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_028586066.1 G494_RS0120850 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000429965.1:WP_028586066.1
          Length = 680

 Score =  507 bits (1305), Expect = e-148
 Identities = 297/672 (44%), Positives = 411/672 (61%), Gaps = 39/672 (5%)

Query: 9   QEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQS 68
           QE  ++ P   F +QA +     ++    + +   E F  +   +LL W K + K LD S
Sbjct: 19  QEEELYYPSVDFIAQANLTDTSVHERF--KLDNFPECF--KEYADLLSWYKYWEKTLDTS 74

Query: 69  NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVF--EADDGSVTRVTYRELHGKVCRF 126
           +AP ++WF  GELNASYNC+DR+L+  N +K AI F  E  +     VTY+EL  +V  F
Sbjct: 75  DAPCWRWFVGGELNASYNCIDRHLEK-NRNKTAIHFVPELLEERTQHVTYQELWVRVNEF 133

Query: 127 ANGLKAL-GIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVG 185
           A  L+   G+++GDRV I+MPM  E  + M ACARLG  HSVVF GFS K+  +R+ D  
Sbjct: 134 AALLQDFAGLKRGDRVTIHMPMCAELPITMLACARLGVIHSVVFAGFSGKACADRIEDSQ 193

Query: 186 AVALITADEQMRGGKALPLKAIADDA--LALGGCEAVRNVIVYRRTGGKVAWTE----GR 239
           +  LI+ D   R GK L  K  AD A   A G  + V  V+++ R  GK + +     GR
Sbjct: 194 SRVLISMDAYYRAGKLLDHKVNADLACEFAQGMGQKVDKVLLWERYPGKYSSSAEMIGGR 253

Query: 240 DRWMEDVSA---GQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMK 296
           D  +  +     GQ    E E + AE PLF++YTSG+TGKPKG QH TGGYL +A  T K
Sbjct: 254 DYSVNTLLKEYYGQ--RVEPERMKAEEPLFLMYTSGTTGKPKGCQHGTGGYLAYATATSK 311

Query: 297 WTFDIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHK 356
           +  DI P+D++WC ADIGW+TGH+YI YGPL+ GA+ V++EGVPTYP+AGR W +     
Sbjct: 312 FIQDIHPEDVYWCAADIGWITGHSYIVYGPLSLGASTVIYEGVPTYPDAGRCWRIAQDLG 371

Query: 357 VSIFYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNER 416
           V+IF+T+PTAIR+L K    +    P +YD  S + + TVGEPI P  W WY + +G  +
Sbjct: 372 VNIFHTSPTAIRALRKLGPEE----PAKYDF-SFKHMTTVGEPIEPAVWKWYQQEVGKGK 426

Query: 417 CPIVDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNG--GIL 474
             IVDT+WQTETGG + T +PG  P+ PGSC    PGI   I D+ G  +  G G  G +
Sbjct: 427 AVIVDTYWQTETGGFLCTTIPGMNPMKPGSCGPGAPGIHPIIYDDQGEILGAGAGKAGNI 486

Query: 475 VVKRPWPAMIRTIWGDPERFRKSYF------PEELGGK--LYLAGDGSIRDKDTGYFTIM 526
            ++ PWP   +TIWGD +RF ++YF      PE    +   YL GD + + +D GY+ ++
Sbjct: 487 CIQNPWPGCFQTIWGDRDRFVETYFGRYNKDPESTDWRDWPYLTGDAAFQAED-GYYRVL 545

Query: 527 GRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGE 586
           GRIDDV+NVSGHR+GT EIESA ++   VAEAAVV   D + G     ++ LK   P   
Sbjct: 546 GRIDDVINVSGHRLGTKEIESASLATAEVAEAAVVPVKDAIKGHVPDLYISLK---PGIT 602

Query: 587 EAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTST 646
            + +IA ++ + V KEIG IAKPK +    ++PKTRSGKIMRR+L S++  +++  D +T
Sbjct: 603 PSPEIAQKVSDTVCKEIGKIAKPKSVWIVADMPKTRSGKIMRRVLASISNEQDV-GDVTT 661

Query: 647 LENPAILEQLKQ 658
           L NP I+ ++K+
Sbjct: 662 LMNPDIVAEIKE 673


Lambda     K      H
   0.319    0.136    0.422 

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: 1281
Number of extensions: 69
Number of successful extensions: 7
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: 660
Length of database: 680
Length adjustment: 39
Effective length of query: 621
Effective length of database: 641
Effective search space:   398061
Effective search space used:   398061
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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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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