Alignments for a candidate for aacS in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Brucella microti CCM 4915

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_002968065.1 BMI_RS00095 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000022745.1:WP_002968065.1
          Length = 662

 Score =  938 bits (2424), Expect = 0.0
 Identities = 452/648 (69%), Positives = 513/648 (79%), Gaps = 2/648 (0%)

Query: 4   ERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVI 63
           + PLW PD   +  S + +F        G S  DY A H WSV +R  FW  VW+ C VI
Sbjct: 13  DNPLWQPDGARIAASNLEQFRIRAERHTGLSLPDYAALHRWSVEDRAGFWQLVWDFCAVI 72

Query: 64  GESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRA 123
           GE G  AL D   M  A+FFPEARLNFAENLLR  G G+A++FRGE+KV  RLTW++L A
Sbjct: 73  GERGNTALTDRGHMRAAKFFPEARLNFAENLLRHKGDGEAIVFRGENKVERRLTWNDLHA 132

Query: 124 LVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRF 183
           LVS+LQQ + ++G+  GDRVA MMPNMPE +ALMLA +S+GA+WSSCSPDFG QGVLDRF
Sbjct: 133 LVSKLQQFMLSEGVQPGDRVAGMMPNMPEAVALMLAASSIGAVWSSCSPDFGVQGVLDRF 192

Query: 184 GQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGV 241
           GQI PKLF  CDGYWYNGKR  V  KV  V   L      VIV Y G++ A+A   E G+
Sbjct: 193 GQIEPKLFFACDGYWYNGKRIAVADKVAEVTAKLPGLKRAVIVTYLGEAEAVADKAEKGI 252

Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
            L   +  F+A P+ F +LPF HPLYILFSSGTTG+PKCIVH AGG LLQHLKEHR H  
Sbjct: 253 ALYAALEPFKAKPVEFTQLPFDHPLYILFSSGTTGIPKCIVHRAGGVLLQHLKEHRLHAD 312

Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
           LRDG+R FYFTTCGWMMWNWLASG+A GATL LYDGSPF PDGNVLFDYAAAE    FGT
Sbjct: 313 LRDGDRFFYFTTCGWMMWNWLASGIASGATLMLYDGSPFYPDGNVLFDYAAAEGMTYFGT 372

Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
           SAK+IDAV K G  P  THDLS+LR ++STGSPLSPEGF+FVY+ IK DV LASISGGTD
Sbjct: 373 SAKFIDAVLKAGLKPGETHDLSALRTISSTGSPLSPEGFAFVYDAIKKDVHLASISGGTD 432

Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
           IVSCFVLG P +PVW+GEIQG GLG+AVDVWND+GKPVRGEKGELVCT+AFPSMP+ FWN
Sbjct: 433 IVSCFVLGVPTEPVWQGEIQGAGLGMAVDVWNDDGKPVRGEKGELVCTKAFPSMPLQFWN 492

Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
           D  G KY+AAYF+RFDN+WCHGDFAEWT HGGIVIHGRSDATLNPGGVRIGTAEIYNQVE
Sbjct: 493 DAQGEKYQAAYFERFDNIWCHGDFAEWTEHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 552

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           QM E+AEALCIGQDW+ DVRVVLFVRLA GV L + L   I+ +IR+GA+PRHVPAKIIA
Sbjct: 553 QMPEIAEALCIGQDWDRDVRVVLFVRLAEGVVLDDDLKARIRTKIRTGATPRHVPAKIIA 612

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649
           V DIPRTKSGKIVELAVRD+VHGR VKN+EALANPEAL+ +  + EL+
Sbjct: 613 VRDIPRTKSGKIVELAVRDIVHGREVKNREALANPEALEFYRDIAELQ 660


