GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Magnetospirillum magneticum AMB-1

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011383117.1 AMB_RS03465 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000009985.1:WP_011383117.1
          Length = 665

 Score =  528 bits (1359), Expect = e-154
 Identities = 316/677 (46%), Positives = 415/677 (61%), Gaps = 26/677 (3%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF KILIANRGEIACRV++TA+++GI+TVAVYS+AD NA+HV+MADEA+ IGP  A +SY
Sbjct: 1   MFDKILIANRGEIACRVMRTAKRLGIRTVAVYSEADANAMHVAMADEAVLIGPAAAAESY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +  D I+EA K +GA+A+HPGYGFLSE   FA A   AGVVFIGPP GAI AMG K  SK
Sbjct: 61  LKGDVILEAAKRTGAQAIHPGYGFLSENAGFAEACAKAGVVFIGPPVGAIHAMGSKAESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           +L + AGV  VPGY G     +E  + +  IGYPV++KASAGGGGKGMR+    + + E 
Sbjct: 121 RLMEAAGVPLVPGYHGKGQTLEELTREAAIIGYPVLVKASAGGGGKGMRVVSEASGLAEA 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
             S+K EA  +FGDD + +E ++ +PRH+EIQV  D HGN VYL ER+CSIQRR+QKVIE
Sbjct: 181 VASAKREAKAAFGDDSLLLETYLGRPRHVEIQVFCDTHGNGVYLFERDCSIQRRHQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIV-DGQKNFYFLEMNTRLQVEHPV 299
           EAP+P L + TR+AMGE A A A+AV Y  AGTVEF+  DG+  F+F+EMNTRLQVEHPV
Sbjct: 241 EAPAPALADETRRAMGEAAVAAAQAVDYVGAGTVEFLYQDGR--FFFIEMNTRLQVEHPV 298

Query: 300 TELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYR 359
           TE+ITG+DLVE  + VA+G KLP  Q  L   G A E+RLYAEDP R+FLP+IG+L    
Sbjct: 299 TEMITGLDLVEWQLLVASGGKLPLAQEQLSRKGHAFEARLYAEDPSRDFLPAIGKLVHLA 358

Query: 360 PPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEG 419
           PP E+      VR DTGV +G +++ +YDPMIAKL  W   R++A+  +R AL  ++V G
Sbjct: 359 PPSEN----RHVRVDTGVRQGDQVTPFYDPMIAKLIVWDEDRDSALRRLRRALADYQVAG 414

Query: 420 IGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTL-RRVAAAAAAMNRVA 478
           +  N+ F+GA+  HP F   +I T FI E Y    Q      P +    A+ A  + R  
Sbjct: 415 VTTNVSFLGAIAAHPAFAALEIDTGFI-ERYRADLQPPAAPVPAMGLAFASLALLLWREE 473

Query: 479 EIRRTRISGTMNNHERHVGVDWVVALQGESYH---VSIAADREGSTVSF-SDGSSLRVTS 534
           +  RT       +   H    W   L  +++H       AD    TV F +DG SL +  
Sbjct: 474 DSARTAARSGDPHSPWHQTNGW--RLNDDNHHDFRFMDGADERRVTVHFVADGWSLDL-- 529

Query: 535 DWTPGQPLAS--LMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKL 592
              P Q L++    + G  L  ++G       +   G D+ V +      ++ L  P   
Sbjct: 530 ---PDQTLSARRATLSGTTLSAEIGGERRTASVVRSGFDITV-LHDGHAWKIKLDDPSAT 585

Query: 593 PPDT---SKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIA 649
             +       L  PMPG VV++ V  GD V  GQ L  VEAMKME+ ++A   G V  I 
Sbjct: 586 AAEREGGDGRLAAPMPGTVVQVLVQPGDAVTAGQPLIVVEAMKMEHAIKAPAEGKVAAIH 645

Query: 650 AAPGASLRVDDVIMEFE 666
              G ++     ++ FE
Sbjct: 646 FKVGDTVAEGVELLAFE 662


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: 1122
Number of extensions: 47
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: 666
Length of database: 665
Length adjustment: 38
Effective length of query: 628
Effective length of database: 627
Effective search space:   393756
Effective search space used:   393756
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