Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Miya:8501869 Length = 846 Score = 440 bits (1132), Expect = e-127 Identities = 304/766 (39%), Positives = 399/766 (52%), Gaps = 61/766 (7%) Query: 96 EGQRVEAGQPLIEFDADYVALNARSLLTLMLVVSGEPFSLLADGLVETGQPLLQLSPSGA 155 EG A Q I D D V A+S L + G G+ E P +P+ + Sbjct: 101 EGVMAAAVQASIGADLDTVLREAQSALAAKAELLGMALPQDGGGVDEAAPPAAGATPAAS 160 Query: 156 VEAVDEEEGDALFSKPLTLPNANGLHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVA 215 E L +PN GLHARPAA A F A + L + + +A+S+ Sbjct: 161 HELT------------LMVPNRLGLHARPAARIVTALGPFVADVQLARGERVVSARSVNR 208 Query: 216 IMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSA------- 268 I L G+T+ AAG DAE A+KAL L AE G+ P AT+SS Sbjct: 209 IATLAVRGGETITFRAAGTDAEQALKALADLAAENFGDL------PDATKSSGRTGVEGP 262 Query: 269 ---------------TLLRGVCASPGSAFGQVV------QVTDPELVITEQGTGGATERA 307 GV ASPG A G V P+L + + E A Sbjct: 263 EGPGEQGRAGVAGVPAAKGGVPASPGIAVGPAVWHRPAFDAPPPDLAAGDPDS----EAA 318 Query: 308 ALTRGLLAANEALQVLQDKAA---GSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAA- 363 L L AA + L L+ + A G +AEIF H+ LL+D T+ A + + E + A Sbjct: 319 RLDGALDAARKELAALERRTAAMAGKQEAEIFVMHRLLLDDATIAGDARQRIAERREPAE 378 Query: 364 FAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQ 423 AW + F+ L + ERAADL DVG RVL+L+ G S L ++L+A Sbjct: 379 AAWYAVIDQAAESFRQLPEGYMRERAADLVDVGARVLRLLTGAPPSGPRLERPSVLLAAD 438 Query: 424 LTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDA 483 L PS A LD VLG VT GGATSH AILAR++G+PA+ G A ++A+G V LD Sbjct: 439 LGPSDMAHLDPALVLGIVTAQGGATSHAAILARSMGIPAVAGAGALAASVADGVTVALDG 498 Query: 484 DKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVE 543 GE+ + P + +E+ R + Q +A A+ PA T DG H+ V AN+ S + Sbjct: 499 STGEVWIAPAPDVLSTIESRRASWLAVRQAALAGAARPAVTVDGRHMHVHANIGSPMDAA 558 Query: 544 HALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKP 603 AL G EGVGL R+EFL+LDR AP EEQ Y A A A+ +VVRTLD+GGDKP Sbjct: 559 PALQNGAEGVGLFRTEFLFLDRVAAPDEEEQRAAYVAAAAAM-PGLPVVVRTLDIGGDKP 617 Query: 604 LAYVPMDA--ETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSEL 661 + Y+ A E NPFLGLRGIR CL R +L Q RA+L +A L +M PMV+ EL Sbjct: 618 VPYLGDFAAGEENPFLGLRGIRFCLARRELFLTQLRALLRAAAEHPLRVMFPMVAHPGEL 677 Query: 662 HLARKILEEEALALGLTELP----KLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYT 717 A+ +LEE AL LP ++GIM+EVP+A +AD A FFSIGTNDL QY Sbjct: 678 AAAKALLEEARAALAAQGLPHGPVEVGIMVEVPAAVALADQLARESAFFSIGTNDLAQYV 737 Query: 718 LAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGV 777 +A DR + +A+ +D+ HPAVLR++ TV A A G V +CG LA A A+P+L+GLG+ Sbjct: 738 MAADRGNAAVADLSDALHPAVLRMVRDTVAAGKAAGIPVAMCGELAGNADAIPLLVGLGL 797 Query: 778 DELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALR 823 DELS++ P IP K VR D+ C +A + L L +AA VR LR Sbjct: 798 DELSMNGPAIPRAKDVVRGCDMTACVRLAGRALELPDAAAVRRLLR 843 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: 1532 Number of extensions: 50 Number of successful extensions: 6 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: 846 Length adjustment: 42 Effective length of query: 796 Effective length of database: 804 Effective search space: 639984 Effective search space used: 639984 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