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 Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate SMc04093 SMc04093 acetyl-CoA synthetase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Smeli:SMc04093
          Length = 649

 Score =  882 bits (2279), Expect = 0.0
 Identities = 422/635 (66%), Positives = 505/635 (79%), Gaps = 5/635 (0%)

Query: 15  DRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGT 74
           +R L++   Y   Y++S+  P+ FWGE GK ++W +PY KVKNTSF  G+VSIKW+EDG 
Sbjct: 14  NRTLLDNATYLEWYRESVADPEKFWGEHGKRIEWFEPYTKVKNTSFE-GDVSIKWFEDGL 72

Query: 75  LNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDV 134
            N++ NC+DRHL+ +G++TAIIWEGD+    K I+Y EL+  VCR AN L E G+KKGD 
Sbjct: 73  TNVSYNCIDRHLKTHGEKTAIIWEGDNPYLDKKITYNELYDKVCRLANVLKEQGVKKGDR 132

Query: 135 VAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGR 194
           V IYMPM+PEAA AMLACARIGA+HSV+FGGFSPEA+AGRI+D  S  VIT DEGVR G+
Sbjct: 133 VTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALAGRIVDCESTFVITCDEGVRGGK 192

Query: 195 SIPLKKNVDDALK---NPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAE 251
            + LK+N D A+      +VT V  V+V++RTGGK+ W  GRDLW+H     A      E
Sbjct: 193 PVALKENTDTAIDIAARQHVT-VSKVLVVRRTGGKVGWAPGRDLWYHQETAAAEPHCPPE 251

Query: 252 EMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVT 311
           +MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYA++T +YVFDY  GDIYWCTADVGWVT
Sbjct: 252 KMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCTADVGWVT 311

Query: 312 GHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKA 371
           GHSY++YGPLA  ATTLMFEGVPN+P   R  +VVDKH+VNI YTAPTAIR+LM  GD  
Sbjct: 312 GHSYIVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSLMGAGDDF 371

Query: 372 IEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATE 431
           ++ + RSSLR+LG+VGEPINPEAWEWY+  +G+E+CPVVDTWWQTETGG +ITPLPGAT+
Sbjct: 372 VKRSSRSSLRLLGTVGEPINPEAWEWYYHVVGDERCPVVDTWWQTETGGILITPLPGATD 431

Query: 432 LKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFST 491
           LK GSATRPFFGVQP +VD++G  ++GA +G+L ITDSWPGQ RT++GDHERF QTYFST
Sbjct: 432 LKPGSATRPFFGVQPQIVDSDGKVVDGAADGNLCITDSWPGQMRTVYGDHERFIQTYFST 491

Query: 492 FKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIP 551
           +K  YF+GDG RRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H  ++EAAVVG P
Sbjct: 492 YKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSEAAVVGYP 551

Query: 552 HNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIM 611
           H IKGQ IY YV+L  GE    EL   +   VR EIGP+ATPD + +   LPKTRSGKIM
Sbjct: 552 HPIKGQGIYCYVSLMAGEVGDDELRQALVKHVRSEIGPIATPDKIQFAPGLPKTRSGKIM 611

Query: 612 RRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           RRILRKIA  D  +LGDTSTLADPGVV+ L+  +Q
Sbjct: 612 RRILRKIAEDDFGSLGDTSTLADPGVVDDLIANRQ 646


Lambda     K      H
   0.317    0.135    0.421 

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: 1476
Number of extensions: 59
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: 652
Length of database: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
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