Alignments for a candidate for aacS in Methylocystis bryophila S285

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Methylocystis bryophila S285

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_085773781.1 B1812_RS16280 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_002117405.1:WP_085773781.1
          Length = 651

 Score =  707 bits (1826), Expect = 0.0
 Identities = 354/645 (54%), Positives = 446/645 (69%), Gaps = 13/645 (2%)

Query: 7   LWVPDREIVERSPMAEFI--DWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIG 64
           +W PD      + +  F   D   E +  +F DY   H WS+    AFW+ +W+  ++IG
Sbjct: 4   VWSPDPAQRASARLTAFARSDRRTEEYAETF-DYAGLHVWSLGHSDAFWSRLWDFFEIIG 62

Query: 65  ESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGD-ALIFRGEDKVSYRLTWDELRA 123
           E G   L DGD+M  AR+FP+ARLNFA+NLLR+  + + A++F+GE +    LT+ EL+ 
Sbjct: 63  EKGGTVLADGDKMPGARWFPQARLNFAQNLLRQRAASEIAIVFQGEKRERRTLTFGELKR 122

Query: 124 LVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRF 183
            V  +   LR+ G+G GDRVA  + N PE +  MLA AS+GA+W+SCSPDFG  GVLDRF
Sbjct: 123 QVGAIAAYLRSAGVGPGDRVAGYLHNGPEAVVGMLAAASLGAVWASCSPDFGVAGVLDRF 182

Query: 184 GQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGV 241
           GQI PK  I CDGY+Y G+  D   + R +A  L A    ++ PY  D    AP+++G  
Sbjct: 183 GQIGPKALIACDGYFYKGQACDRLEQAREIAAGLSALRAVLVAPYIHD----APSLKGFA 238

Query: 242 TLA---DFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRF 298
                 D +A     PL F  LPF HPLY++FSSGTTG PKCIVH AGG LLQH+KEH+ 
Sbjct: 239 MAELWPDVLAKHDGAPLDFALLPFDHPLYVVFSSGTTGSPKCIVHGAGGCLLQHMKEHQL 298

Query: 299 HCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAV 358
           HC +R G+R+F+ TT GWMMWNWL S LA  AT+ LYDG P   +G  LFD A  E   +
Sbjct: 299 HCDVRPGDRVFFATTTGWMMWNWLVSALASRATILLYDGFPMDRNGAALFDLAEREHATL 358

Query: 359 FGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISG 418
           FG SA ++ A +K G  PARTHDL+S+RL+ STGSPLSPEGF +VY  + P+ QLAS+SG
Sbjct: 359 FGVSAGFLRAAQKLGVAPARTHDLASMRLLASTGSPLSPEGFDYVYRDVAPNAQLASMSG 418

Query: 419 GTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVM 478
           GTDI+SCFVLGN  +PV RGEIQG GLG+AV+VWND+G  + G +GELVCT+ FPSMP+ 
Sbjct: 419 GTDILSCFVLGNSWRPVIRGEIQGAGLGMAVEVWNDDGARIVGAEGELVCTQPFPSMPIE 478

Query: 479 FWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYN 538
           FWNDP G KY++AYF  F N+W HGDFA  TP GG +IHGRSDATLNP GVRIGTAEIY 
Sbjct: 479 FWNDPGGEKYKSAYFSDFANIWRHGDFATETPSGGFIIHGRSDATLNPQGVRIGTAEIYR 538

Query: 539 QVEQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAK 598
            VE   +V E L + QD  D  R++LFV+L  G  ++  L+  IK+R+R  ASPRHVPA 
Sbjct: 539 IVEAFMQVEECLAVCQDASDGQRILLFVKLRAGERMSSELSAGIKHRLREEASPRHVPAA 598

Query: 599 IIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFA 643
           II   ++P T+SGK+VELAVRDVVHGRPVKN+EALANPE+LD FA
Sbjct: 599 IIEAPELPHTRSGKLVELAVRDVVHGRPVKNREALANPESLDFFA 643


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: 1449
Number of extensions: 73
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_085773781.1 B1812_RS16280 (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.661999.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-264  864.3   0.0   2.9e-264  864.1   0.0    1.0  1  NCBI__GCF_002117405.1:WP_085773781.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002117405.1:WP_085773781.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.1   0.0  2.9e-264  2.9e-264       5     650 ..       3     648 ..       1     649 [. 0.97

