GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Sphingomonas koreensis DSMZ 15582

Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate Ga0059261_1646 Ga0059261_1646 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)

Query= SwissProt::P45597
         (838 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1646 Ga0059261_1646
           Phosphocarrier protein HPr/phosphoenolpyruvate--protein
           phosphotransferase (EC 2.7.3.9)/PTS system IIA
           component, Glc family (TC 4.A.1)
          Length = 830

 Score =  473 bits (1216), Expect = e-137
 Identities = 286/673 (42%), Positives = 379/673 (56%), Gaps = 31/673 (4%)

Query: 167 TIAYPSGLHARPATRWAETARGFSARAQVRAGDQAADAKSLVGLLQLGLRAGDSITVSAK 226
           T+  P G+HARPA R  E AR F A   +  GD+  DA+S VGLL LG R GD + V A+
Sbjct: 171 TLILPHGIHARPAARLGECARQFEAEIHLLHGDKRGDARSTVGLLALGTRLGDELVVQAR 230

Query: 227 GSDAPALLKRLRAVMDSLTAQEKADAERAAQRRAAPVIGWTPPQAQPA-IVGIGASPGVA 285
           GSDA A L  + A++ S       D    A   A  +     P  QP  I G+ ASPG+A
Sbjct: 231 GSDAEAALAAIVALLGS-------DMGEGAPAHAPAIAVPAAPVLQPGQIGGVIASPGLA 283

Query: 286 IGIVHRLRAAQTEVADQPIGLGDGGVLLHDALTRTRQQLAAIQDDTQRRLGASDAAIFKA 345
           +G   RLR     V  +  G+      L  A T  R ++ A  D      G S AA+ +A
Sbjct: 284 MGPAARLRQTAIAVEREGKGVDAERTALDAARTEVRVRIGARADAA----GGSVAAVMRA 339

Query: 346 QAELLNDTDLITRTCQLMVEGHGVAWSWHQAVEQIASGLAALGNPVLAGRAADLRDVGRR 405
              LL+D +L       +  G+   ++W  AV    + L A GN  L  R  DL D+ R+
Sbjct: 340 HLALLDDPELAAGAETRIAAGNSAGYAWRGAVHDQIAALKATGNAHLIERTDDLVDIERQ 399

Query: 406 VL-------AQLDPAAAGAGLTDLPEQPCILLAGDLSPSDTANLDTDCVLGLATAQGGPT 458
           VL       A+ D  AAGA          IL+A DL PS   ++      G+   +GGPT
Sbjct: 400 VLGVLTGIPAEADAIAAGA----------ILVADDLLPSQLVSIAASKPAGICLVRGGPT 449

Query: 459 SHTAILSRTLGLPALVAAGGQLLDIEDGVTAIIDGSSGRLYINPSELDLDAARTHIAEQQ 518
           SH AIL   +GLPALVA G  +  IEDG   ++D  +G +  +PS+ D DA    +A+++
Sbjct: 450 SHVAILCAGMGLPALVAMGDAIEAIEDGTALLLDAEAGHVTPDPSQADADAFAARLAKRE 509

Query: 519 AIREREAAQRALPAETTDGHHIDIGANVNLPEQVAMALTQGAEGVGLMRTEFLFLERGST 578
           A R+   A      +T DG  I++ AN+   E    A  QGAEG GL+R+EFLFL+R   
Sbjct: 510 ARRDAARAAAGNACQTADGVRIELFANLGTVEDAKAAAAQGAEGSGLVRSEFLFLDREDA 569

Query: 579 PTEDEQYQTYLAMARALDGRPLIVRALDIGGDKQVAHLELPHEENPFLGVRGARLLLRRP 638
           P+EDEQ+  Y  +A AL G+P+IVR LD+GGDK  A++    EENP LG+RG R+ L   
Sbjct: 570 PSEDEQHAAYQGIADALPGKPVIVRLLDVGGDKPAAYIPFDAEENPALGLRGIRVGLAHR 629

Query: 639 DLLEPQLRALYRAAKDGARLSIMFPMITSVPELISLREICARIRAELD-APELPIGIMIE 697
           DLLE Q+RA+ R    G +  IM PM+ SV E+ ++RE+  R+R E+     + +G+M+E
Sbjct: 630 DLLETQIRAILRVQPVG-QCRIMLPMVASVSEIRAVREVVERLRGEMGIETPIEVGVMVE 688

Query: 698 VPAAAAQADVLARHADFFSIGTNDLTQYVLAIDRQNPELAAEADSLHPAVLRMIRSTIDG 757
            PAAA  AD+LA  ADF SIGTNDLTQYVLA+DR NP +A+  D++HPAVLRMI  T   
Sbjct: 689 TPAAAITADLLAAEADFLSIGTNDLTQYVLAMDRGNPAVASGVDAMHPAVLRMIAETCRR 748

Query: 758 ARKHDRWVGVCGGLAGDPFGASLLAGLGVQELSMTPNDIPAVKARLRGRALSALQQLAEQ 817
           A    RWVGVCGGLA DP    +L GLG  ELS  P  +P  KA +R   L+  +  AE+
Sbjct: 749 ATAKGRWVGVCGGLASDPAAVPILIGLGATELSTVPGFVPEAKAIVRSVTLADARDHAER 808

Query: 818 ALQCETAEQVRAL 830
           AL C +A +VRAL
Sbjct: 809 ALHCSSAAEVRAL 821


Lambda     K      H
   0.318    0.134    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: 1793
Number of extensions: 108
Number of successful extensions: 6
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: 838
Length of database: 830
Length adjustment: 42
Effective length of query: 796
Effective length of database: 788
Effective search space:   627248
Effective search space used:   627248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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