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_3942 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated

Query= reanno::WCS417:GFF780
         (952 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3942
          Length = 759

 Score =  334 bits (857), Expect = 1e-95
 Identities = 205/565 (36%), Positives = 326/565 (57%), Gaps = 24/565 (4%)

Query: 404 IAAAPGIAIGPAHIQVLQVFDYPLRGESCAIERER----LHSALADVRRDIQGLIERSQS 459
           +  +PG A+G A + +L   D  +  +    + +       +A+  VR D++ L  +  +
Sbjct: 181 VPGSPGAAVGTA-VVMLPPADLDVVPDKAITDIDAELGLFKTAIEGVRADMRALSAKLAT 239

Query: 460 KAI---REIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLA 516
           +     R +F  +  MLDD  L  EV T +K G+ A+ A   V+     + E + DA L 
Sbjct: 240 QLRPEERALFDVYLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLR 299

Query: 517 ERAADLRDIGRRVLAQLCGVETSQEPSEPY----ILVMDEVGPSDVARLDPARVAGILTA 572
           ERA+D++D+GRR+LA L   +  ++ +  Y    ILV +E+ P+ +  +   ++AG+++ 
Sbjct: 300 ERASDVKDLGRRLLAYL---QQERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAGLVSV 356

Query: 573 RGGATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVD-ADAATLQRATV 631
            G   +H AI+ARA+GIP ++G          G  +++DG  G ++ + +D    Q A V
Sbjct: 357 LGSGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADV 416

Query: 632 ERDTREQRLQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIF 691
             + ++  L    A R  P +T DGH + ++ N G  A VA A ++GAEG+GL RTE+ F
Sbjct: 417 VEEEKQLSL-GLDALRDLPCVTLDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPF 475

Query: 692 MAHPQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIR 751
           M + + P E  Q A YR  L     +P+ +R+LD+GGDK L Y+PI +E+NPFLG RGIR
Sbjct: 476 MINQRFPSEKEQLAIYREQLAAFHPQPVTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIR 534

Query: 752 LTLQRPQIMEAQLRALLRSADN-RPLRIMFPMVGSVDEWRAARDMTERLRLEI-----PV 805
           +TL  P+I   Q RA+L++++    LRI+ PM+    E   A  +  R   E+      V
Sbjct: 535 VTLDHPEIFLVQARAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRDEGTDV 594

Query: 806 ADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAV 865
               +G+MIE+P+A      LA++VDF SVG+NDLTQY LA+DR +P ++   D LHPAV
Sbjct: 595 PMPPIGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAV 654

Query: 866 LQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFS 925
           LQ +   VR AHA GK V +CGE+A DP A  +L+ +G D LS++A ++P+VK  +R+ +
Sbjct: 655 LQALQNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQIN 714

Query: 926 LSEAQGLAQKALAVGSPAEVRALVE 950
           LS+AQ L  + + + +P  + + ++
Sbjct: 715 LSKAQELLAEVMTIDNPQVIHSSLQ 739


Lambda     K      H
   0.318    0.135    0.385 

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: 1438
Number of extensions: 73
Number of successful extensions: 3
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: 952
Length of database: 759
Length adjustment: 42
Effective length of query: 910
Effective length of database: 717
Effective search space:   652470
Effective search space used:   652470
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 (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