Alignments for a candidate for aacS in Desulfoscipio geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Desulfoscipio geothermicus DSM 3669

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_092485810.1 BM299_RS14405 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_900115975.1:WP_092485810.1
          Length = 650

 Score =  726 bits (1875), Expect = 0.0
 Identities = 354/649 (54%), Positives = 460/649 (70%), Gaps = 4/649 (0%)

Query: 4   ERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV- 62
           ++PLWVP  E  +++ M  FI++   ++G++F+DY   +DWSV+    FW A+WE C++ 
Sbjct: 2   KKPLWVPSEERKQKANMTAFINFVNNKYGKNFSDYSELYDWSVNCSADFWAAMWEFCEIK 61

Query: 63  IGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELR 122
                +  +++ D M+ +R+FP A+LNFAENLLR      A+IF+GE +V  RLT+ +L 
Sbjct: 62  ASRPYDSVVINQDDMIGSRWFPGAKLNFAENLLRYRDEQTAIIFKGEGQVPVRLTYAQLF 121

Query: 123 ALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDR 182
             V RL ++LR  G+ AGDRVA  MPNM ET+  MLA  S+GAIWSSCSPDFG +GVLDR
Sbjct: 122 DRVVRLARSLRHLGVAAGDRVAGFMPNMTETVIAMLAATSIGAIWSSCSPDFGIKGVLDR 181

Query: 183 FGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGG 240
           FGQI P++    +GY+YNGK+ D   +V  + + + +    V+VPY  D A     +   
Sbjct: 182 FGQIQPRVLFTANGYYYNGKQHDSLGRVVRIIEEIPSVEKVVVVPYT-DPAPDLGAIPNA 240

Query: 241 VTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300
           V  ADF+A      + F +LPF HP+YI++SSGTTGVPKCIVH AGGTL+QHLKE + H 
Sbjct: 241 VLFADFMAPESGLEIEFAQLPFDHPVYIMYSSGTTGVPKCIVHGAGGTLIQHLKELKLHT 300

Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360
            L+  + +FYFTTCGWMMWNWL S LA+GAT+ LYDGSPF P    LF  A  ER  VFG
Sbjct: 301 DLKREDTIFYFTTCGWMMWNWLVSSLALGATILLYDGSPFYPGPEALFKMAQDERVTVFG 360

Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420
           TSAKY+ A+ K G  P  T DL+ L+ + STGSPLS E F +VY  IK DV L+SISGGT
Sbjct: 361 TSAKYLAAIEKEGVKPRETFDLTPLKAILSTGSPLSVESFEYVYRDIKEDVCLSSISGGT 420

Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480
           DI+SCF LGNP+ PV+ GE+Q  GLG+ V  ++D G+PV  +KGELVCT +FPSMPV FW
Sbjct: 421 DIISCFALGNPIGPVYAGELQCRGLGMEVHAFDDSGRPVVNQKGELVCTSSFPSMPVCFW 480

Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540
           ND    KY  AYF  + NVW HGD+ E T  GGI+I+GRSDATLNPGGVRIGTAEIY QV
Sbjct: 481 NDESNEKYTNAYFSMYSNVWNHGDYIEITDTGGIIIYGRSDATLNPGGVRIGTAEIYRQV 540

Query: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
           E ++E+ ++L +GQ+W++DVRV+LFV+LA  V L   L ++IK  IR   +PRHVPAK+I
Sbjct: 541 EALEEIKDSLVVGQNWDNDVRVILFVKLAENVVLNGDLIKKIKTTIRVNTTPRHVPAKVI 600

Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649
           AV DIP T SGK VE+AVR+++H  PVKN++ALANPEALDL+  + EL+
Sbjct: 601 AVDDIPYTISGKKVEMAVRNIIHNEPVKNRDALANPEALDLYRDIPELQ 649


Lambda     K      H
   0.322    0.139    0.441 

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: 1240
Number of extensions: 46
Number of successful extensions: 3
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: 650
Length of database: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space:   374544
Effective search space used:   374544
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate WP_092485810.1 BM299_RS14405 (acetoacetate--CoA ligase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01217.hmm
# target sequence database:        /tmp/gapView.1283960.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01217  [M=652]
Accession:   TIGR01217
Description: ac_ac_CoA_syn: acetoacetate-CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-295  967.5   0.0   1.6e-295  967.3   0.0    1.0  1  NCBI__GCF_900115975.1:WP_092485810.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900115975.1:WP_092485810.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  967.3   0.0  1.6e-295  1.6e-295       4     651 ..       3     649 ..       1     650 [] 0.99

