Alignments for a candidate for prpE in Epibacterium ulvae U95

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Epibacterium ulvae U95

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_090218642.1 CV091_RS00310 propionyl-CoA synthetase

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



>NCBI__GCF_002796795.1:WP_090218642.1
          Length = 632

 Score =  804 bits (2077), Expect = 0.0
 Identities = 386/631 (61%), Positives = 469/631 (74%), Gaps = 6/631 (0%)

Query: 1   MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLY-EWFADARVNTCYNAVD 59
           MSY++ Y  W+ +P  FW +A E I W + P + + D   G+Y  WF  A  NTCYNAVD
Sbjct: 1   MSYADAYASWQKDPVAFWKKAGEGIDWFT-PAEKIFDPDMGVYGRWFTGATCNTCYNAVD 59

Query: 60  RHVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMI 119
           RHV+ G GE+ AI YDSP+T TK   S+ +++  V+ LA  +R +GVEKGDRVIIYMPM+
Sbjct: 60  RHVDAGHGERLAISYDSPVTDTKATFSFAQVKEEVSALAAVMRDQGVEKGDRVIIYMPMV 119

Query: 120 PEALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLL 179
           P+A+ AMLACARLGAVHSVVFGGFA  ELA RIDD+ PK +I+ASCG+EP R + YKPLL
Sbjct: 120 PQAIFAMLACARLGAVHSVVFGGFAPKELATRIDDSAPKLVISASCGIEPNRVIAYKPLL 179

Query: 180 DGAIDLATHKPDFCVIFQREQEVAELIEGRDVNWH----GFQYGVEPAECVPVEGNHPAY 235
           D AI+L++ KPD C+I QRE    +L  G D+++       +      ECVPV    P Y
Sbjct: 180 DEAIELSSSKPDSCIILQREALTCDLKAGYDIDYTQAVTAAKADARGTECVPVLATDPLY 239

Query: 236 ILYTSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGP 295
           ILYTSGTTGQPKGV+R T G +VA+ W+M   Y V PG+VFWAASDVGWVVGHSYICY P
Sbjct: 240 ILYTSGTTGQPKGVVRDTGGHMVAMQWSMHAHYGVKPGEVFWAASDVGWVVGHSYICYAP 299

Query: 296 LIHGNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDL 355
           LI G  T+V+EGKP+GTPDAG FWRVI ++KV + FTAPTAFRA+K+EDPKGE + +YDL
Sbjct: 300 LIAGCGTVVYEGKPVGTPDAGAFWRVIQDNKVTALFTAPTAFRAIKKEDPKGELIDQYDL 359

Query: 356 SCLKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPA 415
           S  + ++LAGER+DP TI WAQ+ LK PVIDHWWQTETGW+++ NP+G+   P KLGSP 
Sbjct: 360 SHFRTLFLAGERSDPATIEWAQKHLKRPVIDHWWQTETGWAMSGNPVGLGSFPIKLGSPG 419

Query: 416 VPMPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYE 475
            PMPGY + +LD+ G+PV PG LG I  KLPLPP   PTLW A DRF+ SYL  FPGYY 
Sbjct: 420 KPMPGYDIHVLDDDGNPVPPGTLGNIVCKLPLPPSGFPTLWQAPDRFQSSYLEEFPGYYA 479

Query: 476 TGDAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQ 535
           T DAG+ DEDGY++IMARTDD+INVAGHRLSTGAMEEVL  HPDVAE AVIGV+D LKGQ
Sbjct: 480 TSDAGIIDEDGYVFIMARTDDIINVAGHRLSTGAMEEVLGAHPDVAESAVIGVADPLKGQ 539

Query: 536 APVGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMV 595
            P+GF   N G +   +++  ++V+LVR KIG VAAFK A  V RLPKTRSGK+LRGTM 
Sbjct: 540 MPLGFYVANDGANRDPDELEKELVQLVRAKIGAVAAFKTALPVKRLPKTRSGKVLRGTMQ 599

Query: 596 NIADGTDWKMPATIDDPAILDEITTALQGLG 626
            IAD   +K+PA IDDP IL EI   L+G G
Sbjct: 600 KIADQKTFKIPAAIDDPEILSEINDVLKGKG 630


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: 1488
Number of extensions: 68
Number of successful extensions: 3
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: 632
Length adjustment: 38
Effective length of query: 591
Effective length of database: 594
Effective search space:   351054
Effective search space used:   351054
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