GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1646
          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:

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