GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Burkholderia phytofirmans PsJN

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA
           acetyltransferase
          Length = 393

 Score =  664 bits (1714), Expect = 0.0
 Identities = 335/392 (85%), Positives = 362/392 (92%)

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

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
           SGQNPARQA IKAGLP  VP MTIN VCGSGLKAVMLAANAI+AGDA+IVVAGGQENMSA
Sbjct: 61  SGQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           APHVLPGSRDGFRMGDAKL+D+MIVDGLWDVYNQYHMG+TAENVAKEYGITRE QD FA 
Sbjct: 121 APHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGVTAENVAKEYGITREQQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQNKAEAAQKAG+FD+EIVPV IPQRKG+P+ F TDEFVR G T +S++GLKPAF K G
Sbjct: 181 LSQNKAEAAQKAGRFDDEIVPVEIPQRKGEPLRFATDEFVRHGVTAESLAGLKPAFSKEG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTAANASGLNDGAAAV+VMSA KA+ LGL PLA IK+YA +G+DPKVMGMGPVPAS+R 
Sbjct: 241 SVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVMGMGPVPASRRC 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L RA WTP DLDLMEINEAFAAQA AV+QQMGWDTSK+NVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LERAGWTPADLDLMEINEAFAAQACAVNQQMGWDTSKINVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM++RDAKKGLASLCIGGGMGVALA+ER
Sbjct: 361 TLLHEMQKRDAKKGLASLCIGGGMGVALALER 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: 594
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 BPHYT_RS09150 BPHYT_RS09150 (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.3708.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.6e-153  497.2   7.9   1.8e-153  497.0   7.9    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS09150  BPHYT_RS09150 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS09150  BPHYT_RS09150 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.0   7.9  1.8e-153  1.8e-153       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 497.0 bits;  conditional E-value: 1.8e-153
                                TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaagl 70 
                                              iv+a+Rt++gk+ggsl+++ a +L+a+vi+++leragl+pe++ evilG+vl+ag+++n+aR+a+++agl
  lcl|FitnessBrowser__BFirm:BPHYT_RS09150   6 IVSAARTAVGKFGGSLAKIAAPELGATVIRAVLERAGLKPEQVSEVILGQVLTAGSGQNPARQAVIKAGL 75 
                                              8********************************************************************* PP

                                TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledql 140
                                              p+ vp++t+n vC+Sgl+Av+laa++i aG+ad+vvaGG E+mS +p++l+ s  r+++++g+akl d++
  lcl|FitnessBrowser__BFirm:BPHYT_RS09150  76 PTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENMSAAPHVLPGS--RDGFRMGDAKLIDSM 143
                                              ***************************************************98..9************** PP

                                TIGR01930 141 lkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkv 204
                                              + d+   v+++++mg+tAen+ak+ygi+Re+qD++a+ S++ka++A+++g+f+deivpve++++   +  
  lcl|FitnessBrowser__BFirm:BPHYT_RS09150 144 IVDGlwdVYNQYHMGVTAENVAKEYGITREQQDAFAALSQNKAEAAQKAGRFDDEIVPVEIPQRkgePLR 213
                                              *******99*****************************************************99999999 PP

                                TIGR01930 205 vskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaav 274
                                              +++De +r ++t+e+La+Lkpaf + +gs vtA+N+s+lnDGAaa+l+ms ++a++lgl+plari ++a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS09150 214 FATDEFVRHGVTAESLAGLKPAFSK-EGS-VTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYAT 281
                                              ***********************95.8*7.**************************************** PP

                                TIGR01930 275 agvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHP 344
                                              +g+dp++mg+gpvpA++++L++ag++  d+dl+EinEAFAaq+ av++++g  d++k+NvnGGAiA+GHP
  lcl|FitnessBrowser__BFirm:BPHYT_RS09150 282 SGLDPKVMGMGPVPASRRCLERAGWTPADLDLMEINEAFAAQACAVNQQMG-WDTSKINVNGGAIAIGHP 350
                                              ***************************************************.88**************** PP

                                TIGR01930 345 lGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                              +GasG+ri++tll+e+++r++k Gla+lC+ggG+G+A+ le
  lcl|FitnessBrowser__BFirm:BPHYT_RS09150 351 IGASGCRILVTLLHEMQKRDAKKGLASLCIGGGMGVALALE 391
                                              *************************************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: 00:00:00.01
# Mc/sec: 9.55
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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