Alignments for a candidate for kbl in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Thauera aminoaromatica S2

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate WP_004309491.1 C665_RS11130 glycine C-acetyltransferase

Query= reanno::ANA3:7026975
         (397 letters)



>NCBI__GCF_000310185.1:WP_004309491.1
          Length = 418

 Score =  539 bits (1388), Expect = e-158
 Identities = 276/399 (69%), Positives = 319/399 (79%), Gaps = 3/399 (0%)

Query: 2   ASTSFYAQINQQLADVKAEGLYKSERVIASPQQTAIQVNH-QEVVNFCANNYLGLANHPE 60
           A   F A ++  +  ++A+G YK+ERVI SPQ   + +    +V+NFCANNYLGLAN P 
Sbjct: 19  ARERFLAHLHGVVDQIRADGFYKAERVIDSPQGAQVHLGTGADVLNFCANNYLGLANDPR 78

Query: 61  LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120
           L+KAAQ GL   GFGMASVRFICGTQ +HKQLEAS+S+FLG EDTILY SCFDAN GLFE
Sbjct: 79  LVKAAQDGLAEDGFGMASVRFICGTQSVHKQLEASISKFLGTEDTILYGSCFDANGGLFE 138

Query: 121 TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT 180
           TLL  EDA+ISD LNHASIIDGVRLCKA+R+RY NNDMADLE QL AA AAG R  LIAT
Sbjct: 139 TLLTEEDAVISDELNHASIIDGVRLCKARRYRYRNNDMADLEAQLQAADAAGVRFKLIAT 198

Query: 181 DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITG 240
           DGVFSMDGVIA+L+ VCDLADKYGALVMVDDSHAVGFVG +GRG+ E+CGV GRVDIITG
Sbjct: 199 DGVFSMDGVIADLKSVCDLADKYGALVMVDDSHAVGFVGTHGRGTAEYCGVEGRVDIITG 258

Query: 241 TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKS--GQAL 298
           TLGKALGG+SGG+TSG KE+I+ LRQRSRPYLFSN+LAPSI  ASI V+E+L S  G  L
Sbjct: 259 TLGKALGGSSGGYTSGHKEIIELLRQRSRPYLFSNTLAPSIAAASIKVMELLASEEGLEL 318

Query: 299 REAVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFP 358
              V EN  +FR +M+  GFTL G DH I+PVM+GDA+LA   A  LL E IYVIGFSFP
Sbjct: 319 CRRVKENGEHFRREMTRLGFTLAGKDHPIVPVMLGDAQLAGRMAEELLKEGIYVIGFSFP 378

Query: 359 VVPKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397
           VVPKG+ARIRTQMSAAHT  Q+D+A+ AF ++ K +  I
Sbjct: 379 VVPKGKARIRTQMSAAHTTAQIDRAVAAFAKVGKALGAI 417


Lambda     K      H
   0.321    0.134    0.385 

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: 572
Number of extensions: 17
Number of successful extensions: 3
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: 397
Length of database: 418
Length adjustment: 31
Effective length of query: 366
Effective length of database: 387
Effective search space:   141642
Effective search space used:   141642
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_004309491.1 C665_RS11130 (glycine C-acetyltransferase)
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.19939.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-201  655.1   2.8   2.1e-201  654.9   2.8    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004309491.1  C665_RS11130 glycine C-acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004309491.1  C665_RS11130 glycine C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  654.9   2.8  2.1e-201  2.1e-201       3     393 .]      25     417 ..      23     417 .. 0.98

  Alignments for each domain:
  == domain 1  score: 654.9 bits;  conditional E-value: 2.1e-201
                                 TIGR01822   3 ailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfG 71 
                                               a+l++ ++ ir++G +k er+i spq+a++++  G +vlnfcannylGl++ p++++aa+d+l e GfG
  lcl|NCBI__GCF_000310185.1:WP_004309491.1  25 AHLHGVVDQIRADGFYKAERVIDSPQGAQVHLGTGADVLNFCANNYLGLANDPRLVKAAQDGLAEDGFG 93 
                                               6788899************************************************************** PP

                                 TIGR01822  72 lssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvr 140
                                               ++svrficGtq++hk+le+ +++flgted+ily+scfdangGlfe+ll+eeda+isd+lnhasiidGvr
  lcl|NCBI__GCF_000310185.1:WP_004309491.1  94 MASVRFICGTQSVHKQLEASISKFLGTEDTILYGSCFDANGGLFETLLTEEDAVISDELNHASIIDGVR 162
                                               ********************************************************************* PP

                                 TIGR01822 141 lckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdech 209
                                               lcka+ryry+n+d++dlea+l++a+aag+r +liatdGvfsmdG+ia+l+ +c+la+ky+alv+vd++h
  lcl|NCBI__GCF_000310185.1:WP_004309491.1 163 LCKARRYRYRNNDMADLEAQLQAADAAGVRFKLIATDGVFSMDGVIADLKSVCDLADKYGALVMVDDSH 231
                                               ********************************************************************* PP

                                 TIGR01822 210 atGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavv 278
                                               a+Gf+G++GrG+ae+++v ++vdiitgtlGkalGG+sGG+t+++ke++ellrqrsrpylfsn+lap++ 
  lcl|NCBI__GCF_000310185.1:WP_004309491.1 232 AVGFVGTHGRGTAEYCGVEGRVDIITGTLGKALGGSSGGYTSGHKEIIELLRQRSRPYLFSNTLAPSIA 300
                                               ********************************************************************* PP

                                 TIGR01822 279 gasikvlell..easnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeG 345
                                               +asikv+ell  e++ el  +++en ++fr +++ +Gf++++ +h+i+pvml+da+la ++ae+ll+eG
  lcl|NCBI__GCF_000310185.1:WP_004309491.1 301 AASIKVMELLasEEGLELCRRVKENGEHFRREMTRLGFTLAGKDHPIVPVMLGDAQLAGRMAEELLKEG 369
                                               *********9334567999************************************************** PP

                                 TIGR01822 346 iyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                               iyviGf++pvvpkG+arir+q+saah+ +q+d+av af+kvG+ lg+i
  lcl|NCBI__GCF_000310185.1:WP_004309491.1 370 IYVIGFSFPVVPKGKARIRTQMSAAHTTAQIDRAVAAFAKVGKALGAI 417
                                               *********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (418 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: 7.94
//
[ok]

This GapMind analysis is from Sep 24 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