVNAEAAVQA 121 Query: 370 TLATVT-LFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWD-LPERAILIAEQLTPS 427 +AT+ F + ++ +A R AD+ +VG+R+++ ++ + A+ L A+++AE+LTP+ Sbjct: 122 EIATIAQTFASMEDSYLAGRIADVREVGRRLIRNLMRHEYQAFSMLNPGAVILAEELTPA 181 Query: 428 QTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGE 487 TA LD R+V GF TV GGA H AI+AR+LG+PA+ GV + L NG V++D +G Sbjct: 182 DTALLDPRRVAGFATVLGGAEGHTAIMARSLGIPAVLGVGGLLAGLKNGITVIVDGVQGR 241 Query: 488 LHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALT 547 + ++P +E R + ++ LPA TRD V + AN+ ++++HAL Sbjct: 242 VIIDPTPEVLEDYRQRRAEREREREQLKGLRKLPAVTRDNTAVTLQANLELPRDLDHALE 301 Query: 548 LGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYV 607 G +G+GLLR+EFL+++R++ P +EQ +I +G R + RT+DVGG+K ++ Sbjct: 302 NGAQGIGLLRTEFLFMNRDQLPDEDEQYTVLRSIVEGMG-GRTVTARTMDVGGEKLAGWM 360 Query: 608 P--MDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLAR 665 NP LGLR +RL L P+LL Q A+L + L I+LPM+ ++E+ R Sbjct: 361 AGRYGEPANPALGLRAVRLGLREPKLLETQLAAMLRAGVHGPLRILLPMICSVAEVQRVR 420 Query: 666 KILEEEALALG------LTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLA 719 +++ + A L LP +G+M+EVP AAL AD A DFFSIGTNDLTQYTLA Sbjct: 421 EMMGQVARRLRRRGVPIADPLPPVGVMVEVPGAALSADALAYAADFFSIGTNDLTQYTLA 480 Query: 720 MDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDE 779 +DR ++A+ D HPAVLRLI T++AA V VCG +A ++ +L+GLGV + Sbjct: 481 IDRGDEQVASLYDPLHPAVLRLIQFTIEAALRARIPVSVCGEIAGDSRYTALLLGLGVRD 540 Query: 780 LSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQYHA 827 LS+ P IP +K +R+LDL + AR ++ ++ + L ++A Sbjct: 541 LSMVPPAIPLVKRRIRKLDLQEATRRARVIMDQSDSGRIAALLDDFNA 588 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: 1011 Number of extensions: 42 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: 590 Length adjustment: 39 Effective length of query: 799 Effective length of database: 551 Effective search space: 440249 Effective search space used: 440249 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: 54 (25.4 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