GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kbl in Sinorhizobium meliloti 1021

Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate SMc01565 SMc01565 2-amino-3-ketobutyrate CoA ligase

Query= BRENDA::P0AB77
         (398 letters)



>FitnessBrowser__Smeli:SMc01565
          Length = 395

 Score =  548 bits (1412), Expect = e-160
 Identities = 271/397 (68%), Positives = 324/397 (81%), Gaps = 2/397 (0%)

Query: 1   MRGEFYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPD 60
           M   F   L ++LE  +  GL+K ER+ITS Q  +I VA G  V+NFCANNYLGLA+  +
Sbjct: 1   MTTAFLSHLRSELEDLKQAGLYKSERVITSKQSGEIEVASGGRVLNFCANNYLGLADSEE 60

Query: 61  LIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFE 120
           L  AAK+ +D +G+GMASVRFICGTQ+ HKELE ++++FLGMED ILYSSCFDANGGLFE
Sbjct: 61  LAQAAKSALDRYGYGMASVRFICGTQEEHKELEARISSFLGMEDTILYSSCFDANGGLFE 120

Query: 121 TLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIAT 180
           TLLG +DAIISDALNHASIIDGVRL KA+R+RYANNDM  LE  LK+A   G+R  +IAT
Sbjct: 121 TLLGEDDAIISDALNHASIIDGVRLSKARRFRYANNDMAALEEELKKAE--GSRFKMIAT 178

Query: 181 DGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITG 240
           DGVFSMDG+IANL+GVCDLA+KY A+VMVDDSHAVGFVG++GRGS E+C V GRVDIITG
Sbjct: 179 DGVFSMDGIIANLQGVCDLAEKYGAMVMVDDSHAVGFVGKHGRGSAEHCGVEGRVDIITG 238

Query: 241 TLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRD 300
           TLGKALGGASGGYT+A+ +VVEWLRQRSRPYLFSN+LAP I AAS+KV E++E G  LR+
Sbjct: 239 TLGKALGGASGGYTSAKADVVEWLRQRSRPYLFSNTLAPVIAAASLKVFELIENGDALRN 298

Query: 301 RLWANARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVV 360
           RL+ANA  FR +MS  GFTLAG  H IIPVMLGDA +AQ+ A  + K+G+YV GF +PVV
Sbjct: 299 RLYANAALFRSEMSGLGFTLAGEGHPIIPVMLGDAALAQEMAARMLKKGVYVVGFSFPVV 358

Query: 361 PKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVI 397
           PKGQARIRTQMSAAH+   + RA+  F  +G++LGVI
Sbjct: 359 PKGQARIRTQMSAAHSEADVRRAIAVFEEVGRELGVI 395


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: 509
Number of extensions: 12
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: 395
Length adjustment: 31
Effective length of query: 367
Effective length of database: 364
Effective search space:   133588
Effective search space used:   133588
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 SMc01565 SMc01565 (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.11996.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.3e-198  644.8   2.1   2.7e-198  644.6   2.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc01565  SMc01565 2-amino-3-ketobutyrate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01565  SMc01565 2-amino-3-ketobutyrate CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.6   2.1  2.7e-198  2.7e-198       3     393 .]       7     395 .]       5     395 .] 0.99

  Alignments for each domain:
  == domain 1  score: 644.6 bits;  conditional E-value: 2.7e-198
                           TIGR01822   3 ailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrf 77 
                                         ++l++ele +++aGl+k+er+its+q+ +i va G  vlnfcannylGl+d  e+ qaak+ald +G+G++svrf
  lcl|FitnessBrowser__Smeli:SMc01565   7 SHLRSELEDLKQAGLYKSERVITSKQSGEIEVASGGRVLNFCANNYLGLADSEELAQAAKSALDRYGYGMASVRF 81 
                                         6899*********************************************************************** PP

                           TIGR01822  78 icGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryena 152
                                         icGtq+ hkele+++++flg+ed+ily+scfdangGlfe+llge+daiisdalnhasiidGvrl ka+r+ry+n+
  lcl|FitnessBrowser__Smeli:SMc01565  82 ICGTQEEHKELEARISSFLGMEDTILYSSCFDANGGLFETLLGEDDAIISDALNHASIIDGVRLSKARRFRYANN 156
                                         *************************************************************************** PP

                           TIGR01822 153 dledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldv 227
                                         d++ le +lk+a+  g+r ++iatdGvfsmdG ia+l+ +c+laeky+a+v+vd++ha+Gf+G++GrGsae ++v
  lcl|FitnessBrowser__Smeli:SMc01565 157 DMAALEEELKKAE--GSRFKMIATDGVFSMDGIIANLQGVCDLAEKYGAMVMVDDSHAVGFVGKHGRGSAEHCGV 229
                                         **********986..66********************************************************** PP

                           TIGR01822 228 ldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklvent 302
                                          ++vdiitgtlGkalGGasGG+t+ak +vve+lrqrsrpylfsn+lap + +as+kv+el+e+++ lr++l +n+
  lcl|FitnessBrowser__Smeli:SMc01565 230 EGRVDIITGTLGKALGGASGGYTSAKADVVEWLRQRSRPYLFSNTLAPVIAAASLKVFELIENGDALRNRLYANA 304
                                         *************************************************************************** PP

                           TIGR01822 303 ryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqld 377
                                           fr++++ +Gf++++  h+iipvml+da laq++a+r+l++G+yv+Gf++pvvpkGqarir+q+saah+e+++ 
  lcl|FitnessBrowser__Smeli:SMc01565 305 ALFRSEMSGLGFTLAGEGHPIIPVMLGDAALAQEMAARMLKKGVYVVGFSFPVVPKGQARIRTQMSAAHSEADVR 379
                                         *************************************************************************** PP

                           TIGR01822 378 kaveafvkvGrelgvi 393
                                         +a+  f +vGrelgvi
  lcl|FitnessBrowser__Smeli:SMc01565 380 RAIAVFEEVGRELGVI 395
                                         **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (395 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 0.00s 00:00:00.01 Elapsed: 00:00:00.03
# Mc/sec: 4.50
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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