Alignments for a candidate for prpE in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Thermocrinis albus DSM 14484

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_012991821.1 THAL_RS03950 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000025605.1:WP_012991821.1
          Length = 630

 Score =  598 bits (1543), Expect = e-175
 Identities = 318/645 (49%), Positives = 425/645 (65%), Gaps = 20/645 (3%)

Query: 5   ESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKV 64
           E +++    + PP     +A +     Y++L  ++ +D EGFWA+ A EL HW + + KV
Sbjct: 6   EVLLKVQEKYYPPAHIVERAWVKD---YESLYAQSVQDREGFWAKVAEEL-HWFRKWDKV 61

Query: 65  LDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVC 124
           LD    P+ +WF   + N SYNCLDR++  G  +KVA ++  +D +  ++TY EL   V 
Sbjct: 62  LDWQ-FPYAQWFVGAKTNISYNCLDRHVLQGRRNKVAYIWVDEDNNERKITYGELLELVS 120

Query: 125 RFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDV 184
           R ANGLK+LG++KGDRV IYMP S+E V  M ACAR+GA HSVVF GFS  +L+ R+ D 
Sbjct: 121 RIANGLKSLGVKKGDRVSIYMPNSIEAVACMLACARIGAIHSVVFAGFSEGALRLRIEDA 180

Query: 185 GAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWME 244
            A  +ITA    R GK + L A  + A+   G   V  VIV+ R G  +          +
Sbjct: 181 KAKVVITASYTKRRGKKIDLLATVNRAI--DGLSFVEKVIVWDRDGDALNGESSLFVSFD 238

Query: 245 DVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPD 304
            +  G    CE E + AE PLF+LYTSG+TGKPKGV H+TGGY++    T K  FD+  D
Sbjct: 239 SLVKGASPHCEPEVMDAEDPLFILYTSGTTGKPKGVLHTTGGYMVGTYYTTKVVFDLHED 298

Query: 305 DLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAP 364
           D++WCTADIGW+TGH+YI YGPLA GAT ++ EG P YP+ GR+W  + +++V+IFYTAP
Sbjct: 299 DVYWCTADIGWITGHSYIVYGPLANGATSIIVEGAPDYPDPGRWWSYVEKYRVNIFYTAP 358

Query: 365 TAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFW 424
           TAIR  ++  E      P QYDLSSLR+LG+VGEPINPEAW WYYK+IG ERC IVDT+W
Sbjct: 359 TAIRMFMRYGEQ----WPAQYDLSSLRVLGSVGEPINPEAWHWYYKHIGRERCVIVDTWW 414

Query: 425 QTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMI 484
           QTETG HMIT +P + P  PG    P   I AA+VD +G ++P    G LV+K PWP+M+
Sbjct: 415 QTETGAHMITTVP-SYPAKPGKAGKPFFTIEAAVVDSSGKELPPNTVGNLVIKSPWPSML 473

Query: 485 RTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTME 544
           RT WG+PER+ K Y+    G   YL GD +  D++ GY  I+GR DDVLNV+GHR+GTME
Sbjct: 474 RTCWGEPERYEK-YWNTIPG--YYLTGDLASYDEE-GYIMILGRADDVLNVAGHRIGTME 529

Query: 545 IESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIG 604
           +ESALV +P VAEAAV+G+P ++ GE+I AFV+LK+     E + K+  E++  V   +G
Sbjct: 530 VESALVDHPAVAEAAVIGKPHEIKGESIKAFVILKKGY---EPSEKLVEEIKQHVRNVLG 586

Query: 605 PIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLEN 649
            IA P +I F + LPKTRSGKIMRR+L++   G  +  D STLE+
Sbjct: 587 AIAVPDEIEFVEKLPKTRSGKIMRRVLKAQELGLPV-GDISTLED 630


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: 1247
Number of extensions: 70
Number of successful extensions: 8
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: 630
Length adjustment: 38
Effective length of query: 622
Effective length of database: 592
Effective search space:   368224
Effective search space used:   368224
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the original publication.

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 Amino acid biosynthesis