GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Shewanella amazonensis SB2B

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)



>lcl|FitnessBrowser__SB2B:6936677 Sama_0864
           phosphoenolpyruvate-protein phosphotransferase PtsP
           (RefSeq)
          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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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