Alignments for a candidate for aacS in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Magnetospirillum magneticum AMB-1

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011383023.1 AMB_RS03000 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000009985.1:WP_011383023.1
          Length = 652

 Score =  811 bits (2096), Expect = 0.0
 Identities = 406/648 (62%), Positives = 487/648 (75%), Gaps = 6/648 (0%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
           LW P +E  E S +A F+     RF     DY     WSV     FW+ VW+   +IG+ 
Sbjct: 5   LWQPSKERAEASALARFMRRADARFQVGATDYAGLWRWSVDRPDQFWSLVWDEVGIIGDR 64

Query: 67  GEKALV--DGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRAL 124
            +  +V  D  RM  AR+FPEARLNFAENLLR+   GDAL+F GEDKV  RL++ ELRAL
Sbjct: 65  PDGGVVVDDAGRMPGARWFPEARLNFAENLLRRDDGGDALVFWGEDKVKRRLSFAELRAL 124

Query: 125 VSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFG 184
           VSRLQQAL A G+G GDRVA  MPNMPE++A MLA AS+GAIWSS SPDFG QGVLDRFG
Sbjct: 125 VSRLQQALSAAGVGKGDRVAGYMPNMPESVAFMLAVASLGAIWSSASPDFGVQGVLDRFG 184

Query: 185 QIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVT 242
           QIAPK+ +  +GY+Y+GK  D   K+ A+   + +    V+VPY  ++A L+  V+  V 
Sbjct: 185 QIAPKVLVAAEGYFYSGKAHDCLEKLAAIVPGIPSLERVVVVPYTREAADLSG-VDKAVH 243

Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
           L DF+A F A  + F RLPF HPLYI++SSGTTG PKCIVHSAGG+L+Q LKEHR HC +
Sbjct: 244 LGDFLAPFPAKAVEFLRLPFDHPLYIMYSSGTTGAPKCIVHSAGGSLIQQLKEHRLHCDV 303

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
           R  +R+FYFTTCGWMMWNWL +GL   ATL LYDG+P    GN+LFD+A AE   +FGTS
Sbjct: 304 RKDDRVFYFTTCGWMMWNWLVAGLGAEATLLLYDGNPSHLGGNILFDFADAEGMTLFGTS 363

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
           AK+IDA+ K G  P +TH L+++R + STGS L+PEGF +VY  +K DVQLASISGGTDI
Sbjct: 364 AKWIDAIAKSGLEPIKTHSLATVRTICSTGSVLAPEGFDYVYAKVKADVQLASISGGTDI 423

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           +SCF+LGNPL PV+RGEIQ  GLG+ V+V+++ G+ + G KGELVCTRAFPSMPV FWND
Sbjct: 424 ISCFMLGNPLVPVYRGEIQCRGLGMKVEVFDENGQSLAGSKGELVCTRAFPSMPVGFWND 483

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPH-GGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
            DGAKYRAAYF++F  +W HGD+ E  P  GGI++ GRSDATLNPGGVRIGTAEIY QVE
Sbjct: 484 DDGAKYRAAYFEKFPGIWTHGDWVELNPETGGIIVFGRSDATLNPGGVRIGTAEIYRQVE 543

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           Q+D+V E+L IGQDW+ DVRVVLFVRL  GV L+  L   IK RIR   +PRHVPAK++ 
Sbjct: 544 QIDDVLESLVIGQDWQADVRVVLFVRLRDGVTLSPELETRIKKRIRDNTTPRHVPAKVVQ 603

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649
           VADIPRTKSGKIVELAVRDVVHGR VKNKEALANPEALDLFAG  EL+
Sbjct: 604 VADIPRTKSGKIVELAVRDVVHGRAVKNKEALANPEALDLFAGRAELE 651


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: 1441
Number of extensions: 65
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: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space:   375768
Effective search space used:   375768
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_011383023.1 AMB_RS03000 (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.14404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-292  955.7   0.0   6.5e-292  955.4   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383023.1  AMB_RS03000 acetoacetate--CoA li


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383023.1  AMB_RS03000 acetoacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  955.4   0.0  6.5e-292  6.5e-292       5     650 ..       4     650 ..       2     652 .] 0.98

