Alignments for a candidate for kbl in Sinorhizobium meliloti 1021

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.2966.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.06
//
[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