Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate Ac3H11_1916 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1916
          Length = 399

 Score =  341 bits (874), Expect = 2e-98
 Identities = 184/393 (46%), Positives = 257/393 (65%), Gaps = 5/393 (1%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           +++A IV+  RTP+G++ +G     RPDDL    +K  + +    +   I+D IIGC+ P
Sbjct: 6   VQDAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGCSFP 65

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           E EQG+NMAR    LA   + V  +TVNR+C+SG+ ++  AA++I +G  D  IAGGAES
Sbjct: 66  EGEQGMNMARIAVGLA-FNHPVGGVTVNRFCASGITALQMAADRIRVGEADVLIAGGAES 124

Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMS--MGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           MS VPM G+    N  +  +  +  ++  MG TAE+VA+++ +SRE QDAFA+ SH  A 
Sbjct: 125 MSLVPMGGNKPSFNAEVFARDEDVGIAYGMGLTAEKVAQQWKISREAQDAFALESHLRAI 184

Query: 178 KALAEGKFKDEIVPVEVTVTEIG-EDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSV 236
           KA   G+F DEI P EV          + +EK+   S DEG RP T+ + L+ L+P F+ 
Sbjct: 185 KAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRPDTSLEGLAKLKPVFAA 244

Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296
            G+VTAGNSSQTSDGA A+++   +     GL PL +F S+A  GVPPE+MGIGP+EAIP
Sbjct: 245 RGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGVPPEIMGIGPIEAIP 304

Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356
            AL+ AGL+  DIG +ELNEAFA+Q++ VI  LG++   VN  GGAIALGHPLG TG   
Sbjct: 305 AALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGLNPANVNPMGGAIALGHPLGATGAIR 364

Query: 357 TLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
             +++H ++R   ++G+VTMC+G G GAAG+ E
Sbjct: 365 AATVVHALRRHKLKYGMVTMCVGTGQGAAGIIE 397


Lambda     K      H
   0.316    0.133    0.377 

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: 426
Number of extensions: 19
Number of successful extensions: 5
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: 391
Length of database: 399
Length adjustment: 31
Effective length of query: 360
Effective length of database: 368
Effective search space:   132480
Effective search space used:   132480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate Ac3H11_1916 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.13002.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   3.5e-139  449.9   1.5   3.9e-139  449.8   1.5    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.8   1.5  3.9e-139  3.9e-139       1     385 []      11     397 ..      11     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 449.8 bits;  conditional E-value: 3.9e-139
                                        TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.an 59 
                                                      iv+a+Rtpig + +g +k+++++dLl+a+ik+++ ++  ldp++i+++i+G+++++geq +n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916  11 IVAATRTPIGrSGRGYFKNTRPDDLLVAAIKSAMLQVpTLDPKAIEDAIIGCSFPEGEQgMN 72 
                                                      8*********9889***********************9*********************999 PP

                                        TIGR01930  60 iaReaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillk 121
                                                      +aR  a+   +++ v ++tvnr+CaSg++A+++aa++i++Geadv++aGG+EsmS vp++ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916  73 MARI-AVGLAFNHPVGGVTVNRFCASGITALQMAADRIRVGEADVLIAGGAESMSLVPMGGN 133
                                                      9996.678889************************************************999 PP

                                        TIGR01930 122 aslrreslklgk.akledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaak 182
                                                      +     s++ +  a++ed      v  ++ mg tAe++a++++isRe qD++al+Sh +a k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916 134 KP----SFNAEVfARDED------VGIAYGMGLTAEKVAQQWKISREAQDAFALESHLRAIK 185
                                                      86....344433044444......5578********************************** PP

                                        TIGR01930 183 Aieegkfkdeivpvevkgk............kkvvskDegirpnttlekLakLkpafkekkg 232
                                                      A+++g+f dei+p+ev ++             ++vs Deg+rp+t+le LakLkp+f+   g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916 186 AQKAGEFTDEITPFEVVERspnlatgevvekRRTVSLDEGPRPDTSLEGLAKLKPVFAA-RG 246
                                                      ****************9999*********99999***********************96.8* PP

                                        TIGR01930 233 stvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaL 294
                                                      s vtAgNssq++DGA+al+++se+++k++gltplar+vs+a  gv+pe+mg+gp++Ai++aL
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916 247 S-VTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGVPPEIMGIGPIEAIPAAL 307
                                                      7.************************************************************ PP

                                        TIGR01930 295 kkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltl 356
                                                      + agl+ +di ++E+nEAFAaq lav++ lg l++++vN  GGAiAlGHPlGa+Ga+  +t+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916 308 RYAGLKSDDIGWYELNEAFAAQSLAVINTLG-LNPANVNPMGGAIALGHPLGATGAIRAATV 368
                                                      *******************************.88**************************** PP

                                        TIGR01930 357 lkeLkergkkyGlatlCvggGqGaAvile 385
                                                      +++L++++ kyG++t+Cvg+GqGaA i+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1916 369 VHALRRHKLKYGMVTMCVGTGQGAAGIIE 397
                                                      **************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (399 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: 00:00:00.01
# Mc/sec: 11.97
//
[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