Alignments for a candidate for fruI in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments 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)



>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.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources