Alignments for a candidate for aacS in Desulfatiglans anilini DSM 4660

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Desulfatiglans anilini DSM 4660

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_028321365.1 H567_RS0110465 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000422285.1:WP_028321365.1
          Length = 651

 Score =  667 bits (1721), Expect = 0.0
 Identities = 336/647 (51%), Positives = 430/647 (66%), Gaps = 4/647 (0%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
           LW P  + ++ S M  F+     RFG++F +Y + + WSV     FW A WE   VI   
Sbjct: 5   LWEPSEQRIQSSNMYRFMQHVNRRFGKTFDEYPSLYAWSVQNIPDFWAAFWEFSGVIASE 64

Query: 67  GEKALVDG-DRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
             + ++D   +M  A++F  ARLNFAENLLR      ALIF+ E + + R T+  L    
Sbjct: 65  PYREVIDDLSKMPGAKWFSGARLNFAENLLRYRDDRTALIFKSEGRETIRWTYRRLYEET 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           + L  AL+  G+  GDRV   MPNMP+T A MLA  S+GA+WSSCSPDFG +GVLDRFGQ
Sbjct: 125 AALAAALKRVGVAPGDRVVGFMPNMPQTTAAMLAAVSLGAVWSSCSPDFGIKGVLDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAP--TVIVPYAGDSAALAPTVEGGVTL 243
           I P +    DGY + GK  D  ++V  + + L +    V+VPY  D   +   V   V  
Sbjct: 185 IKPTVLFTADGYPFKGKTFDSLARVAEILEDLPSTRQVVVVPYTQDRPDIG-AVPRAVLY 243

Query: 244 ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLR 303
            DF        + F +LPF HPLYI++SSGTTG+PKC+V S GG L+ HLKE   H  L+
Sbjct: 244 DDFKEASPPPEMEFAQLPFDHPLYIMYSSGTTGLPKCMVQSTGGILVHHLKELMLHTDLK 303

Query: 304 DGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSA 363
             + +FYFTTCGWMMWNWL S LA+GATL L+DG+PF P  + L++ A  E+  VFGTSA
Sbjct: 304 REDTIFYFTTCGWMMWNWLTSSLALGATLVLFDGNPFHPAADALWELAQDEKITVFGTSA 363

Query: 364 KYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIV 423
            Y+ A+   G  P    DL  LR + STGSPL  EGF FVY  IK D+QLASI+GGTD+ 
Sbjct: 364 GYLAALENAGVKPGHAFDLGPLRALLSTGSPLPVEGFEFVYRDIKQDLQLASIAGGTDLN 423

Query: 424 SCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWNDP 483
            CF LGNP+ PV+ GE+Q  GL + V+ ++D G+ V  +KGELVCT  +PSMP+ FW+DP
Sbjct: 424 GCFALGNPMGPVYAGELQCRGLAMKVEAFDDNGRSVIDQKGELVCTAPWPSMPIYFWDDP 483

Query: 484 DGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQM 543
           DG+KY AAYFD + NVW HGDF E    GG+VI+GRSDATLNPGGVRIGTAEIY QVEQ 
Sbjct: 484 DGSKYHAAYFDVYPNVWRHGDFIEINDRGGVVIYGRSDATLNPGGVRIGTAEIYRQVEQF 543

Query: 544 DEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAVA 603
            EV ++L +GQDW++DVRV+LFV+ A G  L + L   +++ IR+ ASPRHVPAKI+AV 
Sbjct: 544 KEVEDSLVVGQDWKNDVRVILFVKTAPGCMLDDDLKARLRSTIRTNASPRHVPAKILAVP 603

Query: 604 DIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           DIP T + K VELAV+  + G+PV NK+AL NPE+LD FAGL EL+S
Sbjct: 604 DIPYTLNMKKVELAVKKTIQGQPVLNKDALRNPESLDFFAGLGELQS 650


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: 1228
Number of extensions: 52
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: 651
Length adjustment: 38
Effective length of query: 612
Effective length of database: 613
Effective search space:   375156
Effective search space used:   375156
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_028321365.1 H567_RS0110465 (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.3994298.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-285  933.6   0.0     3e-285  933.4   0.0    1.0  1  NCBI__GCF_000422285.1:WP_028321365.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000422285.1:WP_028321365.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  933.4   0.0    3e-285    3e-285       5     652 .]       4     650 ..       1     650 [. 0.99

