Alignments for a candidate for ackA in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Derxia gummosa DSM 723

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_034410959.1 H566_RS0107210 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_000482785.1:WP_034410959.1
          Length = 409

 Score =  395 bits (1014), Expect = e-114
 Identities = 211/395 (53%), Positives = 267/395 (67%), Gaps = 7/395 (1%)

Query: 5   LLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRP-HFKVVNSDGSTRYDTYLP- 62
           + V+NAGSSS+KF+L++   +  A  L+  G + +LG    H    +  G    +   P 
Sbjct: 10  IAVVNAGSSSLKFSLFDEDGDTLA--LVLHGNVEALGGADAHLLARDPSGRVLAEQRWPG 67

Query: 63  EGTSHDDAMAVLIGWIETTFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFDRLA 122
           +   H  AM  ++  +        ++AVGHR+VHGG+ F  P  +   V+ +L     LA
Sbjct: 68  QQPDHAAAMTEVVACMRAALGGRHVAAVGHRIVHGGSEFTAPARLDAAVLDRLARLAPLA 127

Query: 123 PLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYGFHG 182
           PLHQPHN++   AL ++ P + Q+ CFDTAFH R PE+A AFALP ++T  GVRRYGFHG
Sbjct: 128 PLHQPHNLAPARALLRVAPQVLQVGCFDTAFHARQPELAQAFALPADITRHGVRRYGFHG 187

Query: 183 LSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLMMGSR 242
           LSYEY+AG L  +   A+A GRV+ AHLG GAS+CA+   RSIA+TMGFTALDGL MG+R
Sbjct: 188 LSYEYLAGALAAL-DPALARGRVIAAHLGNGASLCALDAGRSIASTMGFTALDGLPMGTR 246

Query: 243 CGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLASDDPHACEAIEL 302
           CG LDPGV+LYL++   MT R+IEDLLYR SGLLGVSGI+ D+R L ASD P A  AIEL
Sbjct: 247 CGNLDPGVLLYLIDSLGMTPRQIEDLLYRRSGLLGVSGIASDLRALEASDAPEARFAIEL 306

Query: 303 FVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDANASLSG 362
           FVYR+ARE+GSLAAALGGLD LVF GGIGEH   +R  +   A WLG+ LD +ANA  +G
Sbjct: 307 FVYRVAREIGSLAAALGGLDGLVFAGGIGEHGVNVRGAIARAAGWLGLRLDAEANAGATG 366

Query: 363 AG--RISAPDSKVSAWAIPTDEDLMIARHVWRLAD 395
               RIS   S V+AW +PTDE+LMIARH  RL D
Sbjct: 367 GDTRRISTAASPVAAWVVPTDEELMIARHARRLLD 401


Lambda     K      H
   0.321    0.137    0.413 

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: 24
Number of successful extensions: 4
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: 409
Length adjustment: 31
Effective length of query: 367
Effective length of database: 378
Effective search space:   138726
Effective search space used:   138726
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_034410959.1 H566_RS0107210 (acetate/propionate family 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.1880312.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-109  351.3   0.0   3.7e-109  351.1   0.0    1.0  1  NCBI__GCF_000482785.1:WP_034410959.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_034410959.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.1   0.0  3.7e-109  3.7e-109       5     403 ..       9     399 ..       6     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: 351.1 bits;  conditional E-value: 3.7e-109
                             TIGR00016   5 kilvlnaGssslkfalldaensekv..llsglverikleeariktvedgek...keeeklaiedheeavkkll 72 
                                            i v+naGssslkf+l+d  + +++  +l+g ve++  ++a++     +++   +++   + +dh++a+++++
  NCBI__GCF_000482785.1:WP_034410959.1   9 AIAVVNAGSSSLKFSLFDEDG-DTLalVLHGNVEALGGADAHLLARDPSGRvlaEQRWPGQQPDHAAAMTEVV 80 
                                           688***************985.4433489************998876555422256677899*********** PP

                             TIGR00016  73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145
                                             + +         ++a++GHR+vhGg++ft  + +++ vl++++++++lAPlH p +l   +a+l   v ++
  NCBI__GCF_000482785.1:WP_034410959.1  81 ACMRA----ALGGRHVAAVGHRIVHGGSEFTAPARLDAAVLDRLARLAPLAPLHQPHNLAPARALL--RVAPQ 147
                                           *9996....557789**************************************************9..88999 PP

                             TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218
                                           + +v +FDtafH   pe a  +alP +  +++gvRrYGfHG+s++y++  +a  l+ +l+  ++i +HlGnGa
  NCBI__GCF_000482785.1:WP_034410959.1 148 VLQVGCFDTAFHARQPELAQAFALPAD-ITRHGVRRYGFHGLSYEYLAGALA-ALDPALARGRVIAAHLGNGA 218
                                           99***********************66.678****************99876.68999*************** PP

                             TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291
                                           s++a+  G+si  +mG+t L+Gl mGtR+G++Dp+++ yl + lg++  +ie++l ++sGllg+sg++sDlR 
  NCBI__GCF_000482785.1:WP_034410959.1 219 SLCALDAGRSIASTMGFTALDGLPMGTRCGNLDPGVLLYLIDSLGMTPRQIEDLLYRRSGLLGVSGIASDLRA 291
                                           ************************************************************************* PP

                             TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364
                                           +++       ea+ A++++v+R+a+ ig+ +a+l g lD++vF gGiGe  ++vr  + ++   lGl+ld e 
  NCBI__GCF_000482785.1:WP_034410959.1 292 LEASD---APEARFAIELFVYRVAREIGSLAAALGG-LDGLVFAGGIGEHGVNVRGAIARAAGWLGLRLDAEA 360
                                           98876...6679**********************76.************************************ PP

                             TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                           n  a+ g+ + ist  s v + v+pt+eel+ia+ a rl
  NCBI__GCF_000482785.1:WP_034410959.1 361 NAGATGGDTRRISTAASPVAAWVVPTDEELMIARHARRL 399
                                           **********************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (409 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: 15.83
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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