GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Phaeobacter inhibens BS107

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF2318 PGA1_c23500 phosphoenolpyruvate-protein phosphotransferase PtsP

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



>lcl|FitnessBrowser__Phaeo:GFF2318 PGA1_c23500
           phosphoenolpyruvate-protein phosphotransferase PtsP
          Length = 746

 Score =  271 bits (694), Expect = 9e-77
 Identities = 177/548 (32%), Positives = 277/548 (50%), Gaps = 15/548 (2%)

Query: 408 VNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVA 467
           + G  A  G   G V + +P+V+      + P  EL+RL  A++++   +  +++ +Q  
Sbjct: 183 MRGTIAQEGAVEGHVWLHEPRVVVTNPIADDPHRELERLHEAVEELRVGVDKMLEVTQTG 242

Query: 468 SIRD--IFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAER 525
                 +   ++           ++  + +GLSAEAA  +E   A  +   + D  L ER
Sbjct: 243 DKEQLQVLEAYRMFANSKGWMRRMEEDIGRGLSAEAAVEKEQSQARARMGQVQDAYLRER 302

Query: 526 AADLRDVGRRVLACLTGVEAE---QAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGG 582
            +DL D+  R+L  LTG  +E   + P++P +L+   + P ++     + + GI+   G 
Sbjct: 303 LSDLDDLSNRLLRILTGQGSETGAELPEDP-VLIARNIGPGELLEYG-RNLRGIVLEEGS 360

Query: 583 ATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAA 642
             SH+AIIARAL IP +V              +++DGE+G + + P    +   R + A 
Sbjct: 361 VGSHAAIIARALAIPLVVHTKRITTEALNGDHIMVDGEQGVVHLRPDDTVVSAFRDKIAM 420

Query: 643 REERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHS 702
           + + +      R   A+TRDG  V +  N G   + P     GAEG+GL RTEL F+  +
Sbjct: 421 QAKAQERYASIRDKQALTRDGRRVHLLMNAGLMADLPSLENSGAEGVGLFRTELQFLVRN 480

Query: 703 QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQ 762
           Q P ++   A Y+RVL+A  G+ +V RTLD+G DK LPY     E NP LG R IR+ L 
Sbjct: 481 QMPKRSELVALYQRVLDAAGGKRVVFRTLDIGSDKVLPYMKPTDEPNPALGWRAIRVGLD 540

Query: 763 RPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVD-------RLRVELPVADL 815
           +P ++  QL+AL+ +A+GRPL +MFP V   +E+R AKA V+       RL   LP   L
Sbjct: 541 KPGVMRMQLQALIRAANGRPLTVMFPFVAQFEEFRDAKAEVEKTLERERRLGHALP-EKL 599

Query: 816 QVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRL 875
           +VG M+E PS A        EV+F SIG NDL Q+  A DR +  +  + D L+ + L  
Sbjct: 600 EVGAMLETPSLAFAPQKFFDEVEFLSIGGNDLKQFFFAADRENERVRKRYDTLNVSYLSF 659

Query: 876 IGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAA 935
           I   VE     G  +  CGE A   +    L  +G+  LS+   S+  VK+ +  +D   
Sbjct: 660 IAQIVERCEKSGTPLSFCGEDAGRPIEAVCLAAMGLRVLSMRPASVGPVKSLLMRVDLND 719

Query: 936 CQRLAQQA 943
            +++   A
Sbjct: 720 IRKIIADA 727


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: 1366
Number of extensions: 63
Number of successful extensions: 5
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: 746
Length adjustment: 42
Effective length of query: 918
Effective length of database: 704
Effective search space:   646272
Effective search space used:   646272
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: 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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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