Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 5208528 Shew_1039 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_07335 (954 letters) >FitnessBrowser__PV4:5208528 Length = 743 Score = 329 bits (844), Expect = 4e-94 Identities = 215/577 (37%), Positives = 317/577 (54%), Gaps = 21/577 (3%) Query: 391 ATVMLAPESGSLIQAVAAAPGIAIGPAHIQVLQAIDYPL-----RGESAAIERERLQNAL 445 A V AP+ + +AA G+ I AH VL + PL R + E L AL Sbjct: 159 AEVKSAPDK-CVYTGTSAASGVVI--AHAMVLGG-EIPLEQQGRRTKQVDEELLALSQAL 214 Query: 446 NQVRSDIQGLIER---AKAKAIREIFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVI 502 + R+ + L +R K ++ IF Q +LDD L E ++ G +A +A V Sbjct: 215 DACRNTLSALSQRFDGENEKEVQSIFSALQLLLDDTSLGGEYGREIQAGWTAISAVSRVS 274 Query: 503 EAAAKEQEALQDALLAERAADLRDVGRRVLAQLCGVETPN-EPDQPYILVMDEVGPSDVA 561 + +QD + ERA D+RD+G+RVL +L + E D P ILV E + +A Sbjct: 275 LRYIDHFQQMQDPYMQERATDIRDLGQRVLRELIEPQKMQLELDVPVILVTKEATATMLA 334 Query: 562 RLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHV 621 ++ GI+T GG +H+AI+ARA G+PA++G + G L+L+ RG++ + Sbjct: 335 EFPQHKLVGIVTELGGVNSHAAILARAFGVPAVIGVEGILNAGIDGKQLILNANRGQVLI 394 Query: 622 DPDAATLQRAKEERDTREQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGA 681 P + + + K AE+ +PA+T D + ++ N G + +AS + +GA Sbjct: 395 SPTPTLIGEYRSLISAEKALQKRYAEELSKPAMTLDERRIHLYLNAGLLSSLASEIAEGA 454 Query: 682 EGIGLLRTELIFMAHSQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAK 741 +G+GL RTE+ FM ++ P EA Q YR+VL+ GRP+V+RTLDVGGDKPL Y PI Sbjct: 455 DGVGLYRTEIPFMLQTRFPSEAEQVEVYRQVLNAALGRPVVMRTLDVGGDKPLSYLPII- 513 Query: 742 EENPFLGVRGIRLTLQRPQVMEAQLRALLR-SADSRPLRIMFPMVGSVDEWRQARAMTER 800 EENPFLG RGIRLTL P++ QLRA+L S L I+ PMV +DE QA A E+ Sbjct: 514 EENPFLGWRGIRLTLDHPELFLVQLRAMLNASGGGEQLHILLPMVCCLDEIDQAIAYLEQ 573 Query: 801 LRLEIPV---ADLQ---LGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHP 854 LE+ DLQ +GIM+EVP+ +AK VDF SVG+NDLTQY LA+DR +P Sbjct: 574 AYLEVKQDVHPDLQRPKIGIMLEVPALLFQLEEVAKRVDFISVGSNDLTQYLLAVDRNNP 633 Query: 855 TLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSAR 914 +S D HP +L+ + A + + VCGELA +P+ V +LV +G +LS++ Sbjct: 634 RVSTLYDSYHPGILRALTQARLACREYRLPISVCGELAGEPMGVLLLVAMGYTQLSMNQG 693 Query: 915 SIAEVKARVRELSLAQVQTLAQAALAVGSADDVRALV 951 S+A++ +R +S + L AL++ + +VR L+ Sbjct: 694 SLAKINYLIRRVSYQDLSELLAQALSLTNGFEVRELL 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: 1178 Number of extensions: 62 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: 743 Length adjustment: 42 Effective length of query: 912 Effective length of database: 701 Effective search space: 639312 Effective search space used: 639312 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