GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Rhodobacter ovatus JA234

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_097029020.1 CRO07_RS00230 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_900207575.1:WP_097029020.1
          Length = 666

 Score = 1243 bits (3215), Expect = 0.0
 Identities = 623/666 (93%), Positives = 648/666 (97%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MFKKILIANRGEIACRVIKTARKMGI+TVAVYSDADRNALHVSMADEAIHIGPPPANQSY
Sbjct: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           IVIDKIMEAIK SGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPS AIEAMGDKITSK
Sbjct: 61  IVIDKIMEAIKQSGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSPAIEAMGDKITSK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           KLA+EAGVSTVPGYMGLIADADEAVKIS++IGYPVMIKASAGGGGKGMRIAW+  E +EG
Sbjct: 121 KLAQEAGVSTVPGYMGLIADADEAVKISDQIGYPVMIKASAGGGGKGMRIAWNAEEAREG 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
           F+SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE
Sbjct: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP
Sbjct: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360

Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420
           PVE+VTPTSVVRNDTGV+EGGEISMYYDPMIAKLCTWAPTREAAIEEMR+ALDTFEVEGI
Sbjct: 361 PVEAVTPTSVVRNDTGVFEGGEISMYYDPMIAKLCTWAPTREAAIEEMRIALDTFEVEGI 420

Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480
           GHNLPFVGAVMDHPRFV GDITTAFIAEEYPDGFQGA LDEPTLRRVAAAAAAMNRVAEI
Sbjct: 421 GHNLPFVGAVMDHPRFVSGDITTAFIAEEYPDGFQGATLDEPTLRRVAAAAAAMNRVAEI 480

Query: 481 RRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPGQ 540
           RR RISGTM+NHER VG DWVV+LQGE +HV IAADREGSTV+F DGSSLR TSDWTPGQ
Sbjct: 481 RRARISGTMDNHERKVGDDWVVSLQGEDFHVGIAADREGSTVTFCDGSSLRCTSDWTPGQ 540

Query: 541 PLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPDTSKYL 600
           PLA +MVDG+PLVMKVGKIPMGFR+RLRGADLKV+VRTPRQAELA+LMPEKLPPDTS++L
Sbjct: 541 PLARVMVDGKPLVMKVGKIPMGFRVRLRGADLKVHVRTPRQAELAVLMPEKLPPDTSRFL 600

Query: 601 LCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGASLRVDD 660
           LCPMPGLVVKINV EGDEVQEGQALATVEAMKMENILRAER+G VK+IAAA G+SLRVDD
Sbjct: 601 LCPMPGLVVKINVEEGDEVQEGQALATVEAMKMENILRAERKGVVKRIAAAAGSSLRVDD 660

Query: 661 VIMEFE 666
           +IMEFE
Sbjct: 661 IIMEFE 666


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: 1446
Number of extensions: 36
Number of successful extensions: 2
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: 666
Length adjustment: 38
Effective length of query: 628
Effective length of database: 628
Effective search space:   394384
Effective search space used:   394384
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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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