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

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.13310.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: 00:00:00.02
# Mc/sec: 7.35
//
[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