Alignments for a candidate for ackA in Clostridium acetobutylicum ATCC 824

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Clostridium acetobutylicum ATCC 824

Align acetate kinase monomer (EC 2.7.2.15) (characterized)
to candidate WP_010965050.1 CA_RS09050 acetate kinase

Query= metacyc::ACKCLOS-MONOMER
         (401 letters)



>NCBI__GCF_000008765.1:WP_010965050.1
          Length = 401

 Score =  804 bits (2077), Expect = 0.0
 Identities = 401/401 (100%), Positives = 401/401 (100%)

Query: 1   MKNLVINCGSSSIKYQFIDMKDETVLAKGLVERIGIKGSVITHKVNGEKYVTETPMEDHK 60
           MKNLVINCGSSSIKYQFIDMKDETVLAKGLVERIGIKGSVITHKVNGEKYVTETPMEDHK
Sbjct: 1   MKNLVINCGSSSIKYQFIDMKDETVLAKGLVERIGIKGSVITHKVNGEKYVTETPMEDHK 60

Query: 61  KAIKLVLDALLNDEYGVIKNIDEISAVGHRIVHGGEKYANSVLIDEDVMKSIEDCVSLAP 120
           KAIKLVLDALLNDEYGVIKNIDEISAVGHRIVHGGEKYANSVLIDEDVMKSIEDCVSLAP
Sbjct: 61  KAIKLVLDALLNDEYGVIKNIDEISAVGHRIVHGGEKYANSVLIDEDVMKSIEDCVSLAP 120

Query: 121 LHNPPHIIGINACKELMPNVPMVAVFDTAFHQTIPDYAYMYAIPYEYYDKYKIRKYGFHG 180
           LHNPPHIIGINACKELMPNVPMVAVFDTAFHQTIPDYAYMYAIPYEYYDKYKIRKYGFHG
Sbjct: 121 LHNPPHIIGINACKELMPNVPMVAVFDTAFHQTIPDYAYMYAIPYEYYDKYKIRKYGFHG 180

Query: 181 TSHKYVSRTAAEFIGKKVEDLKMVVCHMGNGASITAVENGKSVDTSMGFTPLGGLAMGTR 240
           TSHKYVSRTAAEFIGKKVEDLKMVVCHMGNGASITAVENGKSVDTSMGFTPLGGLAMGTR
Sbjct: 181 TSHKYVSRTAAEFIGKKVEDLKMVVCHMGNGASITAVENGKSVDTSMGFTPLGGLAMGTR 240

Query: 241 SGDMDPAVVTFLMDKLNINASEVNNLLNKKSGIEGLSGISSDMRDIKKGNYVDKDPKAML 300
           SGDMDPAVVTFLMDKLNINASEVNNLLNKKSGIEGLSGISSDMRDIKKGNYVDKDPKAML
Sbjct: 241 SGDMDPAVVTFLMDKLNINASEVNNLLNKKSGIEGLSGISSDMRDIKKGNYVDKDPKAML 300

Query: 301 AYSVFNYKIKQFIGSYTAVMNGLDCLVFTGGIGENSFENRREICKNMDYLGIKIDDKKND 360
           AYSVFNYKIKQFIGSYTAVMNGLDCLVFTGGIGENSFENRREICKNMDYLGIKIDDKKND
Sbjct: 301 AYSVFNYKIKQFIGSYTAVMNGLDCLVFTGGIGENSFENRREICKNMDYLGIKIDDKKND 360

Query: 361 ETMGIPMDISAEGSKVRVLVIPTNEELMIARDTKDIVGKLK 401
           ETMGIPMDISAEGSKVRVLVIPTNEELMIARDTKDIVGKLK
Sbjct: 361 ETMGIPMDISAEGSKVRVLVIPTNEELMIARDTKDIVGKLK 401


Lambda     K      H
   0.317    0.136    0.390 

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: 778
Number of extensions: 28
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 WP_010965050.1 CA_RS09050 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

# 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/TIGR00016.hmm
# target sequence database:        /tmp/gapView.2291792.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00016  [M=405]
Accession:   TIGR00016
Description: ackA: acetate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-163  527.7   3.8   9.6e-163  527.5   3.8    1.0  1  NCBI__GCF_000008765.1:WP_010965050.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008765.1:WP_010965050.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.5   3.8  9.6e-163  9.6e-163       5     401 ..       2     394 ..       1     398 [. 0.96

  Alignments for each domain:
  == domain 1  score: 527.5 bits;  conditional E-value: 9.6e-163
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                           k lv+n+Gsss+k++ +d+++ e+vl++glveri +++++i+ +++ ++k  +++ +edh++a+k +l++l +
  NCBI__GCF_000008765.1:WP_010965050.1   2 KNLVINCGSSSIKYQFIDMKD-ETVLAKGLVERIGIKGSVITHKVN-GEKYVTETPMEDHKKAIKLVLDALLN 72 
                                           679*****************7.*****************7776555.578889999****************9 PP

                             TIGR00016  78 .dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                            +  ++k+ +ei+++GHR+vhGgek+++sv+++++v+k+i+d ++lAPlHnp++++gi+a +  + +++++ v
  NCBI__GCF_000008765.1:WP_010965050.1  73 dEYGVIKNIDEISAVGHRIVHGGEKYANSVLIDEDVMKSIEDCVSLAPLHNPPHIIGINACK--ELMPNVPMV 143
                                           7889**********************************************************..88999**** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDtafHqtip+ ay+Ya+Py++y+++++R+YGfHGtshkyv+++aa+ ++k+++dl+++vcH+GnGas++a
  NCBI__GCF_000008765.1:WP_010965050.1 144 AVFDTAFHQTIPDYAYMYAIPYEYYDKYKIRKYGFHGTSHKYVSRTAAEFIGKKVEDLKMVVCHMGNGASITA 216
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild. 294
                                           v+nGks+dtsmG+tPL Gl+mGtRsGd+Dpa++++l+++l+  ++e++++lnkksG+ g+sg+ssD+Rdi + 
  NCBI__GCF_000008765.1:WP_010965050.1 217 VENGKSVDTSMGFTPLGGLAMGTRSGDMDPAVVTFLMDKLNINASEVNNLLNKKSGIEGLSGISSDMRDIKKg 289
                                           **********************************************************************983 PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           ++ +++ +a lA++v+ ++i+++ig+y+a ++g lD +vFtgGiGen+ e r++++++++ lG+k+d ++n  
  NCBI__GCF_000008765.1:WP_010965050.1 290 NYVDKDPKAMLAYSVFNYKIKQFIGSYTAVMNG-LDCLVFTGGIGENSFENRREICKNMDYLGIKIDDKKND- 360
                                           5669999************************88.*************************************9. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDal 401
                                            ++g    is e skv+vlviptneel+ia+D+ 
  NCBI__GCF_000008765.1:WP_010965050.1 361 ETMGIPMDISAEGSKVRVLVIPTNEELMIARDTK 394
                                           67888999************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (401 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.66
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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