Alignments for a candidate for aacS in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Burkholderia phytofirmans PsJN

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate BPHYT_RS23420 BPHYT_RS23420 acetoacetyl-CoA synthase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__BFirm:BPHYT_RS23420
          Length = 1021

 Score =  415 bits (1067), Expect = e-120
 Identities = 258/650 (39%), Positives = 338/650 (52%), Gaps = 18/650 (2%)

Query: 1   MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAV--WE 58
           M A  P++    E V  S M+ F        G  FADY   H +S  E   FW     W 
Sbjct: 13  MYAREPVFQNLPERVAGSRMSRFTAALENFTGERFADYPELHAYSTREFRRFWQCFLQWT 72

Query: 59  HCKVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGD---ALIFRGEDKVSYR 115
                G   E A V GD    A FFP   LN+A+++L    + D   AL  R  D     
Sbjct: 73  EGMEWGGKAEPACV-GDECETASFFPNVELNYAQSVLGSKIAPDESPALTARYADGRRET 131

Query: 116 LTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFG 175
           +T  ELR  V+RL  +L   G+  GDR  A+M N    I   LA  ++GA  S+ +P+ G
Sbjct: 132 MTRGELRERVARLACSLNELGLCPGDRAVAIMRNDAHAIIAALAVTALGATLSTAAPETG 191

Query: 176 EQGVLDRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAP 235
            Q +LDRF  + P++               + S V AVA +L  PT+      D   L  
Sbjct: 192 VQAILDRFEPLEPRILFAHTTQRSFDTAGSIASHVAAVAAAL--PTLTHVVCLDETPLPS 249

Query: 236 TV-EGGVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLK 294
           TV +   +L D I    A    + R PF HPL+I+FSSGTTG PKCIVH AGGTLL+HLK
Sbjct: 250 TVSQPQHSLRDLIVQGDAARFAWRRFPFNHPLFIMFSSGTTGKPKCIVHGAGGTLLEHLK 309

Query: 295 EHRFHCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAE 354
           EH+ H  L  G++L++ T+C WMMWNW  S LA G  +  YDG     + + L+   A E
Sbjct: 310 EHQLHSDLGPGDKLYFHTSCSWMMWNWQLSALASGVEIVTYDGP--VSEVDTLWRMVADE 367

Query: 355 RFAVFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLA 414
           R  VFGTS  Y+      G  P     L +LR M STG+ L    F +V   +KP +QL 
Sbjct: 368 RVTVFGTSPAYLKMCEDAGLKPGEQFGLHALRAMMSTGAVLYDSQFEWVRAYVKP-LQLQ 426

Query: 415 SISGGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPS 474
           SISGGTDI+ CFVLGNP  PV+ GE Q   LGL V  WN EG P     GELVC   FPS
Sbjct: 427 SISGGTDIIGCFVLGNPNLPVYAGEAQCRSLGLDVQAWN-EGAPT-SMTGELVCVNPFPS 484

Query: 475 MPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTA 534
            P+ F+ D DG+++ AAYF     VW HGD  E++  G   +HGRSD  LN  G+ +   
Sbjct: 485 RPLGFFGDADGSRFHAAYFKANPGVWTHGDIIEFSAQGSARLHGRSDGVLNVRGINVSPG 544

Query: 535 EIYNQVEQMDEVAEALCIGQDWED----DVRVVLFVRLARGVELTEALTREIKNRIRSGA 590
           EIY  V  + E+ +++ + Q   D      RVVL + L RG +++ AL   ++  +    
Sbjct: 545 EIYRIVSGIGEINQSMVVAQTTHDASGSGQRVVLLLVLRRGAKMSAALASRVRRELMLQG 604

Query: 591 SPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALD 640
           S   VP  I  V  +P T +GK  E A RD V+G PV+N  +LANP  ++
Sbjct: 605 SAALVPDVIAEVEALPVTHNGKASEAAARDAVNGLPVRNLSSLANPGCVE 654


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: 1744
Number of extensions: 100
Number of successful extensions: 8
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: 1021
Length adjustment: 41
Effective length of query: 609
Effective length of database: 980
Effective search space:   596820
Effective search space used:   596820
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: 56 (26.2 bits)