  Alignments for each domain:
  == domain 1  score: 864.1 bits;  conditional E-value: 2.9e-264
                             TIGR01217   5 vlwepdaervkdarlarfraavgerfGa.algdydalyrwsvdeldafwkavwefsdvvfssaekevvddskm 76 
                                           ++w pd  + ++arl+ f      +       dy+ l+ ws+ + dafw+ +w+f++++++++   + d++km
  NCBI__GCF_002117405.1:WP_085773781.1   3 IVWSPDPAQRASARLTAFARSDRRTEEYaETFDYAGLHVWSLGHSDAFWSRLWDFFEIIGEKGGTVLADGDKM 75 
                                           68****************866544444414569**************************************** PP

                             TIGR01217  77 laarffpgarlnyaenllrkkgs.edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpn 148
                                           ++ar+fp+arln+a+nllr++ + e a+++++e++e   +tf el+rqv  +aa lr+ Gv++Gdrvagyl n
  NCBI__GCF_002117405.1:WP_085773781.1  76 PGARWFPQARLNFAQNLLRQRAAsEIAIVFQGEKRERRTLTFGELKRQVGAIAAYLRSAGVGPGDRVAGYLHN 148
                                           *******************9776388899******************************************** PP

                             TIGR01217 149 ipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlra 221
                                            peav+ +la+as+Ga+w+scspdfG+ gvldrf+qi pk l+++dgy y+G+  dr e+ re+a +l+ lra
  NCBI__GCF_002117405.1:WP_085773781.1 149 GPEAVVGMLAAASLGAVWASCSPDFGVAGVLDRFGQIGPKALIACDGYFYKGQACDRLEQAREIAAGLSALRA 221
                                           ************************************************************************* PP

                             TIGR01217 222 vvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhl 294
                                           v++ py+ d+ +l+     a  + d+la  + a+l f  lpfdhply++fssGttG pk+ivh aGG l+qh+
  NCBI__GCF_002117405.1:WP_085773781.1 222 VLVAPYIHDAPSLKG-FAMAELWPDVLAKHDGAPLDFALLPFDHPLYVVFSSGTTGSPKCIVHGAGGCLLQHM 293
                                           ********9988887.778889*************************************************** PP

                             TIGR01217 295 kehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyv 367
                                           keh+lhcd+++gdr+++ tt+Gwmmwn+lvs+la  at+ lydG p+  ++ +lfdlaere +t++G sa ++
  NCBI__GCF_002117405.1:WP_085773781.1 294 KEHQLHCDVRPGDRVFFATTTGWMMWNWLVSALASRATILLYDGFPMDRNGAALFDLAEREHATLFGVSAGFL 366
                                           ************************************************************************* PP

                             TIGR01217 368 savrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGe 440
                                            a +k g+ parthdl ++rl+astGspl+pegf+yvy+ ++++ +las+sGGtdi+scfv++n+  pv +Ge
  NCBI__GCF_002117405.1:WP_085773781.1 367 RAAQKLGVAPARTHDLASMRLLASTGSPLSPEGFDYVYRDVAPNAQLASMSGGTDILSCFVLGNSWRPVIRGE 439
                                           ************************************************************************* PP

                             TIGR01217 441 iqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                           iq+ glG+ave+w+++G  + g++Gelv+t+p+psmp++fwnd+ G ky++ayf+ + ++w+hGd+++ tp G
  NCBI__GCF_002117405.1:WP_085773781.1 440 IQGAGLGMAVEVWNDDGARIVGAEGELVCTQPFPSMPIEFWNDPGGEKYKSAYFSDFANIWRHGDFATETPSG 512
                                           ************************************************************************* PP

                             TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikd 586
                                           g +ihGrsdatlnp+Gvr+G+aeiy +ve++ +vee+l + q+  d ++r+ lfvkl +G  ++ +l   ik+
  NCBI__GCF_002117405.1:WP_085773781.1 513 GFIIHGRSDATLNPQGVRIGTAEIYRIVEAFMQVEECLAVCQDASD-GQRILLFVKLRAGERMSSELSAGIKH 584
                                           **********************************************.689*********************** PP

                             TIGR01217 587 airaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleel 650
                                           ++r ++sprhvp+ iie +++p+t sGk ve+av+dvv+G+pv+n++al+npe+ld++++ ++l
  NCBI__GCF_002117405.1:WP_085773781.1 585 RLREEASPRHVPAAIIEAPELPHTRSGKLVELAVRDVVHGRPVKNREALANPESLDFFAQTPRL 648
                                           **********************************************************998875 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 21.00
//
[ok]

This GapMind analysis is from Apr 09 2024. 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