Alignments for a candidate for ackA in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Dechloromonas agitata is5

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_027458048.1 K420_RS0110665 acetate/propionate family kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000519045.1:WP_027458048.1
          Length = 768

 Score =  344 bits (883), Expect = 4e-99
 Identities = 177/400 (44%), Positives = 259/400 (64%), Gaps = 2/400 (0%)

Query: 2   RVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERELPDHEE 61
           +V+V+N G S I + + + E       GI +    + +R+   VG ++  +E       +
Sbjct: 166 KVIVLNVGISQIHFGIYDTEESGADVHGIIDHADQQTTRIAVTVGPQQKTMEHAPFKLSD 225

Query: 62  ALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAPL 121
             K++               +++ AVGHRVVHGG +F  SV++   V+  IEE++  APL
Sbjct: 226 LFKVMQEATALLGPAFTFHPEDVTAVGHRVVHGGNKFSSSVVITPAVIADIEELAVFAPL 285

Query: 122 HNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHGT 181
           HNPAN+ GI+ A K+ P VP+VAVFDTAFHQT+   AYLY +PYE Y+++ IRRYGFHGT
Sbjct: 286 HNPANVAGIRVAQKVFPNVPHVAVFDTAFHQTLAPYAYLYGLPYELYKQHGIRRYGFHGT 345

Query: 182 SHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTRS 241
           SHRYVS +AAE+L + L EL+II+CH+G GAS+ A+ +G+ +DT+MG TP +GL+M +RS
Sbjct: 346 SHRYVSLKAAEVLQRPLGELEIISCHLGIGASLCAIDHGRSIDTTMGMTPTDGLIMPSRS 405

Query: 242 GDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKLV 301
           G +DPA+   +ME+  +SP+++  ++N +SG+ G+S G SSD+RDIE AA +G     L 
Sbjct: 406 GSIDPAVMIHLMEQHHMSPEQLSTLVNSESGLKGIS-GISSDIRDIEAAAAEGHHRALLA 464

Query: 302 LEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNEE 361
            + Y Y++ K IGAY AAM G+D + FT  VGE S   R   C  LEF+G+KLD++KN  
Sbjct: 465 HKAYCYQVRKNIGAYVAAMGGIDVLAFTGDVGETSATVRSLACQGLEFMGIKLDEEKNRN 524

Query: 362 TIRGKE-GIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
             R  +  +IST DS V VLVV  ++E ++A +T   +E+
Sbjct: 525 LGRFDDFAVISTDDSPVTVLVVANDDERLVAWETLRAIER 564


Lambda     K      H
   0.318    0.138    0.391 

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: 720
Number of extensions: 37
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: 403
Length of database: 768
Length adjustment: 36
Effective length of query: 367
Effective length of database: 732
Effective search space:   268644
Effective search space used:   268644
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: 53 (25.0 bits)

Align candidate WP_027458048.1 K420_RS0110665 (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.2600497.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-135  436.9   0.0   4.1e-135  436.5   0.0    1.1  1  NCBI__GCF_000519045.1:WP_027458048.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000519045.1:WP_027458048.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.5   0.0  4.1e-135  4.1e-135       4     402 ..     165     560 ..     162     563 .. 0.93

  Alignments for each domain:
  == domain 1  score: 436.5 bits;  conditional E-value: 4.1e-135
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                            k++vln G s + f ++d+e+s    ++g++++   + +ri  v+ g ++++ + a  + +   k + ++  
  NCBI__GCF_000519045.1:WP_027458048.1 165 GKVIVLNVGISQIHFGIYDTEESGAD-VHGIIDHADQQTTRIA-VTVGPQQKTMEHAPFKLSDLFKVMQEATA 235
                                           59*******************97777.8********9999777.56665555555555555555555544332 PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                               + + + ++++++GHRvvhGg+kf++sv++t  v+++i++++ +APlHnpa++ gi+ ++  kv +++++
  NCBI__GCF_000519045.1:WP_027458048.1 236 LlGPAFTFHPEDVTAVGHRVVHGGNKFSSSVVITPAVIADIEELAVFAPLHNPANVAGIRVAQ--KVFPNVPH 306
                                           2357889999*****************************************************..89999*** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtafHqt++  aylY+lPy+lyk++g+RrYGfHGtsh+yv+ +aa++l++pl +l++i+cHlG Gas++
  NCBI__GCF_000519045.1:WP_027458048.1 307 VAVFDTAFHQTLAPYAYLYGLPYELYKQHGIRRYGFHGTSHRYVSLKAAEVLQRPLGELEIISCHLGIGASLC 379
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+  G+sidt+mG+tP +Gl+m +RsG+iDpa++ +l+e++ +s +++ +++n +sGl gisg+ssD+Rdi++
  NCBI__GCF_000519045.1:WP_027458048.1 380 AIDHGRSIDTTMGMTPTDGLIMPSRSGSIDPAVMIHLMEQHHMSPEQLSTLVNSESGLKGISGISSDIRDIEA 452
                                           ************************************************************************* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           + +eg+++a lA k y++ ++k ig+y+a++ g +D + Ftg +Ge++a+vr l++++le++G+kld+e+n +
  NCBI__GCF_000519045.1:WP_027458048.1 453 AAAEGHHRALLAHKAYCYQVRKNIGAYVAAMGG-IDVLAFTGDVGETSATVRSLACQGLEFMGIKLDEEKNRN 524
                                           *******************************76.************************************986 PP

                             TIGR00016 368 a.rsgkesvisteeskvkvlviptneelviaeDalr 402
                                             r+ + +vist++s v+vlv+  ++e ++a ++lr
  NCBI__GCF_000519045.1:WP_027458048.1 525 LgRFDDFAVISTDDSPVTVLVVANDDERLVAWETLR 560
                                           5589999*********************99988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (768 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: 23.36
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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