Alignments for a candidate for ackA in Pontimonas salivibrio CL-TW6

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pontimonas salivibrio CL-TW6

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_104914114.1 C3B54_RS08495 acetate kinase

Query= BRENDA::P0CW05
         (408 letters)



>NCBI__GCF_002950575.1:WP_104914114.1
          Length = 384

 Score =  344 bits (883), Expect = 2e-99
 Identities = 186/401 (46%), Positives = 258/401 (64%), Gaps = 26/401 (6%)

Query: 2   KVLVINAGSSSLKYQLIDMTNESALAIGLCERIGIDNSIITQKRFDGKKLEKQTDLPNHK 61
           +VLV+N+GSSS+KYQ+ID+ +E  +  G  +R+GID                  D   HK
Sbjct: 3   QVLVVNSGSSSVKYQVIDLPSEQVVDKGQRDRVGIDGG----------------DFATHK 46

Query: 62  IALEEVVKALTDSEFGVIKSMDEINAVGHRVVHGGEKFNSSALINEGVEQAIKDCFELAP 121
            A+ ++V +L  +          ++ VGHRVVHGG +F    LI++ V   I+    LAP
Sbjct: 47  EAIADIVASLPANV--------SLDLVGHRVVHGGARFTRPVLIDQDVISGIEKVRALAP 98

Query: 122 LHNPPNMMGISSCQEIMPGVPMVAVFDTAFHHTIPPYAYMYALPYELYEKYGIRKYGFHG 181
           LHNP N+ GI +  E+MP +P VAVFDTAF  T+ P AY YALP +L EKYGIRKYGFHG
Sbjct: 99  LHNPANLEGIHAVTEVMPQLPQVAVFDTAFFSTLSPAAYDYALPRDLVEKYGIRKYGFHG 158

Query: 182 TSHFYVAKRAAAMLGKPEQDVKVITCHLGNGSSITAVKGGKSIETTMGFTPLEGVAMGTR 241
           TSH YV    + ++   E+ V+V++ HLGNGSS+ AV+GG +++T+MG TPL G+ MGTR
Sbjct: 159 TSHDYVTGELSRLMPPSEKPVRVVSFHLGNGSSVAAVRGGVAVDTSMGLTPLAGLVMGTR 218

Query: 242 CGSIDPAVVPFIMEKEGLSTREIDTLMNKKSGVLGVSSLSNDFRDLDEAASKGNQKAELA 301
            G IDP+VV ++  + GLS  ++D ++N+ SG+LG+S  S D RDL E A  G+  A  A
Sbjct: 219 SGDIDPSVVLYLQREAGLSPEQVDEVLNRNSGLLGLSGHS-DMRDLYEHAEHGDPDALHA 277

Query: 302 LEIFAYKIKKVIGEYIAVLNGVDAIVFTAGIGENSASIRKRILADLDGIGIKIDEEKNKI 361
           L+++ ++ K  +G Y+A L G+DAIVFT GIGENS  +R   ++DL+G+GI IDE +NK 
Sbjct: 278 LDVWTWRAKHYLGAYLAQLGGLDAIVFTGGIGENSPELRLSAVSDLEGLGIHIDESRNKA 337

Query: 362 R-GQEIDISTPDATVRVLVIPTNEELTIARDTKEICETEVK 401
             G+   IS   ++V + VIPTNEEL IAR     CE+  K
Sbjct: 338 ESGEPRLISADGSSVSLWVIPTNEELHIARIATRHCESARK 378


Lambda     K      H
   0.317    0.135    0.379 

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: 385
Number of extensions: 11
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: 408
Length of database: 384
Length adjustment: 31
Effective length of query: 377
Effective length of database: 353
Effective search space:   133081
Effective search space used:   133081
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_104914114.1 C3B54_RS08495 (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.3423799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-131  423.2   0.0   7.7e-130  419.2   0.0    1.9  1  NCBI__GCF_002950575.1:WP_104914114.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002950575.1:WP_104914114.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.2   0.0  7.7e-130  7.7e-130       4     402 ..       2     371 ..       1     374 [. 0.97

  Alignments for each domain:
  == domain 1  score: 419.2 bits;  conditional E-value: 7.7e-130
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +++lv+n+Gsss+k++++d   se+v+ +g  +r+ +++                 +++ h+ea++ ++ +l 
  NCBI__GCF_002950575.1:WP_104914114.1   2 TQVLVVNSGSSSVKYQVIDLP-SEQVVDKGQRDRVGIDGG----------------DFATHKEAIADIVASLP 57 
                                           589******************.799988888888888776................7889************9 PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                           +       + +++l+GHRvvhGg +ft  v+++++v+++i+++  lAPlHnpa+legi+av+  +v+++ ++v
  NCBI__GCF_002950575.1:WP_104914114.1  58 A-------NVSLDLVGHRVVHGGARFTRPVLIDQDVISGIEKVRALAPLHNPANLEGIHAVT--EVMPQLPQV 121
                                           5.......6799**************************************************..999999*** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDtaf  t+   ay YalP++l +++g+R+YGfHGtsh yvt ++++l+  +++ +++++ HlGnG+sv+a
  NCBI__GCF_002950575.1:WP_104914114.1 122 AVFDTAFFSTLSPAAYDYALPRDLVEKYGIRKYGFHGTSHDYVTGELSRLMPPSEKPVRVVSFHLGNGSSVAA 194
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           v+ G ++dtsmGltPL+GlvmGtRsGdiDp+++ yl+ + gls +++ e+ln++sGllg+sg  sD+Rd++++
  NCBI__GCF_002950575.1:WP_104914114.1 195 VRGGVAVDTSMGLTPLAGLVMGTRSGDIDPSVVLYLQREAGLSPEQVDEVLNRNSGLLGLSG-HSDMRDLYEH 266
                                           **************************************************************.99******** PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                            e+g+ +a  Al+v++ R ++y+g+y+a+l g lDaivFtgGiGen+ e+r  ++++le lG+++d+ +n+ a
  NCBI__GCF_002950575.1:WP_104914114.1 267 AEHGDPDALHALDVWTWRAKHYLGAYLAQLGG-LDAIVFTGGIGENSPELRLSAVSDLEGLGIHIDESRNK-A 337
                                           ******************************76.*************************************9.9 PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalr 402
                                           +sg+ ++is + s+v + viptneel ia+ a+r
  NCBI__GCF_002950575.1:WP_104914114.1 338 ESGEPRLISADGSSVSLWVIPTNEELHIARIATR 371
                                           *****************************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (384 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: 00:00:00.01
# Mc/sec: 14.65
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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