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.21354.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: 00:00:00.02
# Mc/sec: 7.43
//
[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:

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:

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:

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:

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