GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Sphingomonas koreensis DSMZ 15582

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ga0059261_4056 Ga0059261_4056 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= metacyc::MONOMER-13589
         (666 letters)



>FitnessBrowser__Korea:Ga0059261_4056
          Length = 626

 Score =  472 bits (1215), Expect = e-137
 Identities = 293/688 (42%), Positives = 394/688 (57%), Gaps = 91/688 (13%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           M   +LIANRGEIACR+I+TARK+GI+TVAVYSDAD +ALHV  AD+A+HIG   A +SY
Sbjct: 1   MINSLLIANRGEIACRIIRTARKLGIRTVAVYSDADAHALHVREADQAVHIGGSQARESY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +V ++++ A K +GAEA+HPGYGFLSE  DFA A+ AAG++++GP   +I AMG K  +K
Sbjct: 61  LVGERVIAAAKETGAEAIHPGYGFLSENADFAEAVVAAGLIWVGPNPDSIRAMGLKDAAK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           KL ++A V   PGY+G     D   + +++IGYPV+IKA AGGGGKGMR      +  + 
Sbjct: 121 KLMQDARVPVTPGYLGEDQSLDRLQREADKIGYPVLIKAVAGGGGKGMRRVDVAEDFADA 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
             S + EAA+SFGDDR+ IEK++  PRHIE+QV  D HGN V+L ER+CS+QRR+QKVIE
Sbjct: 181 LASCQREAASSFGDDRVLIEKYILAPRHIEVQVFGDSHGNIVHLFERDCSMQRRHQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQK-----NFYFLEMNTRLQV 295
           EAP+P +D++ R A+ E A   A+AV Y  AGT+EFI D  +       +F+EMNTRLQV
Sbjct: 241 EAPAPGMDKSARFAVCEAAVKAARAVNYVGAGTIEFIADASQGLHADRIWFMEMNTRLQV 300

Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355
           EHPVTE ITG+DLVE  +RVA+GE LP +Q ++ I+G A+E+RLYAEDP R FLPS G+L
Sbjct: 301 EHPVTEAITGVDLVEWQLRVASGEPLPLRQEEIAISGHAIEARLYAEDPARGFLPSTGKL 360

Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415
                PV +       R DTGV  G  IS +YDPMIAKL   + TRE AI  +R  L   
Sbjct: 361 EVLDFPVNA-------RVDTGVEAGSVISPFYDPMIAKLIVHSDTREEAIALLRSELSYL 413

Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475
            V  +  N  F+  ++    FV+  + T  I        +G VL    L      AA + 
Sbjct: 414 TVWPVRTNAGFLFRLLGDGDFVRAQLDTGLIER------RGEVLTIDPL----PTAADLT 463

Query: 476 RVAEIRRTRI-SGTMN--------NHERHVGVDWVVALQGE-----SYHVSIAA-----D 516
           R      T I S T++           R       +A+ GE     + H  IA+     +
Sbjct: 464 RATYWLETDIPSDTLSMAHGLEGFRLNRSPVTQRALAVNGERIVFTADHGDIASHFYGHE 523

Query: 517 REGSTVSFSDGSSLRVTSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNV 576
           R+G+ +    G++ RVT+D T G   A+   DG  L    G+I                 
Sbjct: 524 RDGAALLVHGGATFRVTADRTDGAAGAA-AGDGSILAPMPGRI----------------- 565

Query: 577 RTPRQAELALLMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENI 636
                                           V + VAEG  V  GQ L  +EAMKME  
Sbjct: 566 --------------------------------VSVEVAEGQAVIAGQKLLVLEAMKMEQA 593

Query: 637 LRAERRGTVKKIAAAPGASLRVDDVIME 664
           L A   GT++ + A  GA ++VD ++++
Sbjct: 594 LTAPFDGTIETLNAVAGAQVQVDALLVK 621


Lambda     K      H
   0.318    0.134    0.386 

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: 1008
Number of extensions: 48
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 666
Length of database: 626
Length adjustment: 38
Effective length of query: 628
Effective length of database: 588
Effective search space:   369264
Effective search space used:   369264
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