Alignments for a candidate for fruI in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas fluorescens GW456-L13

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate PfGW456L13_5075 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1146
         (953 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5075
          Length = 953

 Score = 1715 bits (4442), Expect = 0.0
 Identities = 886/953 (92%), Positives = 917/953 (96%)

Query: 1   MLELTIEQISMGQSAVDKATALQLLADRLVTDGLVADGYLAGLQAREAQGSTFLGQGIAI 60
           MLELT+EQISMGQSAVDK+ ALQLLA  LV DGLVA+GYLAGLQAREAQGSTFLGQGIAI
Sbjct: 1   MLELTVEQISMGQSAVDKSAALQLLAGHLVADGLVAEGYLAGLQAREAQGSTFLGQGIAI 60

Query: 61  PHGTPQTRDLVFSTGVRLMQFPDGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120
           PHGTP+TRDLVF+TGVRLMQFPDGVDWGDG IVYLAIGIAAKSDEHLRLLQLLTRALGET
Sbjct: 61  PHGTPETRDLVFTTGVRLMQFPDGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET 120

Query: 121 DLGQALRRASTAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180
           DLGQALRRA +AEALLKLLQGAPQELALDAQMIGLGV+A+DFEELVWRGARLLRQADCVS
Sbjct: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVAAEDFEELVWRGARLLRQADCVS 180

Query: 181 NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLSGLFCLASLGE 240
           NGF+ VLQQV+ALPLGDGLWWLHSEQTVKRPGLAFVTPD+P+RYLGQPL+GLFCLASLGE
Sbjct: 181 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDRPLRYLGQPLTGLFCLASLGE 240

Query: 241 AHQALLERLCALLIEGRGHELGRATSSRAVLEVLGGEVPADWPSARIALANTHGLHARPA 300
           AHQALLERLCALLIEGRGHELGRATSSR VLEVLGGEVPADWPSARIALAN HGLHARPA
Sbjct: 241 AHQALLERLCALLIEGRGHELGRATSSRKVLEVLGGEVPADWPSARIALANAHGLHARPA 300

Query: 301 KILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEFIAEPTIAADALPA 360
           KILAQLAKSFEG+IRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLE IAEP IAADALPA
Sbjct: 301 KILAQLAKSFEGDIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEIIAEPGIAADALPA 360

Query: 361 LLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQAIAAAPGIAIGPAHIQV 420
           LLAAIEEGLGEEVEPLP VSQ REV+AD+AEV+LAP+SGS++QAIAAAPG AIGPAHIQV
Sbjct: 361 LLAAIEEGLGEEVEPLPPVSQAREVVADMAEVVLAPSSGSVVQAIAAAPGFAIGPAHIQV 420

Query: 421 QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAKAIREIFITHQEMLDDPELT 480
            Q IDYPLRGESA IERERL+ ALA VRRDI+GLIERSK+KAIREIFITHQEMLDDPELT
Sbjct: 421 LQTIDYPLRGESAGIERERLQHALAQVRRDIQGLIERSKSKAIREIFITHQEMLDDPELT 480

Query: 481 DEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVETP 540
           DEVDTRLKQGESAEAAWMAVIEAAA+QQE+LQDALLAERAADLRDIGRRVL QLSG+ETP
Sbjct: 481 DEVDTRLKQGESAEAAWMAVIEAAARQQETLQDALLAERAADLRDIGRRVLMQLSGIETP 540

Query: 541 AEPEQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600
           +EP+QPYILVMDEVGPSDVARLDP RVAGILTARGGATAHSAIVARALGIPALVGAG  V
Sbjct: 541 SEPDQPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPGV 600

Query: 601 LLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAV 660
           LLL PGT LL+DGQRGRLHVDADAATLQRAT ERDTRE RLKAAAE RHQPALT DGHAV
Sbjct: 601 LLLAPGTALLLDGQRGRLHVDADAATLQRATAERDTREQRLKAAAELRHQPALTIDGHAV 660

Query: 661 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDGLAGRPL 720
           EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAH Q PDEATQEVEYRRVLDGLAGRPL
Sbjct: 661 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHPQVPDEATQEVEYRRVLDGLAGRPL 720

Query: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIM 780
           VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQ+MEAQLRALLRAADNRPLRIM
Sbjct: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM 780

Query: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840
           FPMVGSVDEWRQARDMTERLR EIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND
Sbjct: 781 FPMVGSVDEWRQARDMTERLRQEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840

Query: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900
           LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL
Sbjct: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900

Query: 901 VGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL 953
           VGLGVDELSV  RSIAEVKARIREL  TQTQTLA+QALAVGSANEVRALVEAL
Sbjct: 901 VGLGVDELSVGARSIAEVKARIRELGFTQTQTLARQALAVGSANEVRALVEAL 953


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: 2405
Number of extensions: 83
Number of successful extensions: 1
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: 953
Length of database: 953
Length adjustment: 44
Effective length of query: 909
Effective length of database: 909
Effective search space:   826281
Effective search space used:   826281
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: 57 (26.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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