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

GapMind for catabolism of small carbon sources

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

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011781912.1 MVAN_RS23940 propionyl-CoA synthetase

Query= reanno::Phaeo:GFF1175
         (629 letters)



>NCBI__GCF_000015305.1:WP_011781912.1
          Length = 623

 Score =  808 bits (2088), Expect = 0.0
 Identities = 381/622 (61%), Positives = 471/622 (75%), Gaps = 2/622 (0%)

Query: 3   YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHV 62
           Y ++++    +P  FW  AA+A++W   P + L D     Y WF DA +NTC N +DRHV
Sbjct: 4   YRDLFDSSITDPVAFWGAAADAVTWTRPPGRILDDSNPPFYRWFPDAELNTCANTLDRHV 63

Query: 63  EQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEA 122
           + GRG+Q A++YDS +T TKR  +Y EL    A  AGALR  GV KGDRV+IYMPMIPEA
Sbjct: 64  DAGRGDQPALVYDSAVTDTKRTYTYAELLEATARFAGALRKLGVGKGDRVVIYMPMIPEA 123

Query: 123 LEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGA 182
           + AMLACARLGAVHSVVFGGFA +ELAVRIDD  P  I++ASCG+EPGR V YKP+LD A
Sbjct: 124 VIAMLACARLGAVHSVVFGGFAPHELAVRIDDVRPTVIVSASCGIEPGRVVEYKPMLDAA 183

Query: 183 IDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGT 242
           + +  H P  CV+ QR++   +L+EGRD++W     G EP + VPV    P Y+LYTSGT
Sbjct: 184 VGMVEHPPRHCVVVQRDRHRCDLVEGRDLDWADVMAGAEPVDPVPVAATDPLYVLYTSGT 243

Query: 243 TGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTT 302
           TG+PKG++R   G  VAL W+M++IY+++PGDVFWAASDVGWVVGHSYI Y PL+ G TT
Sbjct: 244 TGKPKGIVRDNGGHAVALLWSMRHIYDIEPGDVFWAASDVGWVVGHSYIVYAPLLLGATT 303

Query: 303 IVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVY 362
           +++EGKP+GTPD G FWRV SEH VK+ FTAPTA RA+++EDP+G++V  YDLS LK ++
Sbjct: 304 VLYEGKPVGTPDPGAFWRVASEHGVKALFTAPTAIRAIRKEDPEGKYVGDYDLSGLKYLF 363

Query: 363 LAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYT 422
           LAGER DPDT  WA E+L +PVIDHWWQTETGW+IAANP+G E LP K GSP VPMPGY 
Sbjct: 364 LAGERLDPDTYHWASEKLGIPVIDHWWQTETGWAIAANPMGTEALPLKAGSPTVPMPGYD 423

Query: 423 VDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMK 482
           V IL + GH    G+ GAI ++LPLPPGTLPTLWNA+DR++ SYLT  PGYY TGD G  
Sbjct: 424 VRILHDHGHECETGQEGAICIRLPLPPGTLPTLWNADDRYQASYLTEHPGYYLTGDGGRF 483

Query: 483 DEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLC 542
           DEDGYL++M R DDVINVAGHRLSTGA+EEVLA HP VAECAVIGV+D +KGQAP G + 
Sbjct: 484 DEDGYLFVMGRIDDVINVAGHRLSTGAIEEVLATHPAVAECAVIGVADEIKGQAPRGLVV 543

Query: 543 LNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTD 602
           + AG  T  + +  ++VKLVR++IG VA+FKL  VV  LPKTRSGKILR TM  IA G D
Sbjct: 544 VKAGAST--DGLADELVKLVRDEIGAVASFKLVDVVPALPKTRSGKILRKTMRGIAAGRD 601

Query: 603 WKMPATIDDPAILDEITTALQG 624
             +P+TI+DPA+LD ++  L+G
Sbjct: 602 EPIPSTIEDPAVLDALSPILRG 623


Lambda     K      H
   0.318    0.137    0.428 

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: 1407
Number of extensions: 52
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: 629
Length of database: 623
Length adjustment: 38
Effective length of query: 591
Effective length of database: 585
Effective search space:   345735
Effective search space used:   345735
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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