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

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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