Alignments for a candidate for aacS in Thioalkalivibrio denitrificans ALJD

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Thioalkalivibrio denitrificans ALJD

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_077279762.1 B1C78_RS13845 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_002000365.1:WP_077279762.1
          Length = 650

 Score =  699 bits (1804), Expect = 0.0
 Identities = 359/649 (55%), Positives = 437/649 (67%), Gaps = 5/649 (0%)

Query: 5   RPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-I 63
           RP+W P +E +ER+ M  F+    E    +  DY A H WSV++   FW+AVW + +V  
Sbjct: 3   RPVWTPPQERIERTHMMSFMRQVREASADA-TDYAALHAWSVADPEGFWSAVWRYGEVRA 61

Query: 64  GESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRA 123
            +     L   DRM  AR+F  ARLNFAENLLR+     ALI   ED     L+  +L A
Sbjct: 62  SQPWSSVLGAPDRMPGARWFAGARLNFAENLLRRRDDRPALIACAEDGSRRELSHAQLHA 121

Query: 124 LVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRF 183
            V RL  AL   G+  GDRVA  +PN PE +  MLA   +GA+WSSCSPDFGEQGVLDRF
Sbjct: 122 QVERLAAALHRDGVEPGDRVAGFVPNRPEAVIAMLAATRLGAVWSSCSPDFGEQGVLDRF 181

Query: 184 GQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGV 241
            QI PK+    DGY++ G+  D  +++  VA  L      V+ PY  DS  +A  V G V
Sbjct: 182 AQINPKVLFSADGYFFKGRTFDSRARLARVAAQLPGLRRVVVFPYVQDSVDVAE-VPGAV 240

Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
               ++   QAG     +LPF HP+YI++SSGTTG PKCIVH AGGTLLQHLKEH  H  
Sbjct: 241 EWDTYMQTSQAGMPQPAQLPFDHPVYIMYSSGTTGKPKCIVHGAGGTLLQHLKEHLLHTD 300

Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
           +  G+R+FYFTTCGWMMWNWL S LA GATL LYDGSPF P    L D A  E   VFGT
Sbjct: 301 IGPGDRVFYFTTCGWMMWNWLVSALATGATLVLYDGSPFHPAPTALMDLAEREGITVFGT 360

Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
           SA YI A+ K G  P  +H L  LR + STGSPL+PE F +VY  +K DV LASISGGTD
Sbjct: 361 SASYIAALEKAGVRPRASHRLEPLRTILSTGSPLAPESFDYVYRDVKADVHLASISGGTD 420

Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
           I+SCF LGNP+ PV+RG++Q  GLG+AV+V+++ G+PVR  KGELVCT  FPSMPV FWN
Sbjct: 421 IISCFALGNPVLPVYRGQLQCRGLGMAVEVFDEAGRPVRERKGELVCTAPFPSMPVGFWN 480

Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
           DPDG++YRAAYF+R+  VW HGD+AE T   G++IHGRSDA LNPGGVRIGTAEIY QV+
Sbjct: 481 DPDGSRYRAAYFERYPGVWAHGDYAEITAQDGLIIHGRSDAVLNPGGVRIGTAEIYRQVD 540

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
            + EV E++ +GQ W    RVVLFV L  G+ L E L   I+  IR   +PRHVPAKI+ 
Sbjct: 541 ALAEVLESVAVGQSWRGSERVVLFVVLREGLTLDEDLRTRIRAVIRENTTPRHVPAKILQ 600

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           V ++PRT+SGKIVELAVRDV+HGR V N EALANP+AL+ F    EL S
Sbjct: 601 VGELPRTRSGKIVELAVRDVIHGRSVGNLEALANPDALEQFRDRPELAS 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: 1364
Number of extensions: 73
Number of successful extensions: 4
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_077279762.1 B1C78_RS13845 (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.7157.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-282  923.3   0.0   3.7e-282  923.2   0.0    1.0  1  lcl|NCBI__GCF_002000365.1:WP_077279762.1  B1C78_RS13845 acetoacetate--CoA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002000365.1:WP_077279762.1  B1C78_RS13845 acetoacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  923.2   0.0  3.7e-282  3.7e-282       4     650 ..       3     647 ..       1     649 [. 0.99

