GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N1B4

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate Pf1N1B4_1146 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1146
          Length = 953

 Score = 1825 bits (4726), Expect = 0.0
 Identities = 953/953 (100%), Positives = 953/953 (100%)

Query: 1   MLELTIEQISMGQSAVDKATALQLLADRLVTDGLVADGYLAGLQAREAQGSTFLGQGIAI 60
           MLELTIEQISMGQSAVDKATALQLLADRLVTDGLVADGYLAGLQAREAQGSTFLGQGIAI
Sbjct: 1   MLELTIEQISMGQSAVDKATALQLLADRLVTDGLVADGYLAGLQAREAQGSTFLGQGIAI 60

Query: 61  PHGTPQTRDLVFSTGVRLMQFPDGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120
           PHGTPQTRDLVFSTGVRLMQFPDGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET
Sbjct: 61  PHGTPQTRDLVFSTGVRLMQFPDGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120

Query: 121 DLGQALRRASTAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180
           DLGQALRRASTAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS
Sbjct: 121 DLGQALRRASTAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180

Query: 181 NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLSGLFCLASLGE 240
           NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLSGLFCLASLGE
Sbjct: 181 NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLSGLFCLASLGE 240

Query: 241 AHQALLERLCALLIEGRGHELGRATSSRAVLEVLGGEVPADWPSARIALANTHGLHARPA 300
           AHQALLERLCALLIEGRGHELGRATSSRAVLEVLGGEVPADWPSARIALANTHGLHARPA
Sbjct: 241 AHQALLERLCALLIEGRGHELGRATSSRAVLEVLGGEVPADWPSARIALANTHGLHARPA 300

Query: 301 KILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEFIAEPTIAADALPA 360
           KILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEFIAEPTIAADALPA
Sbjct: 301 KILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEFIAEPTIAADALPA 360

Query: 361 LLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQAIAAAPGIAIGPAHIQV 420
           LLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQAIAAAPGIAIGPAHIQV
Sbjct: 361 LLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQAIAAAPGIAIGPAHIQV 420

Query: 421 QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAKAIREIFITHQEMLDDPELT 480
           QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAKAIREIFITHQEMLDDPELT
Sbjct: 421 QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAKAIREIFITHQEMLDDPELT 480

Query: 481 DEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVETP 540
           DEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVETP
Sbjct: 481 DEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVETP 540

Query: 541 AEPEQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600
           AEPEQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV
Sbjct: 541 AEPEQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600

Query: 601 LLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAV 660
           LLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAV
Sbjct: 601 LLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAV 660

Query: 661 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDGLAGRPL 720
           EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDGLAGRPL
Sbjct: 661 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDGLAGRPL 720

Query: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIM 780
           VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIM
Sbjct: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIM 780

Query: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840
           FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND
Sbjct: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840

Query: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900
           LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL
Sbjct: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900

Query: 901 VGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL 953
           VGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL
Sbjct: 901 VGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL 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: 2467
Number of extensions: 74
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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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