Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_092483768.1 BM299_RS10535 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::psRCH2:GFF3291 (960 letters) >NCBI__GCF_900115975.1:WP_092483768.1 Length = 588 Score = 422 bits (1084), Expect = e-122 Identities = 235/563 (41%), Positives = 346/563 (61%), Gaps = 17/563 (3%) Query: 408 VNGIAASPGIAIGPVLVRKP-QVIDYPKRG----ESPVIELQRLDAALDKVHADIGTLID 462 + G S GI G VL+ +P + + P R E EL+RL A +K + ++ LI+ Sbjct: 6 IRGTGVSEGIRSGKVLLYQPLRNQNLPGRAVISEEEVNHELERLQLAREKAYRELHALIE 65 Query: 463 ESQVASIRD---IFTTHQAMLKDPALREEVQVRL-QKGLSAEAAWMEEIESAAQQQEALH 518 +++ +D I QA L DPA E++ + Q+ +AE A E +E A E ++ Sbjct: 66 RARIELGKDKAAILMAQQAFLNDPAFYPEMEKEIRQQKYTAEKAVTEVVERFAGLFEGMN 125 Query: 519 DKLLAERAADLRDVGRRVLACLTGVEAEQAPD--EPYILVMDEVAPSDVATLNAQRVAGI 576 D+ L ER+AD+RDVG R+++CL G + Q + E ILV D++APSD LN + + G Sbjct: 126 DQYLRERSADVRDVGNRLVSCLQGKKGLQLAEIKEEVILVADDLAPSDTVQLNKKYILGF 185 Query: 577 LTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQA 636 +T GG TSH+AI++R+LGIPAIVG G + + L++DG G +V P+ +++ Sbjct: 186 VTRVGGKTSHTAILSRSLGIPAIVGIGEAIKQIHDGDWLIIDGSTGACIVNPNPRLMKEY 245 Query: 637 RSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTEL 696 +R E+ E A T DG VE++ANIG+ E A+ GAEGIGL RTE Sbjct: 246 EEKRKIEEQALRQLEEFTFKPAATTDGFRVEMSANIGSPAEAKPALEQGAEGIGLYRTEF 305 Query: 697 VFMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRG 756 +FMN +Q P++ Q Y++V+ +E RP+++RTLD+GGDK LPY +P E NPFLG R Sbjct: 306 LFMNEAQMPSEEKQFEAYKQVVATMENRPVIIRTLDIGGDKELPYLSLPKEMNPFLGYRA 365 Query: 757 IRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPV---- 812 IRLSL + +++ TQLRA+L ++ ++IMFPM+ +++EWR AKA++ +R L Sbjct: 366 IRLSLDQRELMVTQLRAILRASAYGKVKIMFPMIASLEEWRQAKAILAEVRDRLTKEGVD 425 Query: 813 --ADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHP 870 ++VG+M+E+PS A++A A+EVDFFSIGTNDL QYTLA+DR + + D LHP Sbjct: 426 FDPSVEVGMMVEVPSTAILADQFAKEVDFFSIGTNDLVQYTLAVDRMNEKVGYLYDHLHP 485 Query: 871 AVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRE 930 AV+ L+ +EA+H GKW G+CG +A D LA PLL+GLG+DE S+ A SI VK + + Sbjct: 486 AVIHLVKKVIEASHREGKWTGMCGGMAGDPLAAPLLIGLGLDEWSMVAGSIKKVKQVISQ 545 Query: 931 LDFAACQRLAQQALMLPGAHEVR 953 ++ CQ+L + L L +VR Sbjct: 546 VNHEECQKLLGEVLELSTTDDVR 568 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: 1006 Number of extensions: 30 Number of successful extensions: 3 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: 588 Length adjustment: 40 Effective length of query: 920 Effective length of database: 548 Effective search space: 504160 Effective search space used: 504160 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: 55 (25.8 bits)
This GapMind analysis is from Apr 09 2024. 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