Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate H281DRAFT_01852 H281DRAFT_01852 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__Burk376:H281DRAFT_01852 Length = 851 Score = 544 bits (1402), Expect = e-159 Identities = 319/681 (46%), Positives = 423/681 (62%), Gaps = 18/681 (2%) Query: 284 SAQVPLANAHGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQ 343 S +V L N G+HARPA V A+ +E EIR+ L G+ SA + KS+ ++ + G Sbjct: 176 SDEVTLPNPAGMHARPAAVFVGAAKKYESEIRL-LHGSNSA--NAKSIVSIMGLATKFGD 232 Query: 344 LLEFMAEPAIASDALPALVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALR 403 + A A +A L R + EG GE+ PA S P + + + +A Sbjct: 233 RVRIQATGPDAGEAASVLARLLAEGSGEKPADAPAFPPTSLAPASGSSGEPAVVKRAQPA 292 Query: 404 AGDQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDE 463 +++ G++ASPG+A+G ++ + QVID + GESP E RL+AA + +I L + Sbjct: 293 DVNELTGVSASPGLAVGKIVQFRQQVIDVKEAGESPQRERVRLEAAHHEARQNIEALKAK 352 Query: 464 SQVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLA 523 S I H +L+DP L + +G SA AW E A E L + LL Sbjct: 353 LTDPSKAQILDAHLELLEDPDLNGMAIGSISEGKSAGFAWRAAFEQQAATLEKLDNPLLR 412 Query: 524 ERAADLRDVGRRVLACLTGVEAEQAPDEPY--ILVMDEVAPSDVATLNAQRVAGILTAGG 581 ERA D+RDVGRRVLA L G++ Q D P IL+ +E++PSD A+L+ +V G T G Sbjct: 413 ERAGDVRDVGRRVLALLAGMQQAQI-DVPAGSILIAEELSPSDTASLDRTKVLGFCTTTG 471 Query: 582 GATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERA 641 GATSH AI+AR+LGIPAI G L LA TL++LDG G L PS ++E+AR + Sbjct: 472 GATSHVAILARSLGIPAICGIDEDALQLADGTLVVLDGSHGSLRRNPSAGEVEKARERIS 531 Query: 642 AREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNH 701 + E++ A+T DGH VE+ ANI A E +AVA GAEG+GLLR+E +F + Sbjct: 532 RQAEKREEEKLAASKLAMTADGHRVEVVANIRNAKEARDAVAAGAEGVGLLRSEFLFDDR 591 Query: 702 SQAPNQATQEAEYRRVLEAL-EGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLS 760 AP++ Q +EY V EAL RPLV+RTLD GGDKPL Y P+P E+NPFLG+RG+R+S Sbjct: 592 DTAPSEDEQASEYCAVAEALGRERPLVIRTLDAGGDKPLSYMPLPKEDNPFLGLRGVRVS 651 Query: 761 LQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMV-----DRLRVELPVADL 815 L RPDI TQLRA+L +A L +MFPMV I+E AK ++ DR + Sbjct: 652 LDRPDIFRTQLRAILRAAPIGNLHVMFPMVAAIEEVLAAKKILLEEAGDRAN------SI 705 Query: 816 QVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRL 875 +VG+MIE+P+AALIA LA+EVDFFSIGTNDLTQYTLA+DRGHP L+ QAD LHPAVLRL Sbjct: 706 KVGVMIEVPAAALIAEPLAREVDFFSIGTNDLTQYTLAMDRGHPKLARQADALHPAVLRL 765 Query: 876 IGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAA 935 IGMTVE AH HGKWVGVCG +A+DA+AVP+LVGLGVDELSVS ++ +KA++ L A Sbjct: 766 IGMTVEGAHKHGKWVGVCGGIASDAIAVPVLVGLGVDELSVSVPAVGSIKAQLARLTMAQ 825 Query: 936 CQRLAQQALMLPGAHEVRAFV 956 ++LA + + L A EVRA + Sbjct: 826 ARQLAAEVVRLGTAAEVRALL 846 Lambda K H 0.317 0.134 0.384 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: 1773 Number of extensions: 73 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: 960 Length of database: 851 Length adjustment: 43 Effective length of query: 917 Effective length of database: 808 Effective search space: 740936 Effective search space used: 740936 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