Alignments for a candidate for fruI in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Paraburkholderia bryophila 376MFSha3.1

Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate H281DRAFT_01977 H281DRAFT_01977 Phosphocarrier protein HPr /phosphoenolpyruvate--protein phosphotransferase /PTS system IIA component, Glc family

Query= SwissProt::P45597
         (838 letters)



>FitnessBrowser__Burk376:H281DRAFT_01977
          Length = 854

 Score =  472 bits (1214), Expect = e-137
 Identities = 290/721 (40%), Positives = 400/721 (55%), Gaps = 16/721 (2%)

Query: 122 IQDPAQLEALFTTDDPAVIVAALTGDRAPDTSAAPATDLAE--RFEWTIAYPSGLHARPA 179
           I + AQ   L   + P +++    G  A  +    AT + E  R + T+ +  GLHARPA
Sbjct: 136 IVERAQGGMLKAGETPLLLLRPRDGAAADASRQLSATSVTEEARAQVTLVHAGGLHARPA 195

Query: 180 TRWAETARGFSARAQVRAGDQAADAKSLVGLLQLGLRAGDSITVSAKGSDAPALLKRLRA 239
            R  E ARGF AR +VR   + A  +S+VGLL LG   G ++ +   G  A A +    A
Sbjct: 196 ARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGQGATVELLGVGPQARAAVD---A 252

Query: 240 VMDSLTAQEKADAERAAQRRAAPVIGWTPPQAQPAIV-----GIGASPGVAIGIVHRLRA 294
           + D LT +   + E    R+++P      P A   +      G+ ASPGVAIG +     
Sbjct: 253 IADELTREAHGEVEEKPARQSSPAPQTVAPAAGETLAPNTLAGVCASPGVAIGKLVCWDD 312

Query: 295 AQTEVADQPIGLGDG-GVLLHDALTRTRQQLAAIQDDTQRRLGASDAAIFKAQAELLNDT 353
           A  +  +Q  G       LL  A+      L     D  +R    +A IF     LL D 
Sbjct: 313 ADIDPPEQASGTSAAESRLLDKAIATVDTDLGTTVRDASQRGAVGEAGIFAVHRVLLEDP 372

Query: 354 DLITRTCQLMVEGHGVAWSWHQAVEQIASGLAALGNPVLAGRAADLRDVGRRVLAQLDPA 413
            L+     L+  G    ++W +A+    + L  + + +LA RAADLRD+ +RVL  L   
Sbjct: 373 TLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYT 432

Query: 414 AAGAGLTDLPEQPCILLAGDLSPSDTANLDTDCVLGLATAQGGPTSHTAILSRTLGLPAL 473
            A A    LP++  +L A + +PSD + LD   V  L  A+GG TSH AIL+R  G+PAL
Sbjct: 433 NAAARA--LPDE-AVLAAEEFTPSDLSALDRSRVTALVMARGGATSHAAILARQAGIPAL 489

Query: 474 VAAGGQLLDIEDGVTAIIDGSSGRLYINPSELDLDAARTHIAEQQAIREREAAQRALPAE 533
           VA G  L  I +G   +++ ++GRL   P+ELD++ AR   +    +RE         A 
Sbjct: 490 VAMGDALYAIPEGTQVVVNATTGRLEFAPTELDVERARLERSRLAGVREANRRTSQEAAV 549

Query: 534 TTDGHHIDIGANVNLPEQVAMALTQGAEGVGLMRTEFLFLERGSTPTEDEQYQTYLAMAR 593
           T DG  I++ AN+   +    A+  GA+ VGL+RTE LF+ R + PT DE  Q+Y  +  
Sbjct: 550 TADGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQGIVD 609

Query: 594 ALDGRPLIVRALDIGGDKQVAHLELPHEENPFLGVRGARLLLRRPDLLEPQLRALYRAAK 653
           AL GR  I+R LD+G DK+V +L LP E NP LG+RG RL   RPDLL+ QLR L     
Sbjct: 610 ALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLSVKP 669

Query: 654 DGARLSIMFPMITSVPELISLREICARIRAELDAPE-LPIGIMIEVPAAAAQADVLARHA 712
            GA + I+ PM+T V ELI +R+       EL   E + +G+MIEVP+AA  AD L++HA
Sbjct: 670 FGA-VRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLSQHA 728

Query: 713 DFFSIGTNDLTQYVLAIDRQNPELAAEADSLHPAVLRMIRSTIDGARKHDRWVGVCGGLA 772
           DF SIGTNDLTQY LA+DR   +LAA++D LHPAVLR+I +T+ GA KH +WVGVCG LA
Sbjct: 729 DFLSIGTNDLTQYTLAMDRCQADLAAQSDGLHPAVLRLIAATVQGASKHGKWVGVCGALA 788

Query: 773 GDPFGASLLAGLGVQELSMTPNDIPAVKARLRGRALSALQQLAEQALQCETAEQVRALEA 832
           GDP    LL GLGV ELS+ P  +P +KAR+R       +Q A+ AL  E+A+ VRA+  
Sbjct: 789 GDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAVSR 848

Query: 833 Q 833
           +
Sbjct: 849 E 849


Lambda     K      H
   0.318    0.134    0.385 

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: 1623
Number of extensions: 79
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: 838
Length of database: 854
Length adjustment: 42
Effective length of query: 796
Effective length of database: 812
Effective search space:   646352
Effective search space used:   646352
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: 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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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