Alignments for a candidate for pccA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Paraburkholderia bryophila 376MFSha3.1

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate H281DRAFT_01343 H281DRAFT_01343 3-methylcrotonoyl-CoA carboxylase, alpha subunit

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Burk376:H281DRAFT_01343
          Length = 677

 Score =  506 bits (1304), Expect = e-147
 Identities = 295/680 (43%), Positives = 393/680 (57%), Gaps = 22/680 (3%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MFNKILIANRGEIACRV  T +++GI++VA+YSDAD  A HV   DEAVHIG   A +SY
Sbjct: 1   MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADADAKHVSACDEAVHIGGATAAESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           + + +++ A RATGAQAVHPGYGFLSEN  FA A EA G++F+GPP  AI AMG K  +K
Sbjct: 61  LRVARIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
            +   A V  VPGY G  ++ +   + ++ IGYPV++KASAGGGGKGMR+    ++    
Sbjct: 121 ALMHAAAVPLVPGYHGDDQNPELLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFLAA 180

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

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAP+P L    +R MGE AVA A+AV Y  AGTVEFI+    +FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGLSAQIKREMGEAAVAAARAVNYVGAGTVEFIMTATGDFYFMEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           E+ITG DLVE  +RVAAG+PL +TQ  +K+ G AIE R+YAE P RGFLPS G L   R 
Sbjct: 301 EMITGQDLVEWQLRVAAGQPLPLTQDQLKIDGHAIEARIYAEHPARGFLPSTGTLKHLRM 360

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           P               G   S +A VR D+GV EG  I+ +YDPMIAKL     TR  A+
Sbjct: 361 PEGVEF------AIHAGAGESRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATREEAL 414

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
             M  AL + EV G   N+ FL  +++   F +GD+ T  I   +   F  V  P  +  
Sbjct: 415 ARMSRALHACEVVGPHTNVEFLQRIVESEPFATGDLDTGLIERHHEALFAPVKKPFKEAL 474

Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVG----TEWVVTLQGAD--FPVTIAADHDG 534
            +A AA                 + +     G      W+      +   P T+A   DG
Sbjct: 475 ALACAALLTREGGTAHGASPWDALSHWRLNSGFTQTLGWLAIESSGETGSPFTVAFARDG 534

Query: 535 STVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTP 594
           +T + +    +R    W+ G  L             +G      R+   G    V     
Sbjct: 535 ATQTLEH-DGVREAFSWSSGAGLHEYRA-------TIGDARATGRVFIDGDTFHVFCLGH 586

Query: 595 RQA-ELARLMPEKLPPDTSK-MLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENIL 652
             A E   L+      +  +  L  PMPG ++ V VE G  V++G  L  +EAMKME+ +
Sbjct: 587 ALAFEWQNLLAHAADAEHGEGRLTAPMPGKVIAVLVEPGAVVEKGTPLIVMEAMKMEHTI 646

Query: 653 RAEKKGVVAKINASAGNSLA 672
            A   G V+++  + G+ +A
Sbjct: 647 GAPAAGTVSEVLYAVGDQVA 666


Lambda     K      H
   0.317    0.134    0.387 

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: 1147
Number of extensions: 51
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 681
Length of database: 677
Length adjustment: 39
Effective length of query: 642
Effective length of database: 638
Effective search space:   409596
Effective search space used:   409596
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources