Alignments for a candidate for fruI in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas stutzeri RCH2

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF3291 Psest_3355 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::psRCH2:GFF3291
         (960 letters)



>FitnessBrowser__psRCH2:GFF3291
          Length = 960

 Score = 1858 bits (4813), Expect = 0.0
 Identities = 960/960 (100%), Positives = 960/960 (100%)

Query: 1   MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI 60
           MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI
Sbjct: 1   MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI 60

Query: 61  PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG 120
           PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG
Sbjct: 61  PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG 120

Query: 121 DLSEGLQQAESPEAIIGLLQGAPQALALDGELVSLGVAADDFDELAWQGVKLLKRAQCVE 180
           DLSEGLQQAESPEAIIGLLQGAPQALALDGELVSLGVAADDFDELAWQGVKLLKRAQCVE
Sbjct: 121 DLSEGLQQAESPEAIIGLLQGAPQALALDGELVSLGVAADDFDELAWQGVKLLKRAQCVE 180

Query: 181 PGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASMGE 240
           PGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASMGE
Sbjct: 181 PGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASMGE 240

Query: 241 AHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPADWPSAQVPLANAHGLHARPA 300
           AHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPADWPSAQVPLANAHGLHARPA
Sbjct: 241 AHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPADWPSAQVPLANAHGLHARPA 300

Query: 301 KVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDALPA 360
           KVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDALPA
Sbjct: 301 KVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDALPA 360

Query: 361 LVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIG 420
           LVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIG
Sbjct: 361 LVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIG 420

Query: 421 PVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVASIRDIFTTHQAML 480
           PVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVASIRDIFTTHQAML
Sbjct: 421 PVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVASIRDIFTTHQAML 480

Query: 481 KDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACL 540
           KDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACL
Sbjct: 481 KDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACL 540

Query: 541 TGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIV 600
           TGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIV
Sbjct: 541 TGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIV 600

Query: 601 GAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANERRMDAAVT 660
           GAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANERRMDAAVT
Sbjct: 601 GAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANERRMDAAVT 660

Query: 661 RDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEA 720
           RDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEA
Sbjct: 661 RDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEA 720

Query: 721 LEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQRPDILETQLRALLASADG 780
           LEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQRPDILETQLRALLASADG
Sbjct: 721 LEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQRPDILETQLRALLASADG 780

Query: 781 RPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVGIMIEIPSAALIAPVLAQEVDFF 840
           RPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVGIMIEIPSAALIAPVLAQEVDFF
Sbjct: 781 RPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVGIMIEIPSAALIAPVLAQEVDFF 840

Query: 841 SIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADA 900
           SIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADA
Sbjct: 841 SIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADA 900

Query: 901 LAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAHEVRAFVGEHC 960
           LAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAHEVRAFVGEHC
Sbjct: 901 LAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAHEVRAFVGEHC 960


Lambda     K      H
   0.317    0.134    0.384 

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: 2681
Number of extensions: 93
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: 960
Length of database: 960
Length adjustment: 44
Effective length of query: 916
Effective length of database: 916
Effective search space:   839056
Effective search space used:   839056
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, or view the source code.

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