Alignments for a candidate for pccA in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Hyphomicrobium sulfonivorans WDL6

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_068459079.1 APY04_RS01365 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_001541235.1:WP_068459079.1
          Length = 667

 Score =  826 bits (2133), Expect = 0.0
 Identities = 433/667 (64%), Positives = 506/667 (75%), Gaps = 1/667 (0%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MFKKILIANRGEIACRVIKTARKMGI+TVAVYSDADR ALHV MADEA+H+GPPPA QSY
Sbjct: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSDADREALHVEMADEAVHLGPPPAAQSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           ++IDKI+EA K++GAEAVHPGYGFLSER  F  ALE AG+VFIGP   AI AMGDKI SK
Sbjct: 61  LLIDKIVEACKSTGAEAVHPGYGFLSEREAFPIALEKAGIVFIGPNPRAIAAMGDKIESK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           + A  A VSTVPGYMG I D   A+KI+ EIGYPVM+KASAGGGGKGMRIA +  EV+EG
Sbjct: 121 RAAAAAKVSTVPGYMGEITDTAHAIKIAEEIGYPVMMKASAGGGGKGMRIANNRREVEEG 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
           +  +++EA  SFGDDR+FIEKF+  PRHIEIQ++ DKHGN ++L ERECSIQRRNQKVIE
Sbjct: 181 YSLAQSEAKASFGDDRMFIEKFIVNPRHIEIQLIGDKHGNVIHLAERECSIQRRNQKVIE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSP LDEATR+AMG QA ALAKAVGY SAGTVEF+    K+FYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPLLDEATRQAMGAQAVALAKAVGYDSAGTVEFVAGQDKSFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           EL+TG+DLVE MIR AAGEKLPF+QSD+KINGWA+ESR+YAEDP+R FLPSIGRL +YRP
Sbjct: 301 ELVTGVDLVELMIRSAAGEKLPFKQSDVKINGWAVESRVYAEDPFRGFLPSIGRLVKYRP 360

Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420
           P E V+    VRNDTGV+EGGEISM+YDPMIAKL T  PTR  AI+    ALD+F ++GI
Sbjct: 361 PEEGVSDGITVRNDTGVFEGGEISMFYDPMIAKLVTHGPTRIEAIDAQAKALDSFYIDGI 420

Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480
            HN+PFV A+M HPR+ +G ++T FIAEE+PDGF     +   L+ VAA AA ++    I
Sbjct: 421 QHNIPFVSALMHHPRWREGALSTGFIAEEFPDGFTARQPEGEALQVVAAVAAVIDHENNI 480

Query: 481 RRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSD-GSSLRVTSDWTPG 539
           RR  I+  M+          VV +  +   V +       +V+F D G+ L +TS+W PG
Sbjct: 481 RRREITHQMSGQPVAFARRRVVKVADQLLPVEVEGGYGNYSVAFPDSGAELELTSEWLPG 540

Query: 540 QPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPDTSKY 599
           +P+ S  +D + + ++V  I  G  L   G    V V T R+AEL  LMP K   DTSKY
Sbjct: 541 EPVWSGTIDDKQVAVQVRPILNGVNLAYGGMQSPVYVYTEREAELVALMPIKQAADTSKY 600

Query: 600 LLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGASLRVD 659
           LLCPMPGLV  INV EG EVQ G ALA VEAMKMENILRAER   VKKI A PG SL VD
Sbjct: 601 LLCPMPGLVKAINVEEGAEVQVGDALAIVEAMKMENILRAERNAKVKKINAKPGDSLAVD 660

Query: 660 DVIMEFE 666
            VI+EFE
Sbjct: 661 AVILEFE 667


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: 1179
Number of extensions: 47
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: 667
Length adjustment: 38
Effective length of query: 628
Effective length of database: 629
Effective search space:   395012
Effective search space used:   395012
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 Apr 09 2024. 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:

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 2024 update 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