Alignments for a candidate for kbl in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Burkholderia phytofirmans PsJN

Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate BPHYT_RS34655 BPHYT_RS34655 2-amino-3-ketobutyrate CoA ligase

Query= BRENDA::P0AB77
         (398 letters)



>FitnessBrowser__BFirm:BPHYT_RS34655
          Length = 399

 Score =  548 bits (1411), Expect = e-160
 Identities = 279/399 (69%), Positives = 325/399 (81%), Gaps = 2/399 (0%)

Query: 1   MRGEFYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPD 60
           MR  +   L   LE  RA+G +K ER+I S Q ADI +A+G+ V+NFCANNYLGLA+   
Sbjct: 1   MRDLYLAHLRGTLEQIRADGFYKSERVIASPQSADIRLANGTDVLNFCANNYLGLADDAR 60

Query: 61  LIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFE 120
           LI AAK G+D+ GFGMASVRFICGTQ  HK+LE+ LAAFL  +D ILYSSCFDANGGLFE
Sbjct: 61  LIDAAKQGLDNDGFGMASVRFICGTQTVHKDLERALAAFLQTDDCILYSSCFDANGGLFE 120

Query: 121 TLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIAT 180
           TLL   DAIISD LNHASIIDGVRL KAKR+RY NND+ +LEA+L EA+ AGAR  LIAT
Sbjct: 121 TLLDENDAIISDELNHASIIDGVRLSKAKRFRYKNNDLADLEAKLIEAKAAGARFTLIAT 180

Query: 181 DGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITG 240
           DGVFSMDG+IANL G+CDLAD+Y ALVMVDDSHAVGFVGE+GRG+ E+C V+ RVDIITG
Sbjct: 181 DGVFSMDGIIANLAGICDLADRYGALVMVDDSHAVGFVGEHGRGTPEHCGVLSRVDIITG 240

Query: 241 TLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMV--EAGSEL 298
           TLGKALGGASGGY AARKE+VE LRQRSRPYLFSN+L P+I AAS+KVLE++  + G++L
Sbjct: 241 TLGKALGGASGGYVAARKEIVELLRQRSRPYLFSNTLTPSIAAASLKVLELLASDEGAQL 300

Query: 299 RDRLWANARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYP 358
           R R+  N   FR +MSA GFTL   +H IIPVMLGDA +A K A  L KEG+YV GF +P
Sbjct: 301 RARVRENGAHFRSKMSALGFTLVPGEHPIIPVMLGDAQLASKMADALLKEGVYVIGFSFP 360

Query: 359 VVPKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVI 397
           VVPKG+ARIRTQMSAAHTPEQI RAV+AF R+G++LGVI
Sbjct: 361 VVPKGRARIRTQMSAAHTPEQIDRAVDAFARVGRELGVI 399


Lambda     K      H
   0.320    0.135    0.388 

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: 532
Number of extensions: 14
Number of successful extensions: 2
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: 398
Length of database: 399
Length adjustment: 31
Effective length of query: 367
Effective length of database: 368
Effective search space:   135056
Effective search space used:   135056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS34655 BPHYT_RS34655 (2-amino-3-ketobutyrate CoA ligase)
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# 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/TIGR01822.hmm
# target sequence database:        /tmp/gapView.18191.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.2e-204  663.4   1.4   6.1e-204  663.2   1.4    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS34655  BPHYT_RS34655 2-amino-3-ketobuty


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS34655  BPHYT_RS34655 2-amino-3-ketobutyrate CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.2   1.4  6.1e-204  6.1e-204       3     393 .]       7     399 .]       5     399 .] 0.99

  Alignments for each domain:
  == domain 1  score: 663.2 bits;  conditional E-value: 6.1e-204
                                TIGR01822   3 ailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGl 72 
                                              a+l++ le ir++G +k+er+i+spq+adir+a+G++vlnfcannylGl+d  ++i+aak++ld+ GfG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS34655   7 AHLRGTLEQIRADGFYKSERVIASPQSADIRLANGTDVLNFCANNYLGLADDARLIDAAKQGLDNDGFGM 76 
                                              68999***************************************************************** PP

                                TIGR01822  73 ssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlc 142
                                              +svrficGtq +hk+le++la+fl+t+d+ily+scfdangGlfe+ll e+daiisd+lnhasiidGvrl 
  lcl|FitnessBrowser__BFirm:BPHYT_RS34655  77 ASVRFICGTQTVHKDLERALAAFLQTDDCILYSSCFDANGGLFETLLDENDAIISDELNHASIIDGVRLS 146
                                              ********************************************************************** PP

                                TIGR01822 143 kakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatG 212
                                              kakr+ry+n+dl+dleakl ea+aagar +liatdGvfsmdG ia+l  ic+la++y+alv+vd++ha+G
  lcl|FitnessBrowser__BFirm:BPHYT_RS34655 147 KAKRFRYKNNDLADLEAKLIEAKAAGARFTLIATDGVFSMDGIIANLAGICDLADRYGALVMVDDSHAVG 216
                                              ********************************************************************** PP

                                TIGR01822 213 flGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasi 282
                                              f+G++GrG+ e ++vl +vdiitgtlGkalGGasGG+ +a+ke+vellrqrsrpylfsn+l+p++ +as+
  lcl|FitnessBrowser__BFirm:BPHYT_RS34655 217 FVGEHGRGTPEHCGVLSRVDIITGTLGKALGGASGGYVAARKEIVELLRQRSRPYLFSNTLTPSIAAASL 286
                                              ********************************************************************** PP

                                TIGR01822 283 kvlell..easnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviG 350
                                              kvlell  +++++lr ++ en  +fr+k++a+Gf++ p+eh+iipvml+da+la+k+a+ ll+eG+yviG
  lcl|FitnessBrowser__BFirm:BPHYT_RS34655 287 KVLELLasDEGAQLRARVRENGAHFRSKMSALGFTLVPGEHPIIPVMLGDAQLASKMADALLKEGVYVIG 356
                                              *****94446899********************************************************* PP

                                TIGR01822 351 ffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                              f++pvvpkG+arir+q+saah+ eq+d+av+af++vGrelgvi
  lcl|FitnessBrowser__BFirm:BPHYT_RS34655 357 FSFPVVPKGRARIRTQMSAAHTPEQIDRAVDAFARVGRELGVI 399
                                              *****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.04
//
[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