Alignments for a candidate for ackA in Sulfuricurvum kujiense DSM 16994

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Sulfuricurvum kujiense DSM 16994

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_013460136.1 SULKU_RS06440 acetate kinase

Query= BRENDA::G4T0C7
         (401 letters)



>NCBI__GCF_000183725.1:WP_013460136.1
          Length = 368

 Score =  347 bits (890), Expect = e-100
 Identities = 181/394 (45%), Positives = 247/394 (62%), Gaps = 33/394 (8%)

Query: 7   NILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQSVIAA 66
           +ILVIN+GSSSIKY +      Q++  GL+E I                           
Sbjct: 2   SILVINAGSSSIKYSIYNTKTLQLIDHGLIEEI--------------------------R 35

Query: 67  DHHQAFKAVFEILG----ENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIAPL 122
           DHH+ F+ +   L     +   +DAIGHRVVHGG+RF  PA VDD  I  + AL  +APL
Sbjct: 36  DHHEGFEVMRTQLQLHNIDITKIDAIGHRVVHGGERFHEPARVDDALIREITALIPLAPL 95

Query: 123 HNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFHGT 182
           HNP N+ GI++  A  P VP  AVFDTAFHQTMPP+AYRY +    Y  + +RR+GFHGT
Sbjct: 96  HNPANIEGIQAARAIAPSVPNFAVFDTAFHQTMPPYAYRYPLAHDLYESFHVRRYGFHGT 155

Query: 183 SHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGTRS 242
           SHHYV+ +A++ + KP +  +LIT H+GNG SA AI  GRS+DTSMG TPLEGL+MGTR 
Sbjct: 156 SHHYVSIQASDLLQKPIESLNLITFHIGNGVSACAIQKGRSIDTSMGMTPLEGLMMGTRC 215

Query: 243 GDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLALD 302
           G +DP+I  ++   +    + +D  LN++SGL  + GTNDLR+++E   +GD  A LA+D
Sbjct: 216 GSIDPSIIGYLMHEKGMSIEEVDTLLNKKSGLLAIAGTNDLRSIIEARKSGDANAALAID 275

Query: 303 LYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSDVT 362
           ++ YR++K +GAY +VL  VDA++FTGG+GE++  +  + CEGL  +GI +D A NS   
Sbjct: 276 MFAYRLRKQLGAYMSVLRGVDAVIFTGGIGEHSPLIHEMVCEGLEHMGICLDRAKNSAFE 335

Query: 363 GAIAEIGLAESRTRILVIKTDEELQIAREAMAVL 396
             I +     S   +LVI TDEE QIA    ++L
Sbjct: 336 TRIHD---EASTVALLVIPTDEERQIALYVQSLL 366


Lambda     K      H
   0.320    0.137    0.400 

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: 451
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: 401
Length of database: 368
Length adjustment: 30
Effective length of query: 371
Effective length of database: 338
Effective search space:   125398
Effective search space used:   125398
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_013460136.1 SULKU_RS06440 (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.3516.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-135  436.2   1.2   1.1e-128  415.4   0.1    2.0  2  lcl|NCBI__GCF_000183725.1:WP_013460136.1  SULKU_RS06440 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013460136.1  SULKU_RS06440 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   1.6e-09   1.6e-09       5      40 ..       2      36 ..       1      44 [. 0.86
   2 !  415.4   0.1  1.1e-128  1.1e-128      60     399 ..      33     361 ..      31     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.6e-09
                                 TIGR00016  5 kilvlnaGssslkfalldaensekvllsglverikl 40
                                               ilv+naGsss+k++++++++  +++ +gl+e+i  
  lcl|NCBI__GCF_000183725.1:WP_013460136.1  2 SILVINAGSSSIKYSIYNTKT-LQLIDHGLIEEIRD 36
                                              79******************5.78889*****9975 PP

  == domain 2  score: 415.4 bits;  conditional E-value: 1.1e-128
                                 TIGR00016  60 aiedheeavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnp 128
                                               +i+dh+e+ + + ++l+  ++i  +  +i++iGHRvvhGge+f e + v+d  +++i  +++lAPlHnp
  lcl|NCBI__GCF_000183725.1:WP_013460136.1  33 EIRDHHEGFEVMRTQLQL-HNI--DITKIDAIGHRVVHGGERFHEPARVDDALIREITALIPLAPLHNP 98 
                                               7899************95.544..5789***************************************** PP

                                 TIGR00016 129 aelegieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraa 197
                                               a++egi+a+    + ++++n avFDtafHqt+p  ay Y+l ++ly+ + vRrYGfHGtsh+yv+ +a+
  lcl|NCBI__GCF_000183725.1:WP_013460136.1  99 ANIEGIQAAR--AIAPSVPNFAVFDTAFHQTMPPYAYRYPLAHDLYESFHVRRYGFHGTSHHYVSIQAS 165
                                               **********..9999***************************************************** PP

                                 TIGR00016 198 kllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsl 266
                                               +ll+kp+++lnli+ H+GnG s +a+++G+sidtsmG+tPLeGl+mGtR+G+iDp+ii yl++++g+s+
  lcl|NCBI__GCF_000183725.1:WP_013460136.1 166 DLLQKPIESLNLITFHIGNGVSACAIQKGRSIDTSMGMTPLEGLMMGTRCGSIDPSIIGYLMHEKGMSI 234
                                               ********************************************************************* PP

                                 TIGR00016 267 deieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFt 335
                                               +e+ ++lnkksGll+i+g ++DlR i+++ + g+ +a+lA++++++R++k +g+y++ l g +Da++Ft
  lcl|NCBI__GCF_000183725.1:WP_013460136.1 235 EEVDTLLNKKSGLLAIAG-TNDLRSIIEARKSGDANAALAIDMFAYRLRKQLGAYMSVLRG-VDAVIFT 301
                                               ******************.****************************************88.******* PP

                                 TIGR00016 336 gGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeD 399
                                               gGiGe +  + e+v+e+le +G+ ld ++n       e+ i  e s+v +lvipt+ee  ia  
  lcl|NCBI__GCF_000183725.1:WP_013460136.1 302 GGIGEHSPLIHEMVCEGLEHMGICLDRAKNS----AFETRIHDEASTVALLVIPTDEERQIALY 361
                                               ****************************999....67899********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (368 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 3.84
//
[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