Alignments for a candidate for ackA in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pseudomonas benzenivorans DSM 8628

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_090447849.1 BLS63_RS21520 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_900100495.1:WP_090447849.1
          Length = 394

 Score =  385 bits (988), Expect = e-111
 Identities = 199/398 (50%), Positives = 264/398 (66%), Gaps = 5/398 (1%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           M  + +LV+NCGSSS+KFA+++       +SGLAE  G  D+ + W+  GG+ ++ + A 
Sbjct: 1   MPARNILVINCGSSSIKFALVNEAHSQFTLSGLAERLGSHDAVLHWQ-RGGERDSLMIAN 59

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
             HR A    +   +         Q+  IGHR+VHGGE FT +  +    +Q I   A L
Sbjct: 60  ADHRAA----LAQLLPLVQAAAGGQLHGIGHRVVHGGEHFTAASRLDEAALQAIRATAPL 115

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPA+L+GI AAI  FP+LPQV VFDTAFHQT+PE A+ YALP  LYREH +RRYG 
Sbjct: 116 APLHNPANLLGIEAAIKLFPKLPQVAVFDTAFHQTLPEHAFRYALPDSLYREHGVRRYGF 175

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH +V   AA++ G  V D + + AHLGNG S  AI+GG+S DTSMGLTPLEGLVMG
Sbjct: 176 HGTSHRFVSHRAAELAGLAVGDSSWLVAHLGNGCSTCAIEGGQSRDTSMGLTPLEGLVMG 235

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TR GD+DP++  HL + LG+ L+ +  LLN++SGLLG+S L+ND R +E+    GH GAT
Sbjct: 236 TRSGDVDPNLHSHLARTLGWNLERIERLLNQESGLLGLSGLSNDMRSLEQAREQGHAGAT 295

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LA+++FCYRLAK +A+ +  L +LD ++FTGGIGENS LIR K +  L++ N  +D   N
Sbjct: 296 LAIEVFCYRLAKSLAAMSCALSQLDGLVFTGGIGENSPLIRSKTVAHLKLLNLALDKQAN 355

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398
                G  G I   G P  +V+PTNEE  IA D + L+
Sbjct: 356 ARTIRGVGGAIHAHGHPRVLVVPTNEERQIALDTLALL 393


Lambda     K      H
   0.321    0.139    0.409 

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: 490
Number of extensions: 27
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: 401
Length of database: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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 WP_090447849.1 BLS63_RS21520 (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.17431.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-139  451.5   0.0   1.3e-139  451.4   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090447849.1  BLS63_RS21520 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447849.1  BLS63_RS21520 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.4   0.0  1.3e-139  1.3e-139       4     403 ..       4     392 ..       1     394 [] 0.96

  Alignments for each domain:
  == domain 1  score: 451.4 bits;  conditional E-value: 1.3e-139
                                 TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkll 72 
                                               + ilv+n+Gsss+kfal++ ++ ++  lsgl+er+ +++a++ + + g+++++ + a +dh++a+++ll
  lcl|NCBI__GCF_900100495.1:WP_090447849.1   4 RNILVINCGSSSIKFALVNEAH-SQFTLSGLAERLGSHDAVLHW-QRGGERDSLMIANADHRAALAQLL 70 
                                               689*****************96.56669************6665.66778899999************* PP

                                 TIGR00016  73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklk 141
                                                 +++         +++ iGHRvvhGge+ft +  +++ +l++i+  ++lAPlHnpa+l giea+   k
  lcl|NCBI__GCF_900100495.1:WP_090447849.1  71 PLVQA-----AAGGQLHGIGHRVVHGGEHFTAASRLDEAALQAIRATAPLAPLHNPANLLGIEAAI--K 132
                                               99984.....78899***************************************************..6 PP

                                 TIGR00016 142 vllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnli 210
                                                 +k ++vavFDtafHqt+pe+a+ YalP sly+e+gvRrYGfHGtsh++v++raa+l + ++ d+  +
  lcl|NCBI__GCF_900100495.1:WP_090447849.1 133 LFPKLPQVAVFDTAFHQTLPEHAFRYALPDSLYREHGVRRYGFHGTSHRFVSHRAAELAGLAVGDSSWL 201
                                               667888*************************************************************** PP

                                 TIGR00016 211 vcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGl 279
                                               v+HlGnG s +a++ G+s dtsmGltPLeGlvmGtRsGd+Dp + s+la tlg  l+ ie++ln++sGl
  lcl|NCBI__GCF_900100495.1:WP_090447849.1 202 VAHLGNGCSTCAIEGGQSRDTSMGLTPLEGLVMGTRSGDVDPNLHSHLARTLGWNLERIERLLNQESGL 270
                                               ********************************************************************* PP

                                 TIGR00016 280 lgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrel 348
                                               lg+sgls+D+R ++++ e+g+  a+lA++v+++R+ak ++++  +l++ lD++vFtgGiGen+  +r +
  lcl|NCBI__GCF_900100495.1:WP_090447849.1 271 LGLSGLSNDMRSLEQAREQGHAGATLAIEVFCYRLAKSLAAMSCALSQ-LDGLVFTGGIGENSPLIRSK 338
                                               **********************************************77.******************** PP

                                 TIGR00016 349 vleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                               ++ +l++l l+ld++ n ++ +g  + i   +++ +vlv+ptnee  ia D+l l
  lcl|NCBI__GCF_900100495.1:WP_090447849.1 339 TVAHLKLLNLALDKQANARTIRGVGGAIH-AHGHPRVLVVPTNEERQIALDTLAL 392
                                               ********************999999997.8999*****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (394 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.33
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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