Alignments for a candidate for aacS in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Sinorhizobium meliloti 1021

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate SMc00774 SMc00774 acetoacetyl-CoA synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__Smeli:SMc00774
          Length = 650

 Score = 1337 bits (3461), Expect = 0.0
 Identities = 650/650 (100%), Positives = 650/650 (100%)

Query: 1   MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC 60
           MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC
Sbjct: 1   MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC 60

Query: 61  KVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDE 120
           KVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDE
Sbjct: 61  KVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDE 120

Query: 121 LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL 180
           LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL
Sbjct: 121 LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL 180

Query: 181 DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGG 240
           DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGG
Sbjct: 181 DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGG 240

Query: 241 VTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300
           VTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC
Sbjct: 241 VTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300

Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360
           GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG
Sbjct: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360

Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420
           TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT
Sbjct: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420

Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480
           DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW
Sbjct: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480

Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540
           NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV
Sbjct: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540

Query: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
           EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII
Sbjct: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600

Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS
Sbjct: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 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: 1804
Number of extensions: 49
Number of successful extensions: 1
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 SMc00774 SMc00774 (acetoacetyl-CoA synthetase)
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.23521.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 1202.2   0.0          0 1202.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00774  SMc00774 acetoacetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00774  SMc00774 acetoacetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1202.1   0.0         0         0       3     652 .]       4     650 .]       2     650 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1202.1 bits;  conditional E-value: 0
                           TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskml 77 
                                         e++lw+pd+e+v+++++a+f++++gerfG++++dyda+++wsv+e++afw+avwe+++v+++s+ek++vd+++ml
  lcl|FitnessBrowser__Smeli:SMc00774   4 ERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGESGEKALVDGDRML 78 
                                         567************************************************************************ PP

                           TIGR01217  78 aarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipea 152
                                         +arffp+arln+aenllrk+gs+dal++++e+k+s+++t++elr++v++l++alra+G+++Gdrva+++pn+pe+
  lcl|FitnessBrowser__Smeli:SMc00774  79 DARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNMPET 153
                                         *************************************************************************** PP

                           TIGR01217 153 vaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipy 227
                                         +a++latasvGaiwsscspdfG++gvldrf+qi+pkl++++dgy+ynGk++d+++kvr+vak+l+  +++v++py
  lcl|FitnessBrowser__Smeli:SMc00774 154 IALMLATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLG--APTVIVPY 226
                                         *****************************************************************..9******* PP

                           TIGR01217 228 vgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcd 302
                                         +gd+++lap+veg++tl+d++a++qa++lvfe+lpf+hplyilfssGttGvpk+ivhsaGGtl+qhlkeh++hc+
  lcl|FitnessBrowser__Smeli:SMc00774 227 AGDSAALAPTVEGGVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
                                         *************************************************************************** PP

                           TIGR01217 303 ltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkp 377
                                         l+dg+rl+y+tt+Gwmmwn+l+sgla+Gatl+lydGsp++p++nvlfd+a++e+++v+Gtsaky++avrk+g++p
  lcl|FitnessBrowser__Smeli:SMc00774 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSAKYIDAVRKGGFTP 376
                                         *************************************************************************** PP

                           TIGR01217 378 arthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlavea 452
                                         arthdls+lrl++stGspl+pegf++vye+ik+dv+lasisGGtdivscfv++np++pv++Geiq+pglGlav++
  lcl|FitnessBrowser__Smeli:SMc00774 377 ARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDV 451
                                         *************************************************************************** PP

                           TIGR01217 453 wdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnp 527
                                         w++eGkpv+gekGelv+t+++psmpv+fwnd+dG+kyr+ayfd++++vw+hGd++e+tp+GgivihGrsdatlnp
  lcl|FitnessBrowser__Smeli:SMc00774 452 WNDEGKPVRGEKGELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNP 526
                                         *************************************************************************** PP

                           TIGR01217 528 nGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskii 602
                                         +Gvr+G+aeiyn+ve++dev+e+l+igq++ed ++rvvlfv+la+G++l+eal++eik++ir+g+sprhvp+kii
  lcl|FitnessBrowser__Smeli:SMc00774 527 GGVRIGTAEIYNQVEQMDEVAEALCIGQDWED-DVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
                                         ********************************.****************************************** PP

                           TIGR01217 603 evagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelks 652
                                         +va+iprt+sGk+ve+av+dvv+G+pv+nk+al+npealdl+++leelks
  lcl|FitnessBrowser__Smeli:SMc00774 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
                                         ***********************************************996 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 9.07
//
[ok]

This GapMind analysis is from Sep 17 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