Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 6936677 Sama_0864 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_07335 (954 letters) >FitnessBrowser__SB2B:6936677 Length = 744 Score = 351 bits (900), Expect = e-100 Identities = 217/567 (38%), Positives = 330/567 (58%), Gaps = 22/567 (3%) Query: 402 LIQAVAAAPGIAIGPAHIQVLQAIDYPLRGESAAI----ERERLQNALNQVRSDIQGLIE 457 L +A+ G+AI AH V+ + E+ A E RL+ A+ + R + L + Sbjct: 169 LFTGTSASTGVAI--AHALVIGGEISLEQPEACATDVDAEVNRLRLAMGRSRDALTALAQ 226 Query: 458 RAKAK---AIREIFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQD 514 + + + IF + Q +L+D L E + G SA+ A V + E ++D Sbjct: 227 KFENDHDDELSSIFTSLQSLLEDASLGGEYQREVLAGWSAETAVSRVSLRYVAQFETMED 286 Query: 515 ALLAERAADLRDVGRRVLAQLCGVETPN---EPDQPYILVMDEVGPSDVARLDPTRVAGI 571 A L ERA+D+RD+G+RVL QL +E +PD+P ILV E S +A ++AGI Sbjct: 287 AYLRERASDIRDLGQRVLRQL--IEPGRMMLDPDKPVILVTREADTSMLAEFPRQKLAGI 344 Query: 572 LTARGGATAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRA 631 +T GG +H+AI+ARALG+PA++G + L+L+ RG L V P + Sbjct: 345 VTEAGGVNSHAAILARALGVPAIMGVEQVLQANLDKQLLVLNASRGILMVSPSPTVVDEY 404 Query: 632 KEERDTREQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTEL 691 + ++ + AE+ EPALT DGH + ++ N G +GV+S + GA+G+GL RTE+ Sbjct: 405 RNLISAQKALDRQYAEELKEPALTLDGHRIHLYLNAGLMSGVSSEIADGADGVGLYRTEI 464 Query: 692 IFMAHSQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRG 751 FM + P E+ Q YR VL AGRP+V+RTLDVGGDKPLPY+PI+ EENPFLG RG Sbjct: 465 PFMLQQRFPSESEQIKVYRSVLQSAAGRPVVMRTLDVGGDKPLPYFPIS-EENPFLGWRG 523 Query: 752 IRLTLQRPQVMEAQLRALLRSA-DSRPLRIMFPMVGSVDEWRQA-----RAMTE-RLRLE 804 IRL+L P++ QLRA+L++A D+ L+I+ PMV S+DE +A +A +E R + Sbjct: 524 IRLSLDHPELFLVQLRAMLQAAGDTDNLKILLPMVSSLDEIDEALLYLDQAFSELRADVN 583 Query: 805 IPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLH 864 +A +G+M+EVP+ +A+ V+F SVG+NDLTQY LA+DR +P +S+ D H Sbjct: 584 PSLARPPVGVMLEVPALLYQLREVAQRVEFVSVGSNDLTQYLLAVDRNNPRVSSLYDSYH 643 Query: 865 PAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVR 924 P VL+ + + ++ H V VCGELA +P+ +LV +G DELS++ S+A++ +R Sbjct: 644 PGVLRALQLALQECRQHKLDVSVCGELAGEPMGALLLVAMGYDELSMNQGSLAKINYLLR 703 Query: 925 ELSLAQVQTLAQAALAVGSADDVRALV 951 + ++++ L + + + DVR LV Sbjct: 704 RVERSELEQLLALVMQMSNGQDVRELV 730 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: 1219 Number of extensions: 45 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: 954 Length of database: 744 Length adjustment: 42 Effective length of query: 912 Effective length of database: 702 Effective search space: 640224 Effective search space used: 640224 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