Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate BWI76_RS23270 BWI76_RS23270 phosphoenolpyruvate--protein phosphotransferase PtsP
Query= reanno::pseudo1_N1B4:Pf1N1B4_1146 (953 letters) >FitnessBrowser__Koxy:BWI76_RS23270 Length = 748 Score = 333 bits (855), Expect = 2e-95 Identities = 214/567 (37%), Positives = 312/567 (55%), Gaps = 20/567 (3%) Query: 402 IQAIAAAPGIAIGPAHIQV-----QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIE 456 I+A+ A+ G+AI + V +QV Y A ERERL AL + + + Sbjct: 171 IRALPASSGVAIAEGWMDVSLPLMEQV--YEASTLDTASERERLTGALEEAANEFRRYSK 228 Query: 457 RSKAKAIRE---IFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQD 513 R A A +E IF + +L D L E+ + +G AE A +IE A+Q +L D Sbjct: 229 RYAAGAQKETAAIFDLYSHLLSDARLRRELFAEVDKGAVAEWAVKKIIEKFAEQFAALSD 288 Query: 514 ALLAERAADLRDIGRRVLAQLS-GVETPAEPEQPYILVMDEVGPSDVARLDPTRVAGILT 572 L ERA DLR +G+R+L L ++ P + +LV DE+ + +A + R+AG++ Sbjct: 289 GYLKERAGDLRTLGQRLLFHLDDSIQGPNTWPERIVLVADELSATTLAEVPQDRLAGVVV 348 Query: 573 ARGGATAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATE 632 G A +H+AI+ RALGIP ++GA LL G L++DG RG L VD + LQ Sbjct: 349 RDGAANSHAAIMVRALGIPTVMGADIQPSLLH-GHTLIVDGYRGELLVDPEPVLLQEYQR 407 Query: 633 ERDTRELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIF 692 + A + + + G V+V N G S + +GIGL RTE+ F Sbjct: 408 LISEENELSRLAEDDLERASELKSGERVKVMLNAGLSPEHEEKLGNFVDGIGLYRTEIPF 467 Query: 693 MAHSQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIR 752 M S P E Q +Y+ +L + + +RTLD+G DK LPY PI+ EENP LG RGIR Sbjct: 468 MLQSGFPSEEEQVAQYQGMLQMFNEKSVTLRTLDIGADKQLPYMPIS-EENPCLGWRGIR 526 Query: 753 LTLQRPQVMEAQLRALLRA-ADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIP------ 805 +TL +P++ Q+RA+LRA A L I+ PMV S+DE +AR + +R E+ Sbjct: 527 ITLDQPEIFLVQVRAMLRANAATGNLSILLPMVTSLDEVDEARRLIDRASREVEEMIGYA 586 Query: 806 VADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPA 865 + +LG+M+EVPS + P LA VDF SVGTNDLTQY LA+DR + +++ D LHP Sbjct: 587 IPRPRLGVMLEVPSMVFMLPQLANRVDFISVGTNDLTQYILAVDRNNTRVASMYDSLHPG 646 Query: 866 VLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIREL 925 VL+ + + R A G + +CGE+A DP+ V +L+G+G LS++GRS+A VK +R + Sbjct: 647 VLRALAMIARDAERFGIDLRLCGEMAGDPMCVTILIGMGYRHLSMNGRSVARVKYLLRRI 706 Query: 926 SLTQTQTLAQQALAVGSANEVRALVEA 952 + + Q L+Q++L EVR V A Sbjct: 707 DINEAQELSQRSLDAQMTAEVRHQVAA 733 Lambda K H 0.318 0.135 0.381 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: 1262 Number of extensions: 59 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: 953 Length of database: 748 Length adjustment: 42 Effective length of query: 911 Effective length of database: 706 Effective search space: 643166 Effective search space used: 643166 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 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