Align candidate BPHYT_RS23420 BPHYT_RS23420 (acetoacetyl-CoA synthase)
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.31967.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.3e-179  584.3   0.0   1.9e-179  583.8   0.0    1.1  1  lcl|FitnessBrowser__BFirm:BPHYT_RS23420  BPHYT_RS23420 acetoacetyl-CoA sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS23420  BPHYT_RS23420 acetoacetyl-CoA synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.8   0.0  1.9e-179  1.9e-179       7     641 ..      20     653 ..      15     663 .. 0.93

  Alignments for each domain:
  == domain 1  score: 583.8 bits;  conditional E-value: 1.9e-179
                                TIGR01217   7 wepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvf..ssaekevvdds 74 
                                              ++   erv+ +r++rf aa  + +G  ++dy +l+ +s +e+  fw+ + ++++ +    +ae + v ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420  20 FQNLPERVAGSRMSRFTAALENFTGERFADYPELHAYSTREFRRFWQCFLQWTEGMEwgGKAEPACV-GD 88 
                                              55556789********************************************986541134444555.55 PP

                                TIGR01217  75 kmlaarffpgarlnyaenllrkkgs...edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdr 141
                                              +  +a ffp+  lnya+ +l  k +    +al  +  +     +t  elr++va+la +l +lG+ +Gdr
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420  89 ECETASFFPNVELNYAQSVLGSKIApdeSPALTARYADGRRETMTRGELRERVARLACSLNELGLCPGDR 158
                                              678899**************98866544677778888889999*************************** PP

                                TIGR01217 142 vagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvre 211
                                               ++++ n ++a+ a la +++Ga  s+++p+ G++++ldrf+ +ep++lf+  + +         ++v++
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 159 AVAIMRNDAHAIIAALAVTALGATLSTAAPETGVQAILDRFEPLEPRILFAHTTQRSFDTAGSIASHVAA 228
                                              *****************************************************9999999999******* PP

                                TIGR01217 212 vakelpdlravvlipyv.gdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpk 280
                                              va  lp+l +vv +    +++   +p       l dl+   +aa+  + + pf+hpl+i+fssGttG pk
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 229 VAAALPTLTHVVCLDETpLPSTVSQP----QHSLRDLIVQGDAARFAWRRFPFNHPLFIMFSSGTTGKPK 294
                                              ************98765133333334....66799****99***************************** PP

                                TIGR01217 281 aivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfd 350
                                              +ivh aGGtl++hlkeh+lh+dl++gd+l+++t++ wmmwn+  s+la G  +v ydG   v + + l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 295 CIVHGAGGTLLEHLKEHQLHSDLGPGDKLYFHTSCSWMMWNWQLSALASGVEIVTYDGP--VSEVDTLWR 362
                                              **********************************************************5..78999**** PP

                                TIGR01217 351 laeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGG 420
                                              +++ e++tv+Gts +y+++++++glkp +++ l+alr+++stG+ l    fe+v   +k+ ++l sisGG
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 363 MVADERVTVFGTSPAYLKMCEDAGLKPGEQFGLHALRAMMSTGAVLYDSQFEWVRAYVKP-LQLQSISGG 431
                                              ******************************************************999987.9******** PP

                                TIGR01217 421 tdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyr 490
                                              tdi+ cfv++np lpvy Ge q+++lGl+v+aw+e G p t  +Gelv+ +p+ps p+ f+ d dGs+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 432 TDIIGCFVLGNPNLPVYAGEAQCRSLGLDVQAWNE-GAP-TSMTGELVCVNPFPSRPLGFFGDADGSRFH 499
                                              *********************************96.666.4679************************** PP

                                TIGR01217 491 kayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedg 560
                                              +ayf+  pgvw+hGd ie++++G+  +hGrsd+ ln  G+ +   eiy +v  + e+++s+v++q ++d 
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 500 AAYFKANPGVWTHGDIIEFSAQGSARLHGRSDGVLNVRGINVSPGEIYRIVSGIGEINQSMVVAQTTHDA 569
                                              *****************************************************************99995 PP

                                TIGR01217 561 ...eervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGk 627
                                                 ++rvvl++ l +Ga+++ al  ++++ + ++ s+  vp+ i ev+ +p t +Gk  e a +d v+G 
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 570 sgsGQRVVLLLVLRRGAKMSAALASRVRRELMLQGSAALVPDVIAEVEALPVTHNGKASEAAARDAVNGL 639
                                              33379***************************************************************** PP

                                TIGR01217 628 pvenkgalsnpeal 641
                                              pv n  +l+np  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS23420 640 PVRNLSSLANPGCV 653
                                              **********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (1021 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 17.76
//
[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