GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Phyllobacterium brassicacearum STM 196

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_106709795.1 CU102_RS04500 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>NCBI__GCF_003010955.1:WP_106709795.1
          Length = 535

 Score =  252 bits (643), Expect = 5e-71
 Identities = 181/537 (33%), Positives = 253/537 (47%), Gaps = 28/537 (5%)

Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLG 342
           G  ASPG A G +++      +      P  E     H  LS   Q   A   + A R  
Sbjct: 9   GKGASPGTAFGQIYLAVDVEETFLSPTDPSAE-----HAILSDAVQGSIAALRELAARSS 63

Query: 343 PSEAAIFAAQAEILNDTDLVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARA 402
              A+I   Q E+L D ++  +A + +  G G A +W  A++   AG    DN  + ARA
Sbjct: 64  TESASILEFQIEMLLDPEITEMAARRIGTGDGAALAWVTALDNYIAGFEQSDNEAVRARA 123

Query: 403 ADLRDVGQRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGG 462
           ADL D+  RVLA    A+      D P    + + +D+SPS   A D +   G+   QG 
Sbjct: 124 ADLFDIKSRVLA----AMTGKPVADFP-VGFVFVGKDISPSVFLAHDWSSGGGIVLFQGS 178

Query: 463 PTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAR 522
             SH ++LAR   +P ++  G     +A     +LDG +G + L P+  ++  A +    
Sbjct: 179 AASHVSMLARAKSVPMVIETGT--FNIAGEEKLLLDGGTGSVVLHPSDEELRQALSTRLS 236

Query: 523 EEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERG 582
                 E EA      RT DG E+ +  NVN    +      G E +GL+RTEFL     
Sbjct: 237 MRPIANEAEAPCSTKLRTADGAEISLSINVNDLSDIIGIDHAGIEGIGLLRTEFLMSSAA 296

Query: 583 DAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLR 642
           D   ED QY  YR +L     +P+ +R LD+GGDK VP      +   FLG+RG RLLL 
Sbjct: 297 DIANEDRQYGIYRQVLEWAGQKPVTIRMLDLGGDKPVP----DRDGTSFLGLRGIRLLLA 352

Query: 643 RPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQ-ALRAACERI----RAELD 697
           RPE L  Q RAL R+A  G       L +M PM+T   E++  +    E +    R  + 
Sbjct: 353 RPEFLRIQARALLRSAVHGN------LKVMLPMVTLPSELEKTVTIFREELTLLQRRRIS 406

Query: 698 APAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPA 757
               P+GIMVEVPA AI  D      +FFS GTNDL QY  A  R +  +A       PA
Sbjct: 407 HRMPPIGIMVEVPATAIMLDTFGA-AEFFSFGTNDLVQYLTAAARDNAAVADIYTHAAPA 465

Query: 758 VLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRL 814
           + RL+  TV  A   G  V VCG +AG+P     L   G+R  S+ P  +  ++ ++
Sbjct: 466 IFRLLEHTVHIAATLGAPVSVCGDMAGEPEYIPALLRCGLRHFSLAPAQLAVIRSQI 522


Lambda     K      H
   0.319    0.134    0.387 

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: 954
Number of extensions: 44
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: 846
Length of database: 535
Length adjustment: 39
Effective length of query: 807
Effective length of database: 496
Effective search space:   400272
Effective search space used:   400272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 (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:

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. 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