GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Burkholderia phytofirmans PsJN

Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate BPHYT_RS02740 BPHYT_RS02740 PTS glucose transporter subunit IIA

Query= SwissProt::P45597
         (838 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02740 BPHYT_RS02740 PTS glucose
           transporter subunit IIA
          Length = 854

 Score =  474 bits (1219), Expect = e-137
 Identities = 295/715 (41%), Positives = 405/715 (56%), Gaps = 28/715 (3%)

Query: 135 DDPAVIVAALTGDRAPDTSAAPATDLAE--RFEWTIAYPSGLHARPATRWAETARGFSAR 192
           + P +++ A  G  A  +    +T++ E  R + T+ +  GLHARPA R  E ARGF AR
Sbjct: 149 ETPLLVLRARDGAAAEASRQLSSTNVTEEARQQVTLVHAGGLHARPAARAREAARGFDAR 208

Query: 193 AQVRAGDQAADAKSLVGLLQLGLRAGDSITVSAKGSDAPALLKRLRAVMDSLTAQEKADA 252
            +VR   + A  +S+VGLL LG  AG+  TV   G   P     + A+ + LT +   + 
Sbjct: 209 VEVRYEGRKAAIESVVGLLGLG--AGEGATVELLGM-GPQAAAAVAAIANELTREAHGEV 265

Query: 253 ERAAQRRAAPVIGWTPPQA--QPA--------IVGIGASPGVAIGIVHRLRAAQTEVADQ 302
           E    R+++P      PQA  +PA        + G+ A+PGVA+G + R   A  +  ++
Sbjct: 266 EEKPARQSSPA-----PQAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEK 320

Query: 303 PIGLGDG-GVLLHDALTRTRQQLAAIQDDTQRRLGASDAAIFKAQAELLNDTDLITRTCQ 361
             G       LL  A+      L     D  +R    +A IF     LL D  L+     
Sbjct: 321 ANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARD 380

Query: 362 LMVEGHGVAWSWHQAVEQIASGLAALGNPVLAGRAADLRDVGRRVLAQLDPAAAGAGLTD 421
           L+  G    ++W +A+    + L  + + +LA RAADLRD+ +RVL  L   +A A    
Sbjct: 381 LISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATA--RT 438

Query: 422 LPEQPCILLAGDLSPSDTANLDTDCVLGLATAQGGPTSHTAILSRTLGLPALVAAGGQLL 481
           LPE+  +L A + +PSD + LD   V  L  A+GG TSH AIL+R  G+PALVA G  L 
Sbjct: 439 LPEE-AVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALH 497

Query: 482 DIEDGVTAIIDGSSGRLYINPSELDLDAARTHIAEQQAIREREAAQRALPAETTDGHHID 541
            I +G   +++ ++GRL   P+ELD++ AR        +RE         A T+DG  I+
Sbjct: 498 AIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIE 557

Query: 542 IGANVNLPEQVAMALTQGAEGVGLMRTEFLFLERGSTPTEDEQYQTYLAMARALDGRPLI 601
           + AN+   +    A+  GA+ VGL+RTE LF+ R + PT DE  Q+Y A+  AL GR  I
Sbjct: 558 VAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAI 617

Query: 602 VRALDIGGDKQVAHLELPHEENPFLGVRGARLLLRRPDLLEPQLRALYRAAKDGARLSIM 661
           +R LD+G DK+V +L LP E NP LG+RG RL   RPDLL+ QLR L      GA + I+
Sbjct: 618 IRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGA-VRIL 676

Query: 662 FPMITSVPELISLREICARIRAELDAPE-LPIGIMIEVPAAAAQADVLARHADFFSIGTN 720
            PM+T V ELI +R+       EL   E + +G+MIEVP+AA  AD LA+HADF SIGTN
Sbjct: 677 LPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTN 736

Query: 721 DLTQYVLAIDRQNPELAAEADSLHPAVLRMIRSTIDGARKHDRWVGVCGGLAGDPFGASL 780
           DLTQY LA+DR   +LAA+AD LHPAVLR+I +T+ GA KH +WVGVCG LAGDP    L
Sbjct: 737 DLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPL 796

Query: 781 LAGLGVQELSMTPNDIPAVKARLRGRALSALQQLAEQALQCETAEQVRALEAQRE 835
           L GLGV ELS+ P  +P +KAR+R       +Q A+ AL  E+A+ VRA  A RE
Sbjct: 797 LVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRA--ASRE 849


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: 1627
Number of extensions: 71
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: 854
Length adjustment: 42
Effective length of query: 796
Effective length of database: 812
Effective search space:   646352
Effective search space used:   646352
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 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