Alignments for a candidate for pccA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Rhodomicrobium vannielii ATCC 17100

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_013420178.1 RVAN_RS13015 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000166055.1:WP_013420178.1
          Length = 674

 Score =  821 bits (2121), Expect = 0.0
 Identities = 431/673 (64%), Positives = 514/673 (76%), Gaps = 8/673 (1%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MFKKILIANRGEIACRVIKTAR+MGI+TVAVYS+ADRNA+HV MADEA+ IGP PA QSY
Sbjct: 1   MFKKILIANRGEIACRVIKTARRMGIKTVAVYSEADRNAVHVEMADEAVLIGPAPAAQSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           ++ +KI+EA K +GAEA+HPGYGFLSE   FA AL+  G+ FIGP   AI+AMGDKI SK
Sbjct: 61  LIAEKIIEAAKKTGAEAIHPGYGFLSENAGFAEALKKEGIAFIGPNIEAIKAMGDKIESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           K A EA VSTVPGY+G+I   ++A+ I+N+IGYPVMIKASAGGGGKGMR+A S  EV+EG
Sbjct: 121 KAAAEARVSTVPGYLGVIESPEQAITIANDIGYPVMIKASAGGGGKGMRVARSADEVREG 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
           F +S  EA +SFGDDR+FIEKFV  PRHIEIQVL DKHGN VY+ ERECSIQRRNQKVIE
Sbjct: 181 FLTSTAEAKSSFGDDRVFIEKFVENPRHIEIQVLGDKHGNVVYVFERECSIQRRNQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSPFLDEATRKAMGEQA AL+KAV Y SAGTVEFIVD +KNFYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPFLDEATRKAMGEQAVALSKAVNYESAGTVEFIVDPKKNFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           E+ITG+DLVE MIRVA GEKLPF+Q DLKINGWA+ESR+YAEDP+R FLPSIGRL +YRP
Sbjct: 301 EMITGLDLVELMIRVAYGEKLPFKQEDLKINGWAVESRVYAEDPFRKFLPSIGRLVKYRP 360

Query: 361 PVESVTPT-SVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEG 419
           PVE      ++VRNDTG  EGGEISM+YDPMIAKL TW PTREAAI+    ALD F ++G
Sbjct: 361 PVEGPRLNGTIVRNDTGTEEGGEISMFYDPMIAKLVTWGPTREAAIDAQAAALDAFYIDG 420

Query: 420 IGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAE 479
           I HN+PF+ A+M HPR+ +G+++T FIAEEYPDGF+    +      + A AA ++ +  
Sbjct: 421 IEHNIPFLSALMQHPRWREGNLSTGFIAEEYPDGFKHREPEGEEREVLVAVAAWIDHINN 480

Query: 480 IRRTRISGTMNNH-ERHVGVDWVVALQGESYHVSIAAD-REGSTVSFSDG-----SSLRV 532
           IRR  ISG + +     +G   +V        V +A D + G+TV+F+D       ++  
Sbjct: 481 IRRRHISGQLPHAVGLRLGAARIVQFGKVEQPVVLAGDYKNGTTVTFTDAEGNPQKTVAF 540

Query: 533 TSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKL 592
            + W  G+P+    VDG+ + ++V  IP GF L   G   K  V T R+AEL  LMPEK 
Sbjct: 541 ETHWWFGKPVWHGKVDGKEVSVQVRVIPNGFDLSYNGVRTKAYVYTNREAELTALMPEKK 600

Query: 593 PPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAP 652
             DTSK LLCPMPGLV+ I+V EG EV+EG+ LA VEAMKM+N+L+AER  TV K+ A P
Sbjct: 601 VADTSKKLLCPMPGLVISISVEEGQEVKEGEQLAIVEAMKMQNVLKAERDVTVTKLRAKP 660

Query: 653 GASLRVDDVIMEF 665
           G SL VD VIMEF
Sbjct: 661 GDSLAVDAVIMEF 673


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: 1171
Number of extensions: 40
Number of successful extensions: 3
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: 674
Length adjustment: 39
Effective length of query: 627
Effective length of database: 635
Effective search space:   398145
Effective search space used:   398145
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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