  Alignments for each domain:
  == domain 1  score: 967.3 bits;  conditional E-value: 1.6e-295
                             TIGR01217   4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevv.ddsk 75 
                                           ++lw+p +er+++a+++ f+++v +++G+ ++dy +ly+wsv+   +fw+a+wef+++ +s++++ vv +++ 
  NCBI__GCF_900115975.1:WP_092485810.1   3 KPLWVPSEERKQKANMTAFINFVNNKYGKNFSDYSELYDWSVNCSADFWAAMWEFCEIKASRPYDSVViNQDD 75 
                                           68**************************************************************987538899 PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpn 148
                                           m+++r+fpga+ln+aenllr +++++a+++++e +++ ++t+++l  +v +la +lr lGv +Gdrvag++pn
  NCBI__GCF_900115975.1:WP_092485810.1  76 MIGSRWFPGAKLNFAENLLRYRDEQTAIIFKGEGQVPVRLTYAQLFDRVVRLARSLRHLGVAAGDRVAGFMPN 148
                                           ************************************************************************* PP

                             TIGR01217 149 ipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlra 221
                                           ++e+v a+la++s+GaiwsscspdfG +gvldrf+qi+p++lf+ +gy+ynGk+hd   +v ++  e+p++++
  NCBI__GCF_900115975.1:WP_092485810.1 149 MTETVIAMLAATSIGAIWSSCSPDFGIKGVLDRFGQIQPRVLFTANGYYYNGKQHDSLGRVVRIIEEIPSVEK 221
                                           ************************************************************************* PP

                             TIGR01217 222 vvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhl 294
                                           vv++py  ++  l   +++a+ ++d++a     e++f qlpfdhp+yi++ssGttGvpk+ivh aGGtl+qhl
  NCBI__GCF_900115975.1:WP_092485810.1 222 VVVVPYTDPAPDLGA-IPNAVLFADFMAPESGLEIEFAQLPFDHPVYIMYSSGTTGVPKCIVHGAGGTLIQHL 293
                                           ********9988887.*************9999**************************************** PP

                             TIGR01217 295 kehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyv 367
                                           ke++lh+dl+  d ++y+tt+Gwmmwn+lvs+la Gat+ lydGsp+ p +++lf++a+ e++tv+Gtsaky+
  NCBI__GCF_900115975.1:WP_092485810.1 294 KELKLHTDLKREDTIFYFTTCGWMMWNWLVSSLALGATILLYDGSPFYPGPEALFKMAQDERVTVFGTSAKYL 366
                                           ************************************************************************* PP

                             TIGR01217 368 savrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGe 440
                                            a++k+g+kp +t+dl+ l++++stGspl+ e+feyvy+ ik dv l+sisGGtdi+scf+++np  pvy Ge
  NCBI__GCF_900115975.1:WP_092485810.1 367 AAIEKEGVKPRETFDLTPLKAILSTGSPLSVESFEYVYRDIKEDVCLSSISGGTDIISCFALGNPIGPVYAGE 439
                                           ************************************************************************* PP

                             TIGR01217 441 iqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                           +q++glG++v+a+d++G+pv ++kGelv+t ++psmpv fwnde   ky +ayf+ y +vw hGdyie+t +G
  NCBI__GCF_900115975.1:WP_092485810.1 440 LQCRGLGMEVHAFDDSGRPVVNQKGELVCTSSFPSMPVCFWNDESNEKYTNAYFSMYSNVWNHGDYIEITDTG 512
                                           ************************************************************************* PP

                             TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikd 586
                                           gi+i+Grsdatlnp+Gvr+G+aeiy +ve+l+e+++slv+gq++++ ++rv+lfvkla+ + l+ +l+k+ik 
  NCBI__GCF_900115975.1:WP_092485810.1 513 GIIIYGRSDATLNPGGVRIGTAEIYRQVEALEEIKDSLVVGQNWDN-DVRVILFVKLAENVVLNGDLIKKIKT 584
                                           *******************************************987.************************** PP

                             TIGR01217 587 airaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelk 651
                                           +ir++ +prhvp+k+i+v++ip+t+sGkkve+av+++++ +pv+n++al+npealdly++++el+
  NCBI__GCF_900115975.1:WP_092485810.1 585 TIRVNTTPRHVPAKVIAVDDIPYTISGKKVEMAVRNIIHNEPVKNRDALANPEALDLYRDIPELQ 649
                                           **************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (650 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 34.48
//
[ok]

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