Alignments for a candidate for prpE in Desulfogranum mediterraneum DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Desulfogranum mediterraneum DSM 13871

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028583435.1 G494_RS0103595 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000429965.1:WP_028583435.1
          Length = 663

 Score =  720 bits (1859), Expect = 0.0
 Identities = 360/631 (57%), Positives = 454/631 (71%), Gaps = 10/631 (1%)

Query: 23  QYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANC 81
           QY  +Y++SI+  + FW E+ + ++ W K +  V     +   V  KW++ G LN++ NC
Sbjct: 37  QYRELYKRSIDDMEGFWAERAEELVSWEKKWDSVLEYDLSVPEV--KWFQGGKLNVSYNC 94

Query: 82  LDRHLQENGDRT--AIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYM 139
           LDRHL ENG R   AIIW+G+     +  +Y+ LH +VCRFAN L + G+KKGD VAIYM
Sbjct: 95  LDRHL-ENGRRNKAAIIWQGEPEEDVRVYTYQMLHTEVCRFANVLKKKGVKKGDRVAIYM 153

Query: 140 PMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLK 199
           PM+PE A+A+LAC R+GAVHSV+F GFS  A+  RI D  +++++T+D  +R G++IPLK
Sbjct: 154 PMIPELAIALLACTRLGAVHSVVFAGFSAIALQSRIQDCEAKVLVTADAVLRGGKAIPLK 213

Query: 200 KNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVE--QASDQHQAEEMNAED 257
            N D AL+  +  SV   +V++R G +I  + GRD WWH+ V     S +   E M+AED
Sbjct: 214 TNADQALEECD--SVGSCIVVQRAGVEIPMEAGRDSWWHEEVAAPDISSECAPEPMDAED 271

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
            LFILYTSGSTGKPKGV+HTTGGYL YA  T ++VFD    D+YWCTAD+GW+TGHSY+L
Sbjct: 272 LLFILYTSGSTGKPKGVVHTTGGYLTYAMHTCQWVFDMKDDDVYWCTADIGWITGHSYIL 331

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPL  GAT+LMFEGVP++P   R  ++VDK +VNI YTAPTAIRALM EG+   +  D 
Sbjct: 332 YGPLGLGATSLMFEGVPSYPAADRFWKIVDKFKVNIFYTAPTAIRALMREGEAHTQRYDL 391

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
           SSLR+LGSVGEPINPEAW WY   IG EK P+VDTWWQTETGG MI+PLP AT LK GSA
Sbjct: 392 SSLRVLGSVGEPINPEAWMWYHVNIGKEKLPIVDTWWQTETGGIMISPLPYATPLKPGSA 451

Query: 438 TRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497
           + P  G+  A+ + EG        G LVI   WPG  R +FGD  R+++TYFS ++N Y 
Sbjct: 452 SYPLPGIDAAIYNEEGEEAAANEGGHLVIRKPWPGMLRGVFGDPARYKKTYFSRYENTYD 511

Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQ 557
             DGAR DEDGY+WI GR+DDV+NVSGHRLGTAEIESALV+H  +AEAA VG+PH +KGQ
Sbjct: 512 PEDGARCDEDGYFWIMGRLDDVINVSGHRLGTAEIESALVSHEAVAEAAAVGMPHPVKGQ 571

Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617
           AI+AYVTL    E S EL AE+R  VR EIGP+ATP+ + W   LPKTRSGKIMRRILRK
Sbjct: 572 AIFAYVTLMSWAEESDELLAELRKHVRAEIGPIATPEAIQWAPGLPKTRSGKIMRRILRK 631

Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLEEKQAI 648
           IAA D  + GDTSTLADP VV+ L++ K+ +
Sbjct: 632 IAANDFKDFGDTSTLADPSVVDHLVDGKKKL 662


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: 1399
Number of extensions: 56
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 652
Length of database: 663
Length adjustment: 38
Effective length of query: 614
Effective length of database: 625
Effective search space:   383750
Effective search space used:   383750
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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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