Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 200507 SO1332 phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI ptt file)
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__MR1:200507 Length = 744 Score = 342 bits (878), Expect = 4e-98 Identities = 218/563 (38%), Positives = 317/563 (56%), Gaps = 14/563 (2%) Query: 410 GIAASPGIAIGPVLVRKPQV-IDYPK-RGESPVIELQRLDAALDKVHADIGTL---IDES 464 G +AS GIAI V ++ ++ P R E V+E RL AA+ + IG L D Sbjct: 172 GTSASSGIAIAHAFVLGGEISLEQPDIRCEDIVLESNRLVAAMGRCKEAIGALSQRFDRE 231 Query: 465 QVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAE 524 Q + IF Q +L D +L E + G AE+A QQ A+ D L E Sbjct: 232 QDEEVASIFNALQLLLDDASLGGEYAREVLLGWEAESAVSRVSLRYIQQFLAMEDPYLKE 291 Query: 525 RAADLRDVGRRVLACLTGVEA-EQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGA 583 RA+D+RD+G++VL L E E PD+P ILV E + +A Q++AGI+T GG Sbjct: 292 RASDIRDLGQKVLRQLIEPERLELEPDKPVILVTKEADATMLAEFPRQKLAGIVTELGGV 351 Query: 584 TSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAR 643 SH+AI+ARALG+PAI G + LL+++ RG+L+V+PS A + + RS +A+ Sbjct: 352 NSHAAILARALGVPAITGVEQLLSADIDQKLLVVNASRGQLMVSPSPAIVSEYRSLISAQ 411 Query: 644 EERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQ 703 + + + +V DG + + N G +A GA+GIGL RTE+ FM + Sbjct: 412 KALQRQYAQELTLPSVMLDGKRIRLYLNAGLLSGVASEIAEGADGIGLYRTEIPFMLQQR 471 Query: 704 APNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQR 763 P+++ Q Y++VL A GRP+V+RTLDVGGDKPLPY+P+ E+NPFLG RGIRLSL Sbjct: 472 FPSESEQVKVYQQVLSAASGRPVVMRTLDVGGDKPLPYFPI-KEDNPFLGWRGIRLSLDH 530 Query: 764 PDILETQLRALL-ASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELP------VADLQ 816 P++ QLRA+L A A+G+ L I+ PMV N+DE A A +++ VEL + + Sbjct: 531 PELFLVQLRAMLQAGAEGKQLSILLPMVSNLDEIDQALAYLEQAHVELKNDVNSNIKMPR 590 Query: 817 VGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLI 876 +GIM+E+P+ +A+ VDF S+G+NDLTQY LA+DR +P +S D HP +LR + Sbjct: 591 IGIMLEVPAMLYQLDEVAKRVDFVSVGSNDLTQYLLAVDRNNPRVSSLFDSYHPGILRAL 650 Query: 877 GMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAAC 936 H + +CGELA + + LLV +G +LS++ S+A + +R + Sbjct: 651 HQARLDCEYHHLDISICGELAGEPMGAILLVAMGYHQLSMNQGSLARINYLLRRVSGEDL 710 Query: 937 QRLAQQALMLPGAHEVRAFVGEH 959 +L QAL L +VR V E+ Sbjct: 711 AQLLAQALSLSNGFQVRELVKEY 733 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: 1333 Number of extensions: 56 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: 960 Length of database: 744 Length adjustment: 42 Effective length of query: 918 Effective length of database: 702 Effective search space: 644436 Effective search space used: 644436 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