Alignments for a candidate for prpE in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Rhodomicrobium vannielii ATCC 17100

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_013417818.1 RVAN_RS00600 propionyl-CoA synthetase

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



>NCBI__GCF_000166055.1:WP_013417818.1
          Length = 646

 Score =  822 bits (2123), Expect = 0.0
 Identities = 389/630 (61%), Positives = 481/630 (76%), Gaps = 6/630 (0%)

Query: 3   YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLY-EWFADARVNTCYNAVDRH 61
           Y +VYE WK +PE FW EAA  I W   P K + D  +G+Y  WF     NT YN +DRH
Sbjct: 11  YFDVYESWKRDPEGFWAEAAREIDWFEQPKK-IFDANEGVYGRWFTGGVTNTAYNCIDRH 69

Query: 62  VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121
           V+ GR +Q AIIYDSP+T   R ++Y +L   VAT AG L+ KG+ KGDRVI+YMPMI E
Sbjct: 70  VKNGRADQPAIIYDSPVTGQVRILTYADLLTEVATFAGVLKEKGIGKGDRVIVYMPMIAE 129

Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181
           AL AMLACAR+GA+HSVVFGGFAANELA+RI+D   KA+I ASCG+E  R +HYKPLLD 
Sbjct: 130 ALIAMLACARIGAIHSVVFGGFAANELAIRIEDTQAKAVITASCGIEVTRVIHYKPLLDH 189

Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEP----AECVPVEGNHPAYIL 237
           AI+L++ KP+ C+I QR QE+A LIEGRD ++       +     A C P+    PAYIL
Sbjct: 190 AIELSSVKPEVCIIVQRPQEIATLIEGRDYDYAALLDDAKARGVSAACEPMAATDPAYIL 249

Query: 238 YTSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLI 297
           YTSGTTG+PKGV+R   G +VAL WTMKN Y++DPG+VFWA+SDVGWVVGHSYI YGPL+
Sbjct: 250 YTSGTTGRPKGVVRDIGGHMVALKWTMKNHYDIDPGEVFWASSDVGWVVGHSYIVYGPLL 309

Query: 298 HGNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSC 357
           HG TTIV+EGKP+GTPDAG FWRVI +HKVK+ FTAPTAFRA+K+EDP+G F+  YD+S 
Sbjct: 310 HGATTIVYEGKPVGTPDAGAFWRVIEQHKVKALFTAPTAFRAIKKEDPQGTFLAHYDVSS 369

Query: 358 LKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVP 417
           LK ++LAGERADP+T+ WA++ LKVPVIDHWWQTETGW+IA N  G+  +P KLGSP   
Sbjct: 370 LKYLFLAGERADPNTVQWAEDLLKVPVIDHWWQTETGWAIAGNCAGLGAMPIKLGSPTFA 429

Query: 418 MPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETG 477
           +PGY + +L+E    VA G+ GA++++LP+PPG LPTLWN +  F + YL  +PGYY+T 
Sbjct: 430 LPGYELHVLNESNEEVARGQTGALSIRLPMPPGCLPTLWNNDQGFIEGYLIEYPGYYKTA 489

Query: 478 DAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAP 537
           DAG  DEDGY+++MARTDD+INVAGHRLSTGA+EEV+A HPDVAECAVIG++D LKGQ  
Sbjct: 490 DAGFIDEDGYVFVMARTDDIINVAGHRLSTGAIEEVVANHPDVAECAVIGIADGLKGQVA 549

Query: 538 VGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNI 597
            GF+ L AG       +  ++V +VR++IGPVAAFK    V+RLPKTRSGKILRGTM  I
Sbjct: 550 AGFVLLKAGVVREINVIEKEIVAMVRDQIGPVAAFKTVLTVNRLPKTRSGKILRGTMRKI 609

Query: 598 ADGTDWKMPATIDDPAILDEITTALQGLGY 627
           ADG  +KMPATIDDPA L+EIT AL+  G+
Sbjct: 610 ADGEAYKMPATIDDPATLEEITAALKAKGF 639


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: 1377
Number of extensions: 49
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: 646
Length adjustment: 38
Effective length of query: 591
Effective length of database: 608
Effective search space:   359328
Effective search space used:   359328
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 Apr 09 2024. 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)
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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 2024 update 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