Alignments for a candidate for aacS in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Rhizobium leguminosarum bv. trifolii WSM1325

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012756113.1 RLEG_RS02080 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000023185.1:WP_012756113.1
          Length = 650

 Score = 1053 bits (2724), Expect = 0.0
 Identities = 506/649 (77%), Positives = 560/649 (86%)

Query: 1   MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC 60
           MQ  RPLWVP  + + +SP+  F++ C   FG S + ++  H WSV+ER  FW+AVW+ C
Sbjct: 1   MQDNRPLWVPSEDAIAKSPIHAFMERCNADFGLSLSGFEDLHAWSVAERENFWSAVWDFC 60

Query: 61  KVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDE 120
            V GE G + L +GDRML+ARFFP+A LNFAENLL   G GDA+IFRGEDK   R +WD 
Sbjct: 61  GVQGERGAEVLANGDRMLEARFFPDATLNFAENLLSGRGDGDAIIFRGEDKAEDRWSWDR 120

Query: 121 LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL 180
           LRALVS+LQQA  A+GIG GDRVAAMMPNMPET+A MLA AS+GAIWSSCSPDFGEQGVL
Sbjct: 121 LRALVSKLQQAFVARGIGKGDRVAAMMPNMPETVAAMLAAASIGAIWSSCSPDFGEQGVL 180

Query: 181 DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGG 240
           DRFGQI P+LFI CD YWY+GK QDV +KV  VAK+L  PTVIV YAG++ A+A    G 
Sbjct: 181 DRFGQIEPRLFIACDAYWYSGKLQDVGAKVATVAKTLAIPTVIVHYAGNAEAVARKTPGA 240

Query: 241 VTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300
           +TL  F+A ++A  + F RL F HPLYILFSSGTTGVPKCIVHSAGGTLLQHLKE R HC
Sbjct: 241 LTLEAFVAPYEAREVEFTRLAFAHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEQRLHC 300

Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360
           GL+ GE+LFYFTTCGWMMWNWL SGLA GATLCL+DGSPF PDGNVLFDYA AE+F +FG
Sbjct: 301 GLQAGEKLFYFTTCGWMMWNWLVSGLASGATLCLFDGSPFAPDGNVLFDYAEAEKFVIFG 360

Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420
           TSAKYIDAVRKGG TP  +HDLSSLRLMTSTGSPLSPEGF+FVYEGIK DVQLASISGGT
Sbjct: 361 TSAKYIDAVRKGGLTPRVSHDLSSLRLMTSTGSPLSPEGFTFVYEGIKKDVQLASISGGT 420

Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480
           DIVSCFVLGNPL+PVWRGEIQG GLGLAVDVWND+GKPVRGEKGELVCT+AFPSMPVMFW
Sbjct: 421 DIVSCFVLGNPLQPVWRGEIQGAGLGLAVDVWNDDGKPVRGEKGELVCTKAFPSMPVMFW 480

Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540
           NDPDGAKYRAAYFDRFDNVWCHGDFAEWT HGG+VIHGRSDATLNPGGVRIGTAEIYNQV
Sbjct: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTEHGGLVIHGRSDATLNPGGVRIGTAEIYNQV 540

Query: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
           EQM EVAEALCIGQDW+DDVRV+LFVRLA  V+LTE L + IK+RIR+GASPRHVPAKII
Sbjct: 541 EQMAEVAEALCIGQDWDDDVRVILFVRLAPDVKLTEDLVKAIKSRIRTGASPRHVPAKII 600

Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649
           AVADIPRTKSGKIVELAVR+VVHGRPVKN+EALANPEAL LFAGL EL+
Sbjct: 601 AVADIPRTKSGKIVELAVREVVHGRPVKNQEALANPEALGLFAGLSELR 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: 1637
Number of extensions: 62
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 WP_012756113.1 RLEG_RS02080 (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.3256179.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 1045.5   0.0          0 1045.3   0.0    1.0  1  NCBI__GCF_000023185.1:WP_012756113.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023185.1:WP_012756113.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1045.3   0.0         0         0       3     652 .]       4     650 .]       2     650 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1045.3 bits;  conditional E-value: 0
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 
                                           +++lw+p ++ +++++++ f + +   fG++l+++++l+ wsv e+++fw+avw+f++v ++++ + + ++++
  NCBI__GCF_000023185.1:WP_012756113.1   4 NRPLWVPSEDAIAKSPIHAFMERCNADFGLSLSGFEDLHAWSVAERENFWSAVWDFCGVQGERGAEVLANGDR 76 
                                           468********************************************************************** PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpn 148
                                           ml+arffp+a+ln+aenll  +g +da+++++e+k   + +++ lr++v++l++a+ a G++kGdrva+++pn
  NCBI__GCF_000023185.1:WP_012756113.1  77 MLEARFFPDATLNFAENLLSGRGDGDAIIFRGEDKAEDRWSWDRLRALVSKLQQAFVARGIGKGDRVAAMMPN 149
                                           ************************************************************************* PP

                             TIGR01217 149 ipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlra 221
                                           +pe+vaa+la+as+GaiwsscspdfG++gvldrf+qiep+l++++d+y+y+Gk +d+  kv+ vak l+   +
  NCBI__GCF_000023185.1:WP_012756113.1 150 MPETVAAMLAAASIGAIWSSCSPDFGEQGVLDRFGQIEPRLFIACDAYWYSGKLQDVGAKVATVAKTLA--IP 220
                                           *********************************************************************..99 PP

                             TIGR01217 222 vvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhl 294
                                           +v++ y+g++e++a k +galtle ++a ++a e++f +l f hplyilfssGttGvpk+ivhsaGGtl+qhl
  NCBI__GCF_000023185.1:WP_012756113.1 221 TVIVHYAGNAEAVARKTPGALTLEAFVAPYEAREVEFTRLAFAHPLYILFSSGTTGVPKCIVHSAGGTLLQHL 293
                                           ************************************************************************* PP

                             TIGR01217 295 kehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyv 367
                                           ke++lhc+l+ g++l+y+tt+Gwmmwn+lvsgla Gatl+l+dGsp+ p++nvlfd+ae+e++ ++Gtsaky+
  NCBI__GCF_000023185.1:WP_012756113.1 294 KEQRLHCGLQAGEKLFYFTTCGWMMWNWLVSGLASGATLCLFDGSPFAPDGNVLFDYAEAEKFVIFGTSAKYI 366
                                           ************************************************************************* PP

                             TIGR01217 368 savrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGe 440
                                           +avrk+gl+p  +hdls+lrl++stGspl+pegf +vye+ik dv+lasisGGtdivscfv++np+ pv++Ge
  NCBI__GCF_000023185.1:WP_012756113.1 367 DAVRKGGLTPRVSHDLSSLRLMTSTGSPLSPEGFTFVYEGIKKDVQLASISGGTDIVSCFVLGNPLQPVWRGE 439
                                           ************************************************************************* PP

                             TIGR01217 441 iqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                           iq+ glGlav++w+++Gkpv+gekGelv+tk++psmpv+fwnd+dG+kyr+ayfd++++vw+hGd++e+t +G
  NCBI__GCF_000023185.1:WP_012756113.1 440 IQGAGLGLAVDVWNDDGKPVRGEKGELVCTKAFPSMPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTEHG 512
                                           ************************************************************************* PP

                             TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikd 586
                                           g+vihGrsdatlnp+Gvr+G+aeiyn+ve++ ev+e+l+igq+++d ++rv+lfv+la+ ++l+e+lvk ik+
  NCBI__GCF_000023185.1:WP_012756113.1 513 GLVIHGRSDATLNPGGVRIGTAEIYNQVEQMAEVAEALCIGQDWDD-DVRVILFVRLAPDVKLTEDLVKAIKS 584
                                           **********************************************.************************** PP

                             TIGR01217 587 airaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelks 652
                                           +ir+g+sprhvp+kii+va+iprt+sGk+ve+av++vv+G+pv+n++al+npeal l+++l+el++
  NCBI__GCF_000023185.1:WP_012756113.1 585 RIRTGASPRHVPAKIIAVADIPRTKSGKIVELAVREVVHGRPVKNQEALANPEALGLFAGLSELRD 650
                                           ***************************************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 18.78
//
[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