Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS26895 RR42_RS26895 3-methylcrotonyl-CoA carboxylase

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



>FitnessBrowser__Cup4G11:RR42_RS26895
          Length = 674

 Score =  501 bits (1289), Expect = e-146
 Identities = 304/691 (43%), Positives = 400/691 (57%), Gaps = 82/691 (11%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF KILIANRGEIACRV  T R++GI+TVAVYSDAD +A HV++ DEA+HIG  PA  SY
Sbjct: 1   MFNKILIANRGEIACRVAATCRRLGIRTVAVYSDADADARHVALCDEAVHIGGAPARDSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +  D I+E  KA+GA+A+HPGYGFLSE   FA A   AG+VFIGPP+ +I AMG K  +K
Sbjct: 61  LRGDHIIEMAKATGAQAIHPGYGFLSENDGFAEACAEAGLVFIGPPASSIRAMGSKSAAK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           +L + A V  VPGY G   +     + ++ IGYPV++KASAGGGGKGMR+     E  EG
Sbjct: 121 RLMEAAAVPLVPGYHGEDQEPALLRREADRIGYPVLLKASAGGGGKGMRVV----EASEG 176

Query: 181 FESS----KNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQ 236
           FE++    + EA+ SFGDDR+ +EK++T+PRHIEIQV AD HGNCVYL ER+CS+QRR+Q
Sbjct: 177 FEAALASVQREASASFGDDRVLVEKYLTRPRHIEIQVFADTHGNCVYLFERDCSVQRRHQ 236

Query: 237 KVIEEAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVE 296
           KV+EEAP+P + E  R+AMGE A A A+AVGY  AGTVEFI +   +FYF+EMNTRLQVE
Sbjct: 237 KVLEEAPAPGMSEERRRAMGEAAVAAAQAVGYVGAGTVEFIANQDGSFYFMEMNTRLQVE 296

Query: 297 HPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLT 356
           HPVTE+ITG DLVE  +RVAAGE LP +Q  L+I+G A+E+R+YAE+P + FLPS G L 
Sbjct: 297 HPVTEMITGQDLVEWQLRVAAGEPLPLRQDQLQIHGHALEARVYAENPDKGFLPSTGTLR 356

Query: 357 RYRPPV-------ESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMR 409
             R P        +     + VR D+GV EG  IS YYDPMIAKL  W   RE A+  M 
Sbjct: 357 YLRTPAAVTFALGQDGNGPAGVRIDSGVREGDTISPYYDPMIAKLIVWGRDREEALARMA 416

Query: 410 LALDTFEVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTL--RRV 467
            AL  + V G+  N+ F+  ++    F   D+ T  I        Q A+   P      V
Sbjct: 417 QALAEYHVVGLSTNIAFLQRLVTSQAFRTADLDTGLIERN-----QAALFPPPAKVGTEV 471

Query: 468 AAAAAAMNRVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDG 527
            A A A    A+ R  R+                              D   +   + + 
Sbjct: 472 IALAVAALVDADTRARRV------------------------------DPADAHSPWQNA 501

Query: 528 SSLRVTSDWT--------PGQPLASLMVDGRPLVMKVGKIPMGFRL-RLRGAD-LKVNVR 577
            + R+ +D T         G+ LASL  DG    + VG+  +  R+  L G+  L +  R
Sbjct: 502 GAWRLNADATSQFRLRTGEGETLASLRSDGGKQWLTVGEQTLPLRVTSLAGSHALDLGER 561

Query: 578 T-----------------PRQAELALLMPEKLPPDTSK---YLLCPMPGLVVKINVAEGD 617
           T                  +Q  L ++ P             L+ PMPG ++ + V  G 
Sbjct: 562 TVKGSTYIEGDALYVFSGKQQTRLEVIDPLAHAGSADAEGGKLVAPMPGRIIAVMVKAGT 621

Query: 618 EVQEGQALATVEAMKMENILRAERRGTVKKI 648
            + +G  L  +EAMKME+ L A   G V+++
Sbjct: 622 VIGKGDPLIVMEAMKMEHTLTAPADGVVQEV 652


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: 1142
Number of extensions: 49
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: 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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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