GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Paraburkholderia bryophila 376MFSha3.1

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate H281DRAFT_04626 H281DRAFT_04626 acetyl-CoA acyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__Burk376:H281DRAFT_04626
          Length = 399

 Score =  353 bits (907), Expect = e-102
 Identities = 193/395 (48%), Positives = 266/395 (67%), Gaps = 8/395 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           +++A IV+ +RTP+GKA +G     RPD+L    ++  + +  G +   I+D I+GCA P
Sbjct: 5   LQDAYIVAASRTPIGKAPRGMFRNTRPDELLVHAIRSAVAQVPGLDTKVIEDAIVGCAIP 64

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQGLN+AR    LAGLP +V  +TVNR+C+SGL ++A AA++I +G  D  IAGG ES
Sbjct: 65  EAEQGLNVARMGALLAGLPNSVGGVTVNRFCASGLTALAMAADRIRVGESDAMIAGGCES 124

Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMS--MGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           MS VPMMG+    +  + ++  +  ++  MG TAE+VA+++ +SRE QDAF+V SH+ A 
Sbjct: 125 MSMVPMMGNKPSLSPHIFDRNEDVGIAYGMGLTAEKVAERWKISREAQDAFSVESHRRAI 184

Query: 178 KALAEGKFKDEIVPVEVTVTEIGEDHKPME---KQFVFSQDEGVRPQTTADILSTLRPAF 234
            A   G+F DEI     T+TE   D    E   K    + DEG R  T+ + L+ LR  F
Sbjct: 185 AAQQAGEFNDEIAAY--TITERFPDLATGEVRVKTREVALDEGPRADTSLEGLAKLRTVF 242

Query: 235 SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEA 294
           +  G+VTAGNSSQTSDGA A++++  +      L PL +F SFAV GVPPE+MGIGP EA
Sbjct: 243 ANKGSVTAGNSSQTSDGAGALIVVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEA 302

Query: 295 IPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGT 354
           IP ALK AGL+  DI   ELNEAFA+Q++ VI++LG+D  K+N  GGAIALGHPLG TG 
Sbjct: 303 IPAALKAAGLKQDDIDWIELNEAFAAQSLAVIQDLGLDPSKINPLGGAIALGHPLGATGA 362

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
               +++H ++RRN ++G+VTMC+G GMGAAG+ E
Sbjct: 363 IRASTVVHGLRRRNYKYGMVTMCVGTGMGAAGIIE 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: 435
Number of extensions: 17
Number of successful extensions: 4
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 H281DRAFT_04626 H281DRAFT_04626 (acetyl-CoA acyltransferase)
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.494031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.5e-143  462.0   2.3   8.4e-143  461.9   2.3    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04626  H281DRAFT_04626 acetyl-CoA acylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04626  H281DRAFT_04626 acetyl-CoA acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.9   2.3  8.4e-143  8.4e-143       1     385 []      10     397 ..      10     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 461.9 bits;  conditional E-value: 8.4e-143
                                    TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaRe 63 
                                                  iv+a Rtpig + +g ++++++++Ll+++i+++++++ gld + i+++i+G++++++eq  n+aR+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626  10 IVAASRTPIGkAPRGMFRNTRPDELLVHAIRSAVAQVpGLDTKVIEDAIVGCAIPEAEQgLNVARM 75 
                                                  8*********988***************************************************** PP

                                    TIGR01930  64 aalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrresl 129
                                                   al aglp+sv ++tvnr+CaSgl+A+a+aa++i++Ge d+++aGG+EsmS vp++ ++     sl
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626  76 GALLAGLPNSVGGVTVNRFCASGLTALAMAADRIRVGESDAMIAGGCESMSMVPMMGNKP----SL 137
                                                  ******************************************************987765....89 PP

                                    TIGR01930 130 klgkakledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivp 195
                                                  +++ +++++    d v  ++ mg tAe++a++++isRe qD+++++Sh++a +A+++g+f+dei  
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626 138 SPHIFDRNE----D-VGIAYGMGLTAEKVAERWKISREAQDAFSVESHRRAIAAQQAGEFNDEIAA 198
                                                  998888888....3.34689********************************************** PP

                                    TIGR01930 196 vevkgk............kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaa 249
                                                  +++ ++            ++ v+ Deg+r++t+le LakL+++f++ kgs vtAgNssq++DGA+a
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626 199 YTITERfpdlatgevrvkTREVALDEGPRADTSLEGLAKLRTVFAN-KGS-VTAGNSSQTSDGAGA 262
                                                  ****99**********998899**********************95.8*7.*************** PP

                                    TIGR01930 250 lllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAa 315
                                                  l+++se+++k+++ltplar+vs+av gv+pe+mg+gp +Ai++aLk agl+ +did++E+nEAFAa
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626 263 LIVVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIPAALKAAGLKQDDIDWIELNEAFAA 328
                                                  ****************************************************************** PP

                                    TIGR01930 316 qvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaA 381
                                                  q lav+++lg ld++k+N  GGAiAlGHPlGa+Ga+   t+++ L++r+ kyG++t+Cvg+G+GaA
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626 329 QSLAVIQDLG-LDPSKINPLGGAIALGHPLGATGAIRASTVVHGLRRRNYKYGMVTMCVGTGMGAA 393
                                                  **********.99***************************************************** PP

                                    TIGR01930 382 vile 385
                                                   i+e
  lcl|FitnessBrowser__Burk376:H281DRAFT_04626 394 GIIE 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: 00:00:00.00
# Mc/sec: 21.77
//
[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