  Alignments for each domain:
  == domain 1  score: 923.2 bits;  conditional E-value: 3.7e-282
                                 TIGR01217   4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd 72 
                                               +++w+p +er++++++  f   v e+     +dy+al+ wsv + + fw+avw++ +v++s++ + v++
  lcl|NCBI__GCF_002000365.1:WP_077279762.1   3 RPVWTPPQERIERTHMMSFMRQVREASAD-ATDYAALHAWSVADPEGFWSAVWRYGEVRASQPWSSVLG 70 
                                               579********************998765.579***********************************9 PP

                                 TIGR01217  73 d.skmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140
                                                 ++m++ar+f garln+aenllr+++  +al+  +e+    ++++++l +qv +laaal + Gv++Gd
  lcl|NCBI__GCF_002000365.1:WP_077279762.1  71 ApDRMPGARWFAGARLNFAENLLRRRDDRPALIACAEDGSRRELSHAQLHAQVERLAAALHRDGVEPGD 139
                                               658****************************************************************** PP

                                 TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209
                                               rvag++pn peav a+la++ +Ga+wsscspdfG++gvldrf+qi+pk+lfs dgy ++G+  d r ++
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 140 RVAGFVPNRPEAVIAMLAATRLGAVWSSCSPDFGEQGVLDRFAQINPKVLFSADGYFFKGRTFDSRARL 208
                                               ********************************************************************* PP

                                 TIGR01217 210 revakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGv 278
                                               ++va +lp lr+vv+ pyv d+  +a  v+ga+++++++ + qa+ ++  qlpfdhp+yi++ssGttG 
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 209 ARVAAQLPGLRRVVVFPYVQDSVDVAE-VPGAVEWDTYMQTSQAGMPQPAQLPFDHPVYIMYSSGTTGK 276
                                               ********************9999987.***************************************** PP

                                 TIGR01217 279 pkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnv 347
                                               pk+ivh aGGtl+qhlkeh lh+d+++gdr++y+tt+Gwmmwn+lvs+latGatlvlydGsp+ pa+ +
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 277 PKCIVHGAGGTLLQHLKEHLLHTDIGPGDRVFYFTTCGWMMWNWLVSALATGATLVLYDGSPFHPAPTA 345
                                               ********************************************************************* PP

                                 TIGR01217 348 lfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllas 416
                                               l+dlaeregitv+Gtsa y+ a++k+g++p  +h l+ lr+++stGspl pe+f+yvy+ +kadv+las
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 346 LMDLAEREGITVFGTSASYIAALEKAGVRPRASHRLEPLRTILSTGSPLAPESFDYVYRDVKADVHLAS 414
                                               ********************************************************************* PP

                                 TIGR01217 417 isGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnded 485
                                               isGGtdi+scf+++np+lpvy+G++q++glG+ave++de G+pv++ kGelv+t p+psmpv fwnd+d
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 415 ISGGTDIISCFALGNPVLPVYRGQLQCRGLGMAVEVFDEAGRPVRERKGELVCTAPFPSMPVGFWNDPD 483
                                               ********************************************************************* PP

                                 TIGR01217 486 GskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvig 554
                                               Gs+yr+ayf++ypgvwahGdy+e+t++ g++ihGrsda lnp+Gvr+G+aeiy +v++l ev es+ +g
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 484 GSRYRAAYFERYPGVWAHGDYAEITAQDGLIIHGRSDAVLNPGGVRIGTAEIYRQVDALAEVLESVAVG 552
                                               ********************************************************************* PP

                                 TIGR01217 555 qeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdv 623
                                               q ++   ervvlfv l +G tlde+l  +i+  ir + +prhvp+ki++v ++prt sGk+ve+av+dv
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 553 QSWRG-SERVVLFVVLREGLTLDEDLRTRIRAVIRENTTPRHVPAKILQVGELPRTRSGKIVELAVRDV 620
                                               ***96.99************************************************************* PP

                                 TIGR01217 624 vaGkpvenkgalsnpealdlyeeleel 650
                                               ++G++v n +al+np+al+ +++ +el
  lcl|NCBI__GCF_002000365.1:WP_077279762.1 621 IHGRSVGNLEALANPDALEQFRDRPEL 647
                                               **********************98887 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.32
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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