Alignments for a candidate for ackA in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Klebsiella variicola At-22

Align propionate kinase (EC 2.7.2.15) (characterized)
to candidate WP_012967795.1 KVAR_RS09600 propionate kinase

Query= BRENDA::O06961
         (402 letters)



>NCBI__GCF_000025465.1:WP_012967795.1
          Length = 401

 Score =  621 bits (1602), Expect = 0.0
 Identities = 311/395 (78%), Positives = 350/395 (88%)

Query: 1   MNEFPVVLVINCGSSSIKFSVLDVATCDVLMAGIADGMNTENAFLSINGDKPINLAHSNY 60
           M EFPVVLVINCGSSSIKFSVLD A+CD L+ G+A+G+N E AFLS+NG +P+ LA   Y
Sbjct: 1   MTEFPVVLVINCGSSSIKFSVLDAASCDCLLNGVAEGINAERAFLSLNGGEPVALAQRGY 60

Query: 61  EDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNIRRVSPLAPLHNY 120
           E AL+AIA  L +RDL DSVALIGHR+AHGG+LFT+SVII++E+I+NIR+VS LAPLHNY
Sbjct: 61  EGALQAIAGALAQRDLIDSVALIGHRVAHGGDLFTESVIISEEVINNIRQVSSLAPLHNY 120

Query: 121 ANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHR 180
           A+LSGI +A+ LFP V QVAVFDTSFHQTLAPEA+LYGLPWEY+ +LGVRRYGFHGTSHR
Sbjct: 121 ASLSGIASAQRLFPQVMQVAVFDTSFHQTLAPEAFLYGLPWEYYQNLGVRRYGFHGTSHR 180

Query: 181 YVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240
           YVSRRA  LL L E++SGL++AHLGNGASICAVRNG+SVDTSMGMTPLEGLMMGTRSGDV
Sbjct: 181 YVSRRALALLGLPEQESGLVIAHLGNGASICAVRNGRSVDTSMGMTPLEGLMMGTRSGDV 240

Query: 241 DFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTF 300
           DFGAMAWIA ET QTLSDLERV N  SGLLGISGLSSDLRVLE+AWHEGH RARLAIKTF
Sbjct: 241 DFGAMAWIAGETRQTLSDLERVANTASGLLGISGLSSDLRVLEQAWHEGHARARLAIKTF 300

Query: 301 VHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSH 360
           VHRIARHIAGHAA+L RLDGIIFTGGIGENSVLIR+LV E L V GL +DV  N+QPNS 
Sbjct: 301 VHRIARHIAGHAAALQRLDGIIFTGGIGENSVLIRRLVSERLAVFGLEMDVARNQQPNSV 360

Query: 361 GERIISANPSQVICAVIPTNEEKMIALDAIHLGNV 395
           GER+ISA+ S+V CAVIPTNEE+MIALDAI LG +
Sbjct: 361 GERLISADASRVRCAVIPTNEERMIALDAIRLGRI 395


Lambda     K      H
   0.320    0.137    0.397 

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: 17
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: 402
Length of database: 401
Length adjustment: 31
Effective length of query: 371
Effective length of database: 370
Effective search space:   137270
Effective search space used:   137270
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_012967795.1 KVAR_RS09600 (propionate 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.2878528.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-159  514.5   0.0   9.7e-159  514.3   0.0    1.0  1  NCBI__GCF_000025465.1:WP_012967795.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012967795.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.3   0.0  9.7e-159  9.7e-159       3     403 ..       4     392 ..       2     394 .. 0.96

  Alignments for each domain:
  == domain 1  score: 514.3 bits;  conditional E-value: 9.7e-159
                             TIGR00016   3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntl 75 
                                           + ++lv+n+Gsss+kf++lda++++  ll+g++e i+ e a+++   +g  +e   la + +e a+++++ +l
  NCBI__GCF_000025465.1:WP_012967795.1   4 FPVVLVINCGSSSIKFSVLDAASCDC-LLNGVAEGINAERAFLS--LNG--GEPVALAQRGYEGALQAIAGAL 71 
                                           5689******************7665.5***********99444..555..688899999************* PP

                             TIGR00016  76 kkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                            +    +++ +++aliGHRv+hGg+ ftesvi+ +ev+++i+++s+lAPlHn+a l+gi ++++l++  ++ +
  NCBI__GCF_000025465.1:WP_012967795.1  72 AQ----RDLIDSVALIGHRVAHGGDLFTESVIISEEVINNIRQVSSLAPLHNYASLSGIASAQRLFP--QVMQ 138
                                           *7....67899****************************************************6665..566* PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDt+fHqt++ ea+lY+lP+++y++lgvRrYGfHGtsh+yv++ra  ll+ p++++ l+++HlGnGas++
  NCBI__GCF_000025465.1:WP_012967795.1 139 VAVFDTSFHQTLAPEAFLYGLPWEYYQNLGVRRYGFHGTSHRYVSRRALALLGLPEQESGLVIAHLGNGASIC 211
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           av+nG+s+dtsmG+tPLeGl+mGtRsGd+D++++ ++a ++ ++l+++e++ n  sGllgisglssDlR++++
  NCBI__GCF_000025465.1:WP_012967795.1 212 AVRNGRSVDTSMGMTPLEGLMMGTRSGDVDFGAMAWIAGETRQTLSDLERVANTASGLLGISGLSSDLRVLEQ 284
                                           ************************************************************************* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           +++eg+ +a+lA+k++vhRia++i+ ++a+l+  lD+i+FtgGiGen++ +r+lv e+l+v+Gl++d ++n++
  NCBI__GCF_000025465.1:WP_012967795.1 285 AWHEGHARARLAIKTFVHRIARHIAGHAAALQR-LDGIIFTGGIGENSVLIRRLVSERLAVFGLEMDVARNQQ 356
                                           *******************************55.*************************************** PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                            +s  e++is + s+v+++viptnee +ia Da+rl
  NCBI__GCF_000025465.1:WP_012967795.1 357 PNSVGERLISADASRVRCAVIPTNEERMIALDAIRL 392
                                           **********************************98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.68
//
[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