Alignments for a candidate for prpE in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Nocardioides daejeonensis MJ31

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_110207905.1 DNK54_RS14895 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_003194585.1:WP_110207905.1
          Length = 644

 Score =  652 bits (1683), Expect = 0.0
 Identities = 340/652 (52%), Positives = 450/652 (69%), Gaps = 19/652 (2%)

Query: 8   MQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQ 67
           M E R F PPE  A+ A +   EAY      AE D EGFWA  A E L W + + +VLD 
Sbjct: 1   MHEERRFPPPEALAAAANVTE-EAYA----RAEADREGFWAEQA-ERLDWGQKWDRVLDW 54

Query: 68  SNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTR-VTYRELHGKVCRF 126
            N PF KWF  G +NA+ NC+DR++  G  +KVAI +  +    TR +TY +L  +V R 
Sbjct: 55  DNPPFAKWFTGGTINAAVNCVDRHVTAGRGEKVAIHWVGEPEDDTRDITYAQLQDEVNRA 114

Query: 127 ANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGA 186
           AN L  LG+ KGDRV IY+PM  E VV M ACARLGA H+VVFGGFSA +L  R+VD GA
Sbjct: 115 ANALTELGVAKGDRVAIYLPMIPEAVVTMLACARLGAPHTVVFGGFSADALASRIVDCGA 174

Query: 187 VALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDV 246
             ++TAD   R G    LK   D+A+A      V +V+V +RTG +VA+ E RD W  ++
Sbjct: 175 RVVVTADGGYRRGAPSALKPAVDEAVAKAD-GLVEHVVVVQRTGQEVAFDETRDLWWHEL 233

Query: 247 SAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPD-D 305
              Q    +AE   AEHPL+V+YTSG+TGKPKG+ H+TGGYL+    +    FD+K D D
Sbjct: 234 MGRQSPQHDAELHDAEHPLYVMYTSGTTGKPKGILHTTGGYLVGTAYSHWAVFDLKADTD 293

Query: 306 LFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPT 365
           ++WCTADIGWVTGH+Y+ YGPLA GATQV++EG P  P+ GR+W++I ++ V+IFYTAPT
Sbjct: 294 VYWCTADIGWVTGHSYLVYGPLANGATQVLYEGTPDSPHKGRWWEIIEKYGVTIFYTAPT 353

Query: 366 AIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQ 425
           AIR+ +K         P ++DLSS+R+LG+VGEPINPEA++WY   IG +R P+VDT+WQ
Sbjct: 354 AIRTFMKWGNDI----PAKFDLSSIRVLGSVGEPINPEAYVWYRSTIGGDRAPVVDTWWQ 409

Query: 426 TETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIR 485
           TETG  MITP+PG T   PGS   PLPGI+A +V++ G  VP+G+GG L+++ PWPAM+R
Sbjct: 410 TETGQIMITPMPGVTHAKPGSAMRPLPGIVADVVNDEGESVPDGSGGYLIIREPWPAMLR 469

Query: 486 TIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEI 545
           T+WGD ER++ +Y+    G  +Y AGDG+ +D+D G   ++GR+DDV+NVSGHR+ T EI
Sbjct: 470 TVWGDDERYKDTYWSRWPG--VYFAGDGAKKDED-GDIWVLGRVDDVMNVSGHRLSTTEI 526

Query: 546 ESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGP 605
           ESALVS+P VAEAAVVG  D+ TG+A+CAFV+L+ S   G+   +I  ELRN V KEIG 
Sbjct: 527 ESALVSHPKVAEAAVVGATDETTGQAVCAFVILRES--AGDGGDEIVAELRNHVAKEIGA 584

Query: 606 IAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
           IAKP+ +     LPKTRSGKIMRRLLR +A+  EI  D +TL + +++  ++
Sbjct: 585 IAKPRQVMIVPELPKTRSGKIMRRLLRDVAENREI-GDVTTLADSSVMSLIQ 635


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: 1405
Number of extensions: 67
Number of successful extensions: 11
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: 644
Length adjustment: 38
Effective length of query: 622
Effective length of database: 606
Effective search space:   376932
Effective search space used:   376932
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 Sep 24 2021. 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