GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Burkholderia phytofirmans PsJN

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate BPHYT_RS23275 BPHYT_RS23275 3-methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Dino:3607308
         (681 letters)



>FitnessBrowser__BFirm:BPHYT_RS23275
          Length = 692

 Score =  494 bits (1272), Expect = e-144
 Identities = 302/700 (43%), Positives = 400/700 (57%), Gaps = 49/700 (7%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MF KILIANRGEIACRV  T +++GI +VA+YSDAD NA HV   DEAVHIG S A +SY
Sbjct: 1   MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADANAKHVAACDEAVHIGGSTAAESY 60

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           + ++++++A R TGA+AVHPGYGFLSEN+ FA A E  G+ FIGPP  AI AMG K  +K
Sbjct: 61  LRVERIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAK 120

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
            +   A V  VPGY G   DA    + +  IGYPV++KASAGGGGKGMR+     +    
Sbjct: 121 ALMHTAAVPLVPGYHGDDQDAQLLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFEAA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
             S K EAA+SFG+DR+ IEK++T+PRH+E+QV AD HG  +YL +R+CS+QRR+QKV+E
Sbjct: 181 LASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLE 240

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300
           EAP+P L    ++ MG+ + A A+AV Y  AGTVEFI+ G  +FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGLAAEIKREMGDAAVAAARAVNYVGAGTVEFIMTGTGDFYFMEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360
           E++TG DLVE  +RVAAGE LP+TQ+ + + G AIE R+YAE P R FLPS G L   R 
Sbjct: 301 EMVTGQDLVEWQLRVAAGEALPLTQEQLKIDGHAIEARIYAEHPARGFLPSTGTLKHLRM 360

Query: 361 PVEVAAGPLEANGKWHGDAPSGPTA-VRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAA 419
           P  V      A     G   SG  A VR D+GV EG  I+ +YDPMIAKL   G  R  A
Sbjct: 361 PEGVEFTLDAAGSGAAGLGESGRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATREEA 420

Query: 420 IEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGF--------EG 471
           +  M  AL   EV G   N+ F+ +++    F  G++ T  I+  +   F        E 
Sbjct: 421 LARMSRALHACEVVGPHTNVEFLQSIVASEPFATGDLDTGLIERHHDALFAPRKKPFKEA 480

Query: 472 VTLGAADLTR----LAAAAAAMFRVAEIR----RTRISGTLDNHERMVGTDWVVTAQDAR 523
           + L  A L +     A  A+    ++  R     T+  G  D      G     +  ++ 
Sbjct: 481 LALACAALLKREGGTAHGASPWDALSHWRLNGGYTQTLGWRDLESGSAGN--AGSDSEST 538

Query: 524 FDVTIDADPGGSTVR---------FADGTAHRVTSRWTPGDSLAT--VEIDGAPMVLKVD 572
           F VT   D G  T+          ++DG+      R T GD+ AT  V +DG    +   
Sbjct: 539 FTVTFARDGGTQTLEHDGVREDFSWSDGSGLH-EYRATIGDARATGRVFVDGDTFHV--- 594

Query: 573 KITSGFRMRFRGADVKVHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGD 632
               G  + F   ++  H       E                L  PMPG V+ + VE G 
Sbjct: 595 -FCLGEALSFEWQNLLAHAADAEGGE--------------GRLTAPMPGKVIAVLVEPGT 639

Query: 633 EVQEGQALCTVEAMKMENILRAEKTATVTKINAGAGDSLA 672
            V++G  L  +EAMKME+ + A    TV+++    GD +A
Sbjct: 640 VVEKGTPLIVMEAMKMEHTIGAPAAGTVSEVLYSVGDQVA 679


Lambda     K      H
   0.318    0.134    0.392 

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: 1211
Number of extensions: 62
Number of successful extensions: 4
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: 681
Length of database: 692
Length adjustment: 39
Effective length of query: 642
Effective length of database: 653
Effective search space:   419226
Effective search space used:   419226
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: 54 (25.4 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