  Alignments for each domain:
  == domain 1  score: 955.4 bits;  conditional E-value: 6.5e-292
                                 TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevv.. 71 
                                                lw+p +er + + larf   +  rf    +dy+ l+rwsvd  d+fw+ vw+ ++++++++   vv  
  lcl|NCBI__GCF_000009985.1:WP_011383023.1   4 LLWQPSKERAEASALARFMRRADARFQVGATDYAGLWRWSVDRPDQFWSLVWDEVGIIGDRPDGGVVvd 72 
                                               59************************************************************9877633 PP

                                 TIGR01217  72 ddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140
                                               d  +m++ar+fp+arln+aenllr+ + +dal++ +e+k++ +++f+elr++v++l++al a Gv+kGd
  lcl|NCBI__GCF_000009985.1:WP_011383023.1  73 DAGRMPGARWFPEARLNFAENLLRRDDGGDALVFWGEDKVKRRLSFAELRALVSRLQQALSAAGVGKGD 141
                                               3459***************************************************************** PP

                                 TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209
                                               rvagy+pn+pe+va +la as+Gaiwss+spdfG++gvldrf+qi+pk+l++ +gy y+Gk hd  ek+
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 142 RVAGYMPNMPESVAFMLAVASLGAIWSSASPDFGVQGVLDRFGQIAPKVLVAAEGYFYSGKAHDCLEKL 210
                                               ********************************************************************* PP

                                 TIGR01217 210 revakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGv 278
                                               ++++ ++p+l++vv++py  +++ l+  v+ a++l d+la + a  ++f +lpfdhplyi++ssGttG+
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 211 AAIVPGIPSLERVVVVPYTREAADLSG-VDKAVHLGDFLAPFPAKAVEFLRLPFDHPLYIMYSSGTTGA 278
                                               *******************97777766.***************************************** PP

                                 TIGR01217 279 pkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnv 347
                                               pk+ivhsaGG l+q lkeh+lhcd+++ dr++y+tt+Gwmmwn+lv+gl + atl lydG p    +n+
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 279 PKCIVHSAGGSLIQQLKEHRLHCDVRKDDRVFYFTTCGWMMWNWLVAGLGAEATLLLYDGNPSHLGGNI 347
                                               ********************************************************************* PP

                                 TIGR01217 348 lfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllas 416
                                               lfd+a++eg+t++Gtsak+++a+ k+gl+p++th l ++r++ stGs l pegf+yvy ++kadv+las
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 348 LFDFADAEGMTLFGTSAKWIDAIAKSGLEPIKTHSLATVRTICSTGSVLAPEGFDYVYAKVKADVQLAS 416
                                               ********************************************************************* PP

                                 TIGR01217 417 isGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnded 485
                                               isGGtdi+scf+++np++pvy+Geiq++glG++ve++de+G+++ g kGelv+t+++psmpv fwnd+d
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 417 ISGGTDIISCFMLGNPLVPVYRGEIQCRGLGMKVEVFDENGQSLAGSKGELVCTRAFPSMPVGFWNDDD 485
                                               ********************************************************************* PP

                                 TIGR01217 486 GskyrkayfdkypgvwahGdyieltp.rGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvi 553
                                               G+kyr+ayf+k+pg+w+hGd++el+p +Ggi+++Grsdatlnp+Gvr+G+aeiy +ve++d+v eslvi
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 486 GAKYRAAYFEKFPGIWTHGDWVELNPeTGGIIVFGRSDATLNPGGVRIGTAEIYRQVEQIDDVLESLVI 554
                                               **************************99***************************************** PP

                                 TIGR01217 554 gqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkd 622
                                               gq+++  ++rvvlfv+l  G+tl+++l  +ik++ir + +prhvp+k+++va+iprt+sGk+ve+av+d
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 555 GQDWQA-DVRVVLFVRLRDGVTLSPELETRIKKRIRDNTTPRHVPAKVVQVADIPRTKSGKIVELAVRD 622
                                               ****98.************************************************************** PP

                                 TIGR01217 623 vvaGkpvenkgalsnpealdlyeeleel 650
                                               vv+G++v+nk+al+npealdl+++ +el
  lcl|NCBI__GCF_000009985.1:WP_011383023.1 623 VVHGRAVKNKEALANPEALDLFAGRAEL 650
                                               **********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (652 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.90
//
[ok]

This GapMind analysis is from Sep 17 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 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