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_011779394.1 MVAN_RS10860 pyruvate carboxylase

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_000015305.1:WP_011779394.1
          Length = 1145

 Score =  371 bits (953), Expect = e-107
 Identities = 206/448 (45%), Positives = 283/448 (63%), Gaps = 12/448 (2%)

Query: 3   SKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIG----PARAAD 58
           SKVLVANRGEIA+R  RA  E+G+ TVAVY   D++  H   ADE+Y IG    P RA  
Sbjct: 6   SKVLVANRGEIAIRAFRAAYEMGIATVAVYPYEDRNSLHRLKADESYQIGEIGHPVRA-- 63

Query: 59  SYLDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTK 118
            YL    ++  A +A  DA++PGYGFL+EN E A    D+  T+VGPSA+ +E  G K +
Sbjct: 64  -YLSVAEIMRVAVEAGCDAVYPGYGFLSENPELAAACADAGITFVGPSANVLELTGNKAR 122

Query: 119 ARSLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVD 178
           A    + A +PV+  +  P+ S +++ A AD   +P+ +KA  GGGGRG++ V     + 
Sbjct: 123 AIQAARAAGLPVLTSSA-PSASVDELVAAADGMEFPLFVKAVSGGGGRGMRRVTDRAALA 181

Query: 179 GQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKV 238
              E A RE E+ F + +VY+E+ +  PRHIEVQILAD  G+V HL ERDCS+QRRHQKV
Sbjct: 182 EAVEAASREAESAFGDPNVYLEQAVLNPRHIEVQILADTAGHVMHLFERDCSVQRRHQKV 241

Query: 239 IEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVED-GEFYFMEVNTRIQVEHT 297
           IE AP+P L ++LR++I + A    +  +Y+ AGTVEFL+++ G   F+E N RIQVEHT
Sbjct: 242 IELAPAPNLPDELRQKICDDAVAFAKEIDYSCAGTVEFLLDERGHHVFIECNPRIQVEHT 301

Query: 298 VTEEVTGLDVVKWQLRVAAGE---ELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTL 354
           VTEE+T +D+V  QLR+A+GE   +L  SQ+ + I G +++ RI  E P   F P TG +
Sbjct: 302 VTEEITDVDLVSSQLRIASGETLADLGLSQETLVIRGAALQCRITTEDPANGFRPDTGRI 361

Query: 355 STYDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGL 414
           + Y  PGG GIR+D     G EIG  +DSM+ KL   G D    + RA RAL EF + G+
Sbjct: 362 TAYRSPGGAGIRLDGGAHLGAEIGAHFDSMLVKLTCRGRDFATAVARAHRALAEFRVRGV 421

Query: 415 RTVIPFHRLMLTDEAFREGSHTTKYLDE 442
            T IPF + ++ D  FR G   T ++D+
Sbjct: 422 STNIPFLQAVIDDPDFRAGRVNTSFIDD 449



 Score = 55.1 bits (131), Expect = 2e-11
 Identities = 33/93 (35%), Positives = 52/93 (55%), Gaps = 2/93 (2%)

Query: 509  KPSGPRKRREESD-EGGQQVIEGDGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMK 567
            +P   R R   SD    ++    + + VAA   G ++ V + EGD V+ G T+  +EAMK
Sbjct: 1041 RPVVVRDRSVASDIPAAEKADRTNPDHVAAPFAG-VVTVNIAEGDKVDAGQTIATIEAMK 1099

Query: 568  MENDVVAERGGTVSQVLVGEGDSVDMGDVLLVL 600
            ME  + A + GTV++V V     V+ GD+L+V+
Sbjct: 1100 MEAGITAPKSGTVARVAVSATAQVEGGDLLVVI 1132


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: 1358
Number of extensions: 58
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 601
Length of database: 1145
Length adjustment: 42
Effective length of query: 559
Effective length of database: 1103
Effective search space:   616577
Effective search space used:   616577
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: 56 (26.2 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