Alignments for a candidate for pccA in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Mycolicibacterium vanbaalenii PYR-1

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_011778918.1 MVAN_RS08390 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_000015305.1:WP_011778918.1
          Length = 600

 Score =  528 bits (1360), Expect = e-154
 Identities = 290/602 (48%), Positives = 388/602 (64%), Gaps = 17/602 (2%)

Query: 3   SKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLD 62
           SKVLVANRGEIAVRV+RA ++ G+++VAVY+E D    HVR ADEA+ +G   +A+SYL 
Sbjct: 10  SKVLVANRGEIAVRVIRAAKDAGLQSVAVYAEPDADAPHVRLADEAFALGGQTSAESYLV 69

Query: 63  HESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSL 122
            E +++AA K+ A+AIHPGYGFL+ENA+FA+ V D+   W+GPS  ++  LG+K  AR +
Sbjct: 70  FEKLLDAAAKSGANAIHPGYGFLSENADFAQAVLDAGLIWIGPSPQSIRDLGDKVTARHI 129

Query: 123 MQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182
              A+ P+VPGT +P   A++V A A +YG PVAIKA  GGGGRG+KV  + +E+   F+
Sbjct: 130 AARAEAPLVPGTPDPVKDADEVVAFAKEYGVPVAIKAAFGGGGRGMKVARTIEEIPELFD 189

Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242
           +A RE  A F     +VE+YL+ PRH+E Q++AD HGNV   G RDCSLQRR QK++EEA
Sbjct: 190 SATREAVAAFGRGECFVERYLDKPRHVEAQVIADMHGNVIVAGTRDCSLQRRFQKLVEEA 249

Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV-EDGEFYFMEVNTRIQVEHTVTEE 301
           P+P L++  R+ I E+A+R  + A Y  AGTVE+LV +DG   F+EVNTR+QVEH VTEE
Sbjct: 250 PAPFLTDAQRKEIHESAKRICKEAGYYGAGTVEYLVGQDGLISFLEVNTRLQVEHPVTEE 309

Query: 302 VTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPG 361
            +G+D+V  Q ++A GE LD ++D     GHS EFRIN E   + F PA G +S ++ P 
Sbjct: 310 TSGIDLVLQQFKIANGEALDITEDPTP-RGHSFEFRINGEDAGRGFLPAPGPVSKFEAPT 368

Query: 362 GIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFH 421
           G G+RMD  V  G  IGG +DSM+AKLIVTG+ R+E L R+ RAL EF++EGL TVIPFH
Sbjct: 369 GPGVRMDSGVETGSVIGGQFDSMLAKLIVTGATRDEALARSRRALAEFNVEGLATVIPFH 428

Query: 422 RLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGD--EEEGEVTERTFTVEV 479
           R ++ D AF             +    IE   +        GD  +EE  +  +T  VEV
Sbjct: 429 RAVVADPAFIGDGEKFD-----VHTRWIETEWDNTVEPFTGGDPIDEEDTIPRQTVVVEV 483

Query: 480 NGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQQVIEGDGESVAAEM 539
            G+R EVSL   G  A+  GGA A  +  K   PRKR      GG       G++V A M
Sbjct: 484 GGRRLEVSLP--GDLALGGGGAPAHGALRKKPKPRKR------GGGGATAASGDAVTAPM 535

Query: 540 QGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLV 599
           QGT++ V V+EG  V  GD V +LEAMKMEN V A + G V+ + V  G ++  G V+  
Sbjct: 536 QGTVVKVAVEEGQTVAAGDLVVVLEAMKMENPVTAHKDGVVTGLSVEAGAAITQGTVVCE 595

Query: 600 LE 601
           L+
Sbjct: 596 LK 597


Lambda     K      H
   0.312    0.132    0.371 

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: 895
Number of extensions: 41
Number of successful extensions: 6
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: 601
Length of database: 600
Length adjustment: 37
Effective length of query: 564
Effective length of database: 563
Effective search space:   317532
Effective search space used:   317532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 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:

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