Alignments for a candidate for prpE in Desulfovibrio oxyclinae DSM 11498

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Desulfovibrio oxyclinae DSM 11498

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_018125632.1 B149_RS0113155 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000375485.1:WP_018125632.1
          Length = 639

 Score =  607 bits (1564), Expect = e-178
 Identities = 310/637 (48%), Positives = 423/637 (66%), Gaps = 14/637 (2%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           ++S++QE RVF P      +A +   E   A   ++E D  G+W   A EL  W K + +
Sbjct: 7   LDSLLQEERVFRPLPQLVIEANVNPQELGAAR-RQSEYDPLGYWEEAADEL-DWFKRWDR 64

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VLD S  PFY+WF     N  YNCLDR+++  N +K+A+++E + G   + TY EL+ +V
Sbjct: 65  VLDDSRKPFYRWFPGARCNIVYNCLDRHIETANKNKLALIWEGEPGDSRKYTYFELYREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
            RFAN L+ LG++KGDRVV+YMP   E VVAM A A++GA HSVVF GFSAK+L++R+ D
Sbjct: 125 NRFANALRTLGVQKGDRVVVYMPPLPETVVAMLAAAKIGAVHSVVFAGFSAKALRQRIND 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A A+ITAD   R G+ L LK   D+AL     + V +++V RRT   V   +GRD W 
Sbjct: 185 AQAKAVITADGFYRNGQVLRLKDTVDEALVGACADCVESMVVVRRTKVGVDMVDGRDFWY 244

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
           ED+   + +T   E + A  PLF++YTSG+TGKPKG+ H  GGY++    T+   FD+KP
Sbjct: 245 EDLVRQERNTAPTEVMEAHEPLFLMYTSGTTGKPKGIVHCHGGYMVGVHRTLTTVFDVKP 304

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
            D+FWCTAD GWVTGH+ + YGPL AG T V++EG P YP A R W+++A++ +SIFYT 
Sbjct: 305 TDIFWCTADPGWVTGHSAVVYGPLLAGTTTVIYEGHPNYPQADRLWNIVAKYGISIFYTV 364

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PT IR L++        H K++DLSSLRLLG+VGEPI+PEAW W YKNIG   CP++DT+
Sbjct: 365 PTVIRMLMRFGVQ----HTKRHDLSSLRLLGSVGEPISPEAWTWLYKNIGRSECPVIDTW 420

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
           WQTETG  MI+PLP  + L PGS T PLPG+ A +VD  G+ V  G GG+LV++ PWPAM
Sbjct: 421 WQTETGMFMISPLP-ISLLKPGSVTKPLPGVKADVVDREGNSVEPGKGGLLVIREPWPAM 479

Query: 484 IRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTM 543
           +  +W D +R+R+ YF +  G   Y AGD + RD+D GY  I GR DDV+N++GHR+G+ 
Sbjct: 480 MTGLWNDEDRYRE-YFEKVPG--CYFAGDVARRDED-GYIWIQGRADDVINIAGHRVGSA 535

Query: 544 EIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEI 603
           E+E+A  ++  V EAAV+G PD + GEA  AFVV++      +E +K   +L+  +  E+
Sbjct: 536 ELEAAFGAHRNVTEAAVIGVPDTIKGEAAKAFVVVRSGAEEDDELIK---DLKRHIRNEL 592

Query: 604 GPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEI 640
           GP+A  K I F   LPKTRSGKIMRR+L++   G EI
Sbjct: 593 GPVAVLKSIEFRRKLPKTRSGKIMRRVLKAEETGTEI 629


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: 1241
Number of extensions: 62
Number of successful extensions: 6
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: 660
Length of database: 639
Length adjustment: 38
Effective length of query: 622
Effective length of database: 601
Effective search space:   373822
Effective search space used:   373822
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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Protein sequences (fasta format)
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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