Alignments for a candidate for prpE in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Williamsia sterculiae CPCC 203464

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_076482594.1 BW971_RS18805 acetate--CoA ligase

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



>NCBI__GCF_900156495.1:WP_076482594.1
          Length = 626

 Score =  686 bits (1769), Expect = 0.0
 Identities = 334/623 (53%), Positives = 425/623 (68%), Gaps = 1/623 (0%)

Query: 3   YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHV 62
           Y + +     +P+ FW+ AA  + W   PT+AL D    +Y WF D  +NT YNA+DRHV
Sbjct: 4   YQDAFTQAAEDPDTFWLGAARGVDWVHEPTRALDDHHAPIYRWFPDGTLNTSYNALDRHV 63

Query: 63  EQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEA 122
             G G++ A+I+DS +T   R  +Y EL + VA  AG L A GV  GDRVIIY+PMIPEA
Sbjct: 64  AAGNGDRPALIWDSAMTGASRTYTYAELLDEVARFAGVLSATGVASGDRVIIYLPMIPEA 123

Query: 123 LEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGA 182
             AMLACAR+GAVHSVVFGGFAA ELA RI DA P A++ AS GLEPGRTV Y P++  A
Sbjct: 124 AIAMLACARIGAVHSVVFGGFAAPELAARIIDADPVAVVTASGGLEPGRTVDYLPIVAAA 183

Query: 183 IDLATHKPDFCVIFQR-EQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241
           ++LA       V+  R E   A    G  ++W            V V    P YILYTSG
Sbjct: 184 LELADAASTTVVVKDRPEIPGAAADHGGWLDWDEQLATATSTPPVTVAATDPLYILYTSG 243

Query: 242 TTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301
           TTG+PKGV+R   G  VAL W+M N+Y++  GDV+W ASDVGWVVGHSYI Y PL  G T
Sbjct: 244 TTGKPKGVVRDNGGHAVALTWSMSNVYDIHAGDVWWTASDVGWVVGHSYIVYAPLFAGAT 303

Query: 302 TIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQV 361
           T+++EGKP+GTPDAG FWRVI EH VK+ FTAPTA RA+++ DP    +++YD+S L+ +
Sbjct: 304 TVMYEGKPVGTPDAGAFWRVIDEHHVKALFTAPTAIRAIRKADPDATELRRYDVSSLRTL 363

Query: 362 YLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGY 421
           + AGER DP+T TWA   L VPV+DHWWQTETGW+I AN  G+E +P K GSP VP+PG+
Sbjct: 364 FAAGERLDPETFTWAGTVLGVPVVDHWWQTETGWAIVANLRGLEPMPLKAGSPTVPVPGF 423

Query: 422 TVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGM 481
            V+++D  G PV  G+ G I V+LPLPPGTL  LWN EDRF+ SYL  F GYY TGD G 
Sbjct: 424 VVEVVDADGTPVGAGDEGNILVRLPLPPGTLTGLWNDEDRFRSSYLRAFDGYYLTGDTGY 483

Query: 482 KDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFL 541
           +D DGY+ ++ R+DDVINVAGHR STG+ E V+A HP VAECAVIG+ D +KGQ P G++
Sbjct: 484 RDRDGYVVVLGRSDDVINVAGHRFSTGSFEAVVASHPAVAECAVIGIHDDIKGQRPSGYV 543

Query: 542 CLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGT 601
            L AG D   + +  ++V  VR++IG VA F+   VV  LPKTRSGKILR TM  IAD  
Sbjct: 544 VLKAGVDIDSDVLRDELVTRVRDEIGSVATFRDVTVVPALPKTRSGKILRKTMRQIADHE 603

Query: 602 DWKMPATIDDPAILDEITTALQG 624
           ++ +P+T++D  +++ +   L G
Sbjct: 604 EYTVPSTVEDATVVEALAQQLGG 626


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: 1327
Number of extensions: 73
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: 626
Length adjustment: 38
Effective length of query: 591
Effective length of database: 588
Effective search space:   347508
Effective search space used:   347508
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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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