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 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate H281DRAFT_00852 H281DRAFT_00852 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__Burk376:H281DRAFT_00852
          Length = 393

 Score =  669 bits (1725), Expect = 0.0
 Identities = 337/392 (85%), Positives = 365/392 (93%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           MTDVVIVSAARTAVGKFGGSLAKI APELGA VI+A LERAG+KPEQVSEVI+GQVLTAG
Sbjct: 1   MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLERAGMKPEQVSEVILGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
           SGQNPARQ+ IKAGLPA VP MTINKVCGSGLKAVMLAANAI+AGDA+IV+AGGQENMSA
Sbjct: 61  SGQNPARQSLIKAGLPAAVPGMTINKVCGSGLKAVMLAANAIIAGDADIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           APHVLPGSRDGFRMGDAKL+D+MIVDGLWDVYNQYHMG+TAENVAKE+ ITRE QD FA 
Sbjct: 121 APHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGVTAENVAKEFDITREQQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQNKAEAAQK+G+FD+EIVPV IPQRKGDPV F TDEFVR G T +S++GLKPAF K G
Sbjct: 181 LSQNKAEAAQKSGRFDDEIVPVEIPQRKGDPVRFATDEFVRHGVTAESLAGLKPAFSKEG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           TVTAANASGLNDGAAAV+VMSA KA+ LGLTPLA IK+YANAGVDPKVMGMGPVPAS+R 
Sbjct: 241 TVTAANASGLNDGAAAVLVMSAKKAEALGLTPLARIKAYANAGVDPKVMGMGPVPASRRC 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L RA W+  DLDLMEINEAFAAQALAVH+QMGWDTSK+NVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LERAGWSVNDLDLMEINEAFAAQALAVHKQMGWDTSKINVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLL+EM++RDAKKGLASLCIGGGMGVALA+ER
Sbjct: 361 TLLYEMQKRDAKKGLASLCIGGGMGVALALER 392


Lambda     K      H
   0.315    0.131    0.369 

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: 599
Number of extensions: 18
Number of successful extensions: 1
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: 393
Length of database: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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_00852 H281DRAFT_00852 (acetyl-CoA acetyltransferase)
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.644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.5e-155  503.1   7.8   2.8e-155  502.9   7.8    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00852  H281DRAFT_00852 acetyl-CoA acety


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00852  H281DRAFT_00852 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.9   7.8  2.8e-155  2.8e-155       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 502.9 bits;  conditional E-value: 2.8e-155
                                    TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaal 66 
                                                  iv+a+Rt++gk+ggsl+++ a +L+a+vi+++lerag++pe++ evilG+vl+ag+++n+aR+ ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00852   6 IVSAARTAVGKFGGSLAKIAAPELGATVIRAVLERAGMKPEQVSEVILGQVLTAGSGQNPARQSLI 71 
                                                  8***************************************************************** PP

                                    TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklg 132
                                                  +aglp  vp++t+n+vC+Sgl+Av+laa++i aG+ad+v+aGG E+mS +p++l+ s  r+++++g
  lcl|FitnessBrowser__Burk376:H281DRAFT_00852  72 KAGLPAAVPGMTINKVCGSGLKAVMLAANAIIAGDADIVIAGGQENMSAAPHVLPGS--RDGFRMG 135
                                                  *******************************************************98..9****** PP

                                    TIGR01930 133 kakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivp 195
                                                  +akl d+++ d+   v+++++mg+tAen+ak+++i+Re+qD++a+ S++ka++A+++g+f+deivp
  lcl|FitnessBrowser__Burk376:H281DRAFT_00852 136 DAKLIDSMIVDGlwdVYNQYHMGVTAENVAKEFDITREQQDAFAALSQNKAEAAQKSGRFDDEIVP 201
                                                  ***************99************************************************* PP

                                    TIGR01930 196 vevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseeva 258
                                                  ve++++   ++ +++De +r ++t+e+La+Lkpaf + +g tvtA+N+s+lnDGAaa+l+ms ++a
  lcl|FitnessBrowser__Burk376:H281DRAFT_00852 202 VEIPQRkgdPVRFATDEFVRHGVTAESLAGLKPAFSK-EG-TVTAANASGLNDGAAAVLVMSAKKA 265
                                                  ****999*999************************95.8*.6************************ PP

                                    TIGR01930 259 kelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekel 324
                                                  ++lgltplari ++a+agvdp++mg+gpvpA++++L++ag+s++d+dl+EinEAFAaq+lav k++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00852 266 EALGLTPLARIKAYANAGVDPKVMGMGPVPASRRCLERAGWSVNDLDLMEINEAFAAQALAVHKQM 331
                                                  ****************************************************************** PP

                                    TIGR01930 325 gsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                  g  d++k+NvnGGAiA+GHP+GasG+ri++tll+e+++r++k Gla+lC+ggG+G+A+ le
  lcl|FitnessBrowser__Burk376:H281DRAFT_00852 332 G-WDTSKINVNGGAIAIGHPIGASGCRILVTLLYEMQKRDAKKGLASLCIGGGMGVALALE 391
                                                  *.88*****************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 7.48
//
[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