  Alignments for each domain:
  == domain 1  score: 933.4 bits;  conditional E-value: 3e-285
                             TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvdd.skm 76 
                                            lwep ++r++++++ rf + v  rfG+++ +y +ly wsv++  +fw+a+wefs+v++s+++ ev+dd skm
  NCBI__GCF_000422285.1:WP_028321365.1   4 LLWEPSEQRIQSSNMYRFMQHVNRRFGKTFDEYPSLYAWSVQNIPDFWAAFWEFSGVIASEPYREVIDDlSKM 76 
                                           79*****************************************************************98689* PP

                             TIGR01217  77 laarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpni 149
                                           ++a++f garln+aenllr ++  +al++++e +e+ + t+  l +  a laaal+++Gv +Gdrv+g++pn+
  NCBI__GCF_000422285.1:WP_028321365.1  77 PGAKWFSGARLNFAENLLRYRDDRTALIFKSEGRETIRWTYRRLYEETAALAAALKRVGVAPGDRVVGFMPNM 149
                                           ************************************************************************* PP

                             TIGR01217 150 peavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlrav 222
                                           p++ aa+la+ s+Ga+wsscspdfG +gvldrf+qi+p +lf+ dgy ++Gk  d   +v+e+  +lp+ r+v
  NCBI__GCF_000422285.1:WP_028321365.1 150 PQTTAAMLAAVSLGAVWSSCSPDFGIKGVLDRFGQIKPTVLFTADGYPFKGKTFDSLARVAEILEDLPSTRQV 222
                                           ************************************************************************* PP

                             TIGR01217 223 vlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlk 295
                                           v++py  dr  +   v+ a+ ++d+  a   +e++f qlpfdhplyi++ssGttG+pk++v+s+GG+lv+hlk
  NCBI__GCF_000422285.1:WP_028321365.1 223 VVVPYTQDRPDIGA-VPRAVLYDDFKEASPPPEMEFAQLPFDHPLYIMYSSGTTGLPKCMVQSTGGILVHHLK 294
                                           *******9999988.*************9******************************************** PP

                             TIGR01217 296 ehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvs 368
                                           e+ lh+dl+  d ++y+tt+Gwmmwn+l s+la Gatlvl+dG p+ pa+++l++la+ e+itv+Gtsa y+ 
  NCBI__GCF_000422285.1:WP_028321365.1 295 ELMLHTDLKREDTIFYFTTCGWMMWNWLTSSLALGATLVLFDGNPFHPAADALWELAQDEKITVFGTSAGYLA 367
                                           ************************************************************************* PP

                             TIGR01217 369 avrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGei 441
                                           a++++g+kp + +dl  lr+++stGspl+ egfe+vy+ ik d++lasi+GGtd+  cf+++np+ pvy Ge+
  NCBI__GCF_000422285.1:WP_028321365.1 368 ALENAGVKPGHAFDLGPLRALLSTGSPLPVEGFEFVYRDIKQDLQLASIAGGTDLNGCFALGNPMGPVYAGEL 440
                                           ************************************************************************* PP

                             TIGR01217 442 qapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGg 514
                                           q++gl ++vea+d++G++v ++kGelv+t p psmp+ fw+d+dGsky++ayfd yp+vw+hGd+ie++ rGg
  NCBI__GCF_000422285.1:WP_028321365.1 441 QCRGLAMKVEAFDDNGRSVIDQKGELVCTAPWPSMPIYFWDDPDGSKYHAAYFDVYPNVWRHGDFIEINDRGG 513
                                           ************************************************************************* PP

                             TIGR01217 515 ivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikda 587
                                           +vi+Grsdatlnp+Gvr+G+aeiy +ve+++eve+slv+gq++++ ++rv+lfvk a+G  ld++l  +++++
  NCBI__GCF_000422285.1:WP_028321365.1 514 VVIYGRSDATLNPGGVRIGTAEIYRQVEQFKEVEDSLVVGQDWKN-DVRVILFVKTAPGCMLDDDLKARLRST 585
                                           ********************************************9.*************************** PP

                             TIGR01217 588 iraglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelks 652
                                           ir+++sprhvp+ki++v++ip+tl+ kkve+avk+ ++G+pv nk+al npe+ld++++l el+s
  NCBI__GCF_000422285.1:WP_028321365.1 586 IRTNASPRHVPAKILAVPDIPYTLNMKKVELAVKKTIQGQPVLNKDALRNPESLDFFAGLGELQS 650
                                           *************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (651 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 37.11
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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