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: 1547
Number of extensions: 64
Number of successful extensions: 2
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: 662
Length adjustment: 38
Effective length of query: 612
Effective length of database: 624
Effective search space:   381888
Effective search space used:   381888
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_002968065.1 BMI_RS00095 (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.1973401.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1038.8   0.0          0 1038.5   0.0    1.0  1  NCBI__GCF_000022745.1:WP_002968065.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022745.1:WP_002968065.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1038.5   0.0         0         0       3     651 ..      13     660 ..      11     661 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1038.5 bits;  conditional E-value: 0
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 
                                           +++lw+pd  r++ ++l++fr  +  ++G++l dy+al+rwsv+++  fw+ vw+f+ v+++++  ++ d  +
  NCBI__GCF_000022745.1:WP_002968065.1  13 DNPLWQPDGARIAASNLEQFRIRAERHTGLSLPDYAALHRWSVEDRAGFWQLVWDFCAVIGERGNTALTDRGH 85 
                                           568********************************************************************** PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpn 148
                                           m aa+ffp+arln+aenllr+kg ++a+++++e+k+  ++t+++l ++v++l++ + + Gv++Gdrvag++pn
  NCBI__GCF_000022745.1:WP_002968065.1  86 MRAAKFFPEARLNFAENLLRHKGDGEAIVFRGENKVERRLTWNDLHALVSKLQQFMLSEGVQPGDRVAGMMPN 158
                                           ************************************************************************* PP

                             TIGR01217 149 ipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlra 221
                                           +peava++la++s+Ga+wsscspdfG++gvldrf+qiepkl+f++dgy+ynGk+  + +kv+ev+ +lp l++
  NCBI__GCF_000022745.1:WP_002968065.1 159 MPEAVALMLAASSIGAVWSSCSPDFGVQGVLDRFGQIEPKLFFACDGYWYNGKRIAVADKVAEVTAKLPGLKR 231
                                           ************************************************************************* PP

                             TIGR01217 222 vvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhl 294
                                            v++ y+g++e++a k e ++ l   l  ++a +++f qlpfdhplyilfssGttG+pk+ivh aGG+l+qhl
  NCBI__GCF_000022745.1:WP_002968065.1 232 AVIVTYLGEAEAVADKAEKGIALYAALEPFKAKPVEFTQLPFDHPLYILFSSGTTGIPKCIVHRAGGVLLQHL 304
                                           ************************************************************************* PP

                             TIGR01217 295 kehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyv 367
                                           keh+lh+dl+dgdr++y+tt+Gwmmwn+l+sg+a Gatl+lydGsp+ p++nvlfd+a++eg+t +Gtsak++
  NCBI__GCF_000022745.1:WP_002968065.1 305 KEHRLHADLRDGDRFFYFTTCGWMMWNWLASGIASGATLMLYDGSPFYPDGNVLFDYAAAEGMTYFGTSAKFI 377
                                           ************************************************************************* PP

                             TIGR01217 368 savrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGe 440
                                           +av k+glkp +thdlsalr++ stGspl+pegf +vy++ik dv+lasisGGtdivscfv+++p+ pv++Ge
  NCBI__GCF_000022745.1:WP_002968065.1 378 DAVLKAGLKPGETHDLSALRTISSTGSPLSPEGFAFVYDAIKKDVHLASISGGTDIVSCFVLGVPTEPVWQGE 450
                                           ************************************************************************* PP

                             TIGR01217 441 iqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                           iq+ glG+av++w+++Gkpv+gekGelv+tk++psmp++fwnd +G ky++ayf++++++w+hGd++e+t +G
  NCBI__GCF_000022745.1:WP_002968065.1 451 IQGAGLGMAVDVWNDDGKPVRGEKGELVCTKAFPSMPLQFWNDAQGEKYQAAYFERFDNIWCHGDFAEWTEHG 523
                                           ************************************************************************* PP

                             TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikd 586
                                           givihGrsdatlnp+Gvr+G+aeiyn+ve+++e++e+l+igq+++  ++rvvlfv+la+G+ ld++l  +i+ 
  NCBI__GCF_000022745.1:WP_002968065.1 524 GIVIHGRSDATLNPGGVRIGTAEIYNQVEQMPEIAEALCIGQDWDR-DVRVVLFVRLAEGVVLDDDLKARIRT 595
                                           ********************************************76.9************************* PP

                             TIGR01217 587 airaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelk 651
                                           +ir+g++prhvp+kii+v++iprt+sGk+ve+av+d+v+G+ v+n++al+npeal++y++++el+
  NCBI__GCF_000022745.1:WP_002968065.1 596 KIRTGATPRHVPAKIIAVRDIPRTKSGKIVELAVRDIVHGREVKNREALANPEALEFYRDIAELQ 660
                                           ***************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (662 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: 21.66
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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