Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E2

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate Pf6N2E2_3339 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= reanno::pseudo5_N2C3_1:AO356_07335
         (954 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3339
          Length = 954

 Score = 1814 bits (4698), Expect = 0.0
 Identities = 945/954 (99%), Positives = 950/954 (99%)

Query: 1   MLELTLEQISMAQTAVDKDAALQLLADKLVADGLVAEGYLAGLQAREAQGSTFLGQGIAI 60
           MLELTLEQISMAQTAVDKDAALQLLADKLVADGLVAEGYLAGLQAREAQGSTFLGQGIAI
Sbjct: 1   MLELTLEQISMAQTAVDKDAALQLLADKLVADGLVAEGYLAGLQAREAQGSTFLGQGIAI 60

Query: 61  PHGTPQTRDLVYSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120
           PHGTPQTRDLV+STGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET
Sbjct: 61  PHGTPQTRDLVHSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120

Query: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180
           DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS
Sbjct: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180

Query: 181 NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE 240
           NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE
Sbjct: 181 NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE 240

Query: 241 AHQALLERLCALLIEGRGHELGRATSSRKVLEVLGGELPADWPSARIGLANAHGLHARPA 300
           AHQALLERLCALLIEGRGHELGRATSSRKVLEVLGGELPADWPSARIGLANAHGLHARPA
Sbjct: 241 AHQALLERLCALLIEGRGHELGRATSSRKVLEVLGGELPADWPSARIGLANAHGLHARPA 300

Query: 301 KILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVLEFIAEPSIANDALPA 360
           KILAQLAKSF+GEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVLEFIAEPSIANDALPA
Sbjct: 301 KILAQLAKSFEGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVLEFIAEPSIANDALPA 360

Query: 361 LLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLIQAVAAAPGIAIGPAHIQ 420
           LLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLIQAVAAAPGIAIGPAHIQ
Sbjct: 361 LLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLIQAVAAAPGIAIGPAHIQ 420

Query: 421 VLQAIDYPLRGESAAIERERLQNALNQVRSDIQGLIERAKAKAIREIFITHQEMLDDPEL 480
           VLQAIDYPLRGESAAIERERLQNALNQVR DIQGLIERAKAKAIREIFITHQEMLDDPEL
Sbjct: 421 VLQAIDYPLRGESAAIERERLQNALNQVRRDIQGLIERAKAKAIREIFITHQEMLDDPEL 480

Query: 481 TDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAERAADLRDVGRRVLAQLCGVET 540
           +DEVDTRLKLGESAQAAWMGV+EAAAKEQEALQDALLAERAADLRDVGRRVLAQLCGVET
Sbjct: 481 SDEVDTRLKLGESAQAAWMGVVEAAAKEQEALQDALLAERAADLRDVGRRVLAQLCGVET 540

Query: 541 PNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAA 600
           PNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAA
Sbjct: 541 PNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAA 600

Query: 601 VLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTREQRLKVAAEQRHEPALTRDGHA 660
           VLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTREQRLKVAAEQRHEPALTRDGHA
Sbjct: 601 VLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTREQRLKVAAEQRHEPALTRDGHA 660

Query: 661 VEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQAPDEATQEAEYRKVLDGLAGRP 720
           VEVFANIGESAGVA AVEQGAEGIGLLRTELIFMAHSQAPDEATQEAEYRKVLDGLAGRP
Sbjct: 661 VEVFANIGESAGVAGAVEQGAEGIGLLRTELIFMAHSQAPDEATQEAEYRKVLDGLAGRP 720

Query: 721 LVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRSADSRPLRI 780
           LVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRSAD+RPLRI
Sbjct: 721 LVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRSADNRPLRI 780

Query: 781 MFPMVGSVDEWRQARAMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTN 840
           MFPMVGSVDEWRQARAMTERLR EIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTN
Sbjct: 781 MFPMVGSVDEWRQARAMTERLRQEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTN 840

Query: 841 DLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPV 900
           DLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPV
Sbjct: 841 DLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPV 900

Query: 901 LVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQAALAVGSADDVRALVEAL 954
           LVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQ ALAVGSADDVRALVEAL
Sbjct: 901 LVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQEALAVGSADDVRALVEAL 954


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: 2355
Number of extensions: 73
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: 954
Length of database: 954
Length adjustment: 44
Effective length of query: 910
Effective length of database: 910
Effective search space:   828100
Effective search space used:   828100
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