Alignments for a candidate for pccA in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Saccharomonospora cyanea NA-134

Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate WP_005458894.1 SACCYDRAFT_RS19840 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::P0DTA4
         (730 letters)



>NCBI__GCF_000244975.1:WP_005458894.1
          Length = 660

 Score =  461 bits (1185), Expect = e-134
 Identities = 282/678 (41%), Positives = 387/678 (57%), Gaps = 55/678 (8%)

Query: 63  FDKILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYL 122
           FD +L+ANRGEIA RVI T +++GI++VAV+SD DA + HV  AD A  VGPA  ++SYL
Sbjct: 2   FDTVLVANRGEIAVRVIATLRRLGIRSVAVYSDADADARHVAEADVARRVGPADAARSYL 61

Query: 123 NMDAIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKL 182
           ++  I+ A   T AQAVHPGYGFLSEN  FAK     G++F+GP   AI AMGDKI +K 
Sbjct: 62  SVPDIVAAAVETGAQAVHPGYGFLSENAAFAKACEDAGIVFVGPPVAAIDAMGDKIRAKE 121

Query: 183 LAKKAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGF 242
               A V  +PG + V  D D     A  +GYPV++K SAGGGGKGMR+  +  E     
Sbjct: 122 TVSAAGVPVVPGANDV-SDVDSVAAAAERVGYPVLLKPSAGGGGKGMRLVREPAELPAAV 180

Query: 243 RFSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEE 302
             + +EA  +FGDDRLL+E+F+ +PRHIEIQVL D+HG  + L ERECS+QRR+QK+VEE
Sbjct: 181 ESAQREARGAFGDDRLLVERFVADPRHIEIQVLADRHGTVVHLGERECSLQRRHQKIVEE 240

Query: 303 APSIFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSK--KNFYFLEMNTRLQVEHPV 360
           APS  LD++TR  MG+ AV  A++V Y  AGTVEF+V S     F+FLEMNTRLQVEHPV
Sbjct: 241 APSTLLDADTRARMGKAAVEAARSVGYVGAGTVEFIVSSSAPDEFFFLEMNTRLQVEHPV 300

Query: 361 TECITGLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRLSQY 420
           TE +TGLDLV+  +RVA G PL   Q D+ ++G AVE RVYAEDP + F +P+ G +   
Sbjct: 301 TELVTGLDLVEWQLRVAAGEPLTFTQDDVRLDGHAVEARVYAEDPARDF-VPTGGTVLGL 359

Query: 421 QEPIHLPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRGVTH 480
            E    P VRVDSG++ G+ ++ +YDPM++K+I +G +R  AL R++ AL +  + GV  
Sbjct: 360 HEASG-PHVRVDSGLRQGTAVASHYDPMLAKVIAWGPDRTSALHRLDRALADTAVLGVPT 418

Query: 481 NIALLREVIINSRFVEGDINTKFLSDVYPDGFKGHKLTEDERNQLLAIAS--SLFVASQL 538
           N+  LR ++ +   V G ++T               L E E + L A       FVA+ L
Sbjct: 419 NVPFLRTLLRHPDVVAGRLDT--------------GLVERELSVLTADPDPVEFFVAAAL 464

Query: 539 RAQRFQEPENSRVPIIKP--QVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTS 596
                  P     P+I P    + W L              N+G T  + V  ++  V  
Sbjct: 465 DRVLSLWPTG---PVIDPWDVPSGWRL------------GGNAGVTMRLRVGAAEALVRV 509

Query: 597 TWNLASPLLSVSIDGTQRTIQCLSRDAGGNMSIQFLGTV--------------YKVHILT 642
               A     V +DG +      +R+ G ++ ++  G                Y      
Sbjct: 510 EGLPAQ--ARVVVDGAEAVSASAARE-GADLVVRVAGEYRRYRRAEACDGAVWYAREGRV 566

Query: 643 KLAAELNKFMLEKAAEDTSSILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMT 702
              +E    +   A    +  + SPMPG V+ V V+PGD V  G  + V+EAMKM++++T
Sbjct: 567 VAVSERPNLLASHAESVAAGPVTSPMPGTVLVVKVEPGDTVKAGTPLLVVEAMKMEHTIT 626

Query: 703 AGKTGKVKSVHCKAGDTV 720
           A   G V  +  +AG  V
Sbjct: 627 APVDGVVSQLDVRAGQQV 644


Lambda     K      H
   0.318    0.134    0.385 

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: 1074
Number of extensions: 51
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 730
Length of database: 660
Length adjustment: 39
Effective length of query: 691
Effective length of database: 621
Effective search space:   429111
Effective search space used:   429111
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