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

GapMind for catabolism of small carbon sources

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

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_011782756.1 MVAN_RS28370 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_000015305.1:WP_011782756.1
          Length = 516

 Score =  486 bits (1252), Expect = e-142
 Identities = 258/528 (48%), Positives = 343/528 (64%), Gaps = 17/528 (3%)

Query: 20  TTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSFVELDEHARHRS 79
           TTA  LA+L  +   A   G E+AVAK+  KG  +AR RI  LLD GSF+E+   A+   
Sbjct: 5   TTAELLAELREKLELAKEPGGEKAVAKREKKGIPSARARIHALLDPGSFLEIGALAKTPG 64

Query: 80  TNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSLGEVFGEKIVKVMDLAMKTG 139
                D D  YGDGVVTG GT++GR V VFS D TVF GS+GE+FG K+ ++M+     G
Sbjct: 65  -----DPDALYGDGVVTGHGTINGRPVGVFSHDQTVFQGSVGEMFGRKVARLMEWVAMVG 119

Query: 140 CPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQISLIMGPCAGGAVYSPAITD 199
           CP++GINDS GARIQ+   +L  YAE+ +R+    G++P+ISLI G CAGGAVYSP  TD
Sbjct: 120 CPIIGINDSAGARIQDTATSLAWYAELGRRHELLRGLVPEISLIFGKCAGGAVYSPIQTD 179

Query: 200 FTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNERSGNAHYLATDEDDAISYVK 259
             V V    +MF+TGPDVIK VTGEDV+ ++LGGA     R GN H +   E  A  YV+
Sbjct: 180 LVVAVRDQGYMFVTGPDVIKDVTGEDVTLDELGGADAQ-ARYGNIHQVVESEAAAFQYVR 238

Query: 260 ELLSFLPSNNLSSSPVF-PGAEVEEGSVADGVGDADLELDALVPDSPNQPYDMREVITRL 318
           + LSFLP N    +P+  PG E E       V   DLELDA+VPD+ NQ YDM E++ R+
Sbjct: 239 DYLSFLPGNAFDDAPIVNPGLEPE-------VTPHDLELDAIVPDADNQAYDMMEILLRI 291

Query: 319 VDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGTLDIDASEKAARFVRFCDA 378
            D+G+  +V     P ++  F R++G  VG++ANQPM ++G +D +AS+KAARFVRFCD+
Sbjct: 292 FDDGDVFQVGEQAGPAIITAFARVDGRPVGIIANQPMYMSGAIDNEASDKAARFVRFCDS 351

Query: 379 FNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVPLVTVITRKAYGGAYDVMG 438
           FN P++ +VD PGF+PG  QE  GII+RG + L A  EA VP VT+  RK+YGGAY VMG
Sbjct: 352 FNTPLVFVVDTPGFMPGVEQEKGGIIKRGGRFLNAVVEADVPKVTITIRKSYGGAYAVMG 411

Query: 439 SKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGEDVEALRARLQQEYEDTLC 498
           SK L AD N AWPTA+IAV+GA+GAA +L +R     A    +V+ +RA   + Y   L 
Sbjct: 412 SKQLTADFNFAWPTARIAVIGAEGAAQLLVKRFPDPTA---PEVQKIRADFIEGYNANLA 468

Query: 499 NPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKKHGNIPL 546
            P++AAERG++D V+ P  TR  + + + +L DK+     +KHG  P+
Sbjct: 469 TPWIAAERGFIDGVVEPHETRLLLRKCMHLLRDKQINRVQRKHGLTPI 516


Lambda     K      H
   0.318    0.136    0.398 

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: 698
Number of extensions: 29
Number of successful extensions: 7
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: 546
Length of database: 516
Length adjustment: 35
Effective length of query: 511
Effective length of database: 481
Effective search space:   245791
Effective search space used:   245791
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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