Alignments for a candidate for prpE in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Sinorhizobium meliloti 1021

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate SMc04095 SMc04095 acyl-COA synthetase

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



>FitnessBrowser__Smeli:SMc04095
          Length = 635

 Score =  819 bits (2115), Expect = 0.0
 Identities = 389/628 (61%), Positives = 466/628 (74%), Gaps = 4/628 (0%)

Query: 3   YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHV 62
           YSEVY  WK +P  FW +AA AI W   P +     G     WF D   NTC+N +DRHV
Sbjct: 5   YSEVYAAWKTDPHGFWADAASAIDWFKRPERIFEPAGGTYGHWFPDGVTNTCHNCLDRHV 64

Query: 63  EQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEA 122
           E GRGEQ A IYDSP+T     ISY +L   V  +A   R  GV+KGDR+IIYMPMIP+A
Sbjct: 65  EAGRGEQLAFIYDSPVTGRIERISYADLLADVKAMAAIYRKLGVDKGDRIIIYMPMIPQA 124

Query: 123 LEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGA 182
             AMLA AR+GAVHSVVFGGFAANELA+RIDD   K +++ASCGLEPGRTV YKPLLD A
Sbjct: 125 AIAMLAAARIGAVHSVVFGGFAANELAMRIDDCQAKIVVSASCGLEPGRTVAYKPLLDQA 184

Query: 183 IDLATHKPDFCVIFQREQEVAELIEGRDVNWH----GFQYGVEPAECVPVEGNHPAYILY 238
           I+ A+HKP  C+I+QR+   AE++ GRD+++       +   E A C PV    P Y+LY
Sbjct: 185 IETASHKPARCLIYQRDMLAAEMVSGRDIDFAEALAAARDAGEEASCTPVASTDPLYVLY 244

Query: 239 TSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIH 298
           TSGTTGQPKGV+R   G +VAL W+M++ + V+ GDVFWAASD+GWVVGHSYI YGPL++
Sbjct: 245 TSGTTGQPKGVVRDNGGHMVALRWSMEHFFGVNAGDVFWAASDIGWVVGHSYIVYGPLLN 304

Query: 299 GNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCL 358
           G T+++FEGKP+GTPD GT+WRVISE  V   FTAPTA RA+++EDP+     +YDLS  
Sbjct: 305 GCTSVLFEGKPVGTPDPGTYWRVISERGVAVMFTAPTALRAIRKEDPEAAHAGRYDLSRF 364

Query: 359 KQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPM 418
           + +YLAGERADPDTI WA+  LKVPVIDHWWQTETGW +A NPLG+  LP K GSPAVP+
Sbjct: 365 RALYLAGERADPDTIRWAERALKVPVIDHWWQTETGWPVAGNPLGLGLLPVKYGSPAVPL 424

Query: 419 PGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGD 478
           PGY V ++D+ GHPV  G LG + +KLPLPPG LPTLWNA+ RF  +YL  +PG+Y+T D
Sbjct: 425 PGYDVQVVDDAGHPVETGTLGNVVIKLPLPPGCLPTLWNADHRFHAAYLEEYPGFYKTAD 484

Query: 479 AGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPV 538
           AG  DEDGY++IMARTDD+INVAGHRLSTGAMEEV A HPDVAECAVIG++D LKGQ P 
Sbjct: 485 AGYVDEDGYIFIMARTDDIINVAGHRLSTGAMEEVCASHPDVAECAVIGIADPLKGQVPA 544

Query: 539 GFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIA 598
           GFL +NA      E++  +VV LVRE+IGPVAAF+ A  V RLPKTRSGKILR T+  I 
Sbjct: 545 GFLVINANVSRETEEIEKEVVGLVRERIGPVAAFRTAVCVKRLPKTRSGKILRSTIQKII 604

Query: 599 DGTDWKMPATIDDPAILDEITTALQGLG 626
           D   W MPATIDDPAILDEIT  L+  G
Sbjct: 605 DRQPWTMPATIDDPAILDEITELLRSKG 632


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: 1426
Number of extensions: 71
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: 635
Length adjustment: 38
Effective length of query: 591
Effective length of database: 597
Effective search space:   352827
Effective search space used:   352827
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 17 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