Alignments for a candidate for prpE in Desulfurobacterium atlanticum DSM 15668

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Desulfurobacterium atlanticum DSM 15668

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_089322819.1 CHB58_RS03975 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_900188395.1:WP_089322819.1
          Length = 631

 Score =  609 bits (1571), Expect = e-178
 Identities = 328/647 (50%), Positives = 435/647 (67%), Gaps = 22/647 (3%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEA-YQALCDEAERDYEGFWARHARELLHWTKPFT 62
           ++S++    +  PPE F   A + + E  Y+   D  E     FWA+ A EL  W + + 
Sbjct: 6   LDSLLHLGTIIKPPEEFVRNANVKNYEEEYKKFLDNPEE----FWAKVADELF-WYEKWD 60

Query: 63  KVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGK 122
           KVL+  N P+ KWF +G+ N + N LDR+++NG  +KVA  +E + G+   VTY  L+  
Sbjct: 61  KVLEW-NLPYAKWFVNGKTNITVNALDRHVKNGRKNKVAFFWEDEFGNEKVVTYGSLYTL 119

Query: 123 VCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLV 182
           V + AN LK  GI+KGDRVVIYMP+ VE V AM ACAR+GA HSVV+ GFS  +L+ R+ 
Sbjct: 120 VNKLANALKNAGIKKGDRVVIYMPLVVEQVAAMLACARIGAVHSVVYAGFSVPALRHRIE 179

Query: 183 DVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRW 242
           D  A  +ITAD  +R G+A+PLK I D+A+   G + V  V+V RR   KV     ++  
Sbjct: 180 DAQAKMVITADMTIRRGRAIPLKQIVDEAVR--GLDNVEKVVVLRRLKPKVDLIGEKEID 237

Query: 243 MEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIK 302
             +        CE E + +E PLF+LYTSGSTGKPKGV H+TGGY++    +MK  FD+K
Sbjct: 238 FYEFIKDADTYCEPEVMDSEDPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLK 297

Query: 303 PDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYT 362
            DD++WCTAD GW+TGH+YI YGPL AGATQV+ EG P YP+ GR+W +I ++ V+IFYT
Sbjct: 298 EDDIYWCTADPGWITGHSYIVYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYT 357

Query: 363 APTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDT 422
           APTAIR  ++A E      P++YDLSSLRLLG+VGEPINPEAWMWY++ IG ERCPIVDT
Sbjct: 358 APTAIRMFMRAGEH----WPEKYDLSSLRLLGSVGEPINPEAWMWYFRVIGKERCPIVDT 413

Query: 423 FWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPA 482
           +WQTETG  MIT + G  P+ PG    P+PG++A +VD+ G+ V    GG LVV+ PWP+
Sbjct: 414 WWQTETGAVMITTIDG-LPMKPGRAGKPVPGVVADVVDKEGNPVEPNKGGFLVVRNPWPS 472

Query: 483 MIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGT 542
           M+RTI  + E++ +SY+    G   Y AGD + +D+D GY  I+GR DDV+NVSGHR+GT
Sbjct: 473 MMRTIHKNKEKY-ESYWNTIPG--CYFAGDVATKDED-GYIMILGRADDVINVSGHRIGT 528

Query: 543 MEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKE 602
           ME+ESALVS+P VAEAAV+G+PD + GE I AFV+LK      EE V     L+  V  E
Sbjct: 529 MEVESALVSHPSVAEAAVIGKPDPVKGERIKAFVILKEGESPSEELV---NSLKKHVRTE 585

Query: 603 IGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLEN 649
           +G +A P +I F D LPKTRSGKIMRR+L++   G +   D STLE+
Sbjct: 586 LGALAVPSEIEFVDKLPKTRSGKIMRRVLKAKELGMD-PGDLSTLED 631


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: 1249
Number of extensions: 66
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: 631
Length adjustment: 38
Effective length of query: 622
Effective length of database: 593
Effective search space:   368846
Effective search space used:   368846
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