Alignments for a candidate for ackA in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Oceanisphaera arctica V1-41

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_104486274.1 UN63_RS08110 acetate kinase

Query= BRENDA::P63411
         (400 letters)



>NCBI__GCF_002936955.1:WP_104486274.1
          Length = 406

 Score =  575 bits (1481), Expect = e-168
 Identities = 280/400 (70%), Positives = 337/400 (84%), Gaps = 2/400 (0%)

Query: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60
           M+SKLVLVLNCGSSSLKFAI+DA +G+E LSG+AECF+LP+ RIKW +DG K  A+LGAG
Sbjct: 1   MTSKLVLVLNCGSSSLKFAILDAESGNERLSGIAECFYLPDTRIKWTLDGHKGSASLGAG 60

Query: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120
           AAH +AL+FIV+ +L Q P L A L A+GHR+VHGGE++T SV+IDESVIQGI+D AS A
Sbjct: 61  AAHQQALDFIVDKLLMQNPVLMANLCAVGHRVVHGGEQFTQSVLIDESVIQGIEDCASLA 120

Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180
           PLHNPAHL+GIA A +SFP+L    VAVFDTAFHQ+MPE +YLYA+PY LY+EHG+RRYG
Sbjct: 121 PLHNPAHLVGIASARRSFPELPQ--VAVFDTAFHQSMPEPAYLYAIPYHLYREHGIRRYG 178

Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240
            HGTSH+++ Q+AA+ LNKP+ ELNII+CHLGNG SV AI+NG+ VDTSMGLTPLEGLVM
Sbjct: 179 MHGTSHYFIAQQAAERLNKPLAELNIISCHLGNGASVCAIKNGESVDTSMGLTPLEGLVM 238

Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300
           GTRSGDIDPAIIFHLHDTLG S D+IN MLTKESGLLGLTE +SDCR+ E+NY    +AK
Sbjct: 239 GTRSGDIDPAIIFHLHDTLGYSTDRINTMLTKESGLLGLTEHSSDCRFAEENYDQLPEAK 298

Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360
           RA+D++C+RLAKYI  Y   +DGRLDA+VFTGGIGEN+ +VREL+L KL +LG ++D E 
Sbjct: 299 RALDIFCYRLAKYIAGYGCALDGRLDAIVFTGGIGENSGLVRELTLSKLSLLGVKLDPEA 358

Query: 361 NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
           NLAARFGK+G I    + PA VIPTNEE VIAQDA  L++
Sbjct: 359 NLAARFGKAGRITTADSTPAWVIPTNEEWVIAQDALALSS 398


Lambda     K      H
   0.318    0.134    0.384 

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: 525
Number of extensions: 9
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: 400
Length of database: 406
Length adjustment: 31
Effective length of query: 369
Effective length of database: 375
Effective search space:   138375
Effective search space used:   138375
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_104486274.1 UN63_RS08110 (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.892029.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-171  554.7   0.0     6e-171  554.6   0.0    1.0  1  NCBI__GCF_002936955.1:WP_104486274.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002936955.1:WP_104486274.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.6   0.0    6e-171    6e-171       1     403 [.       1     396 [.       1     398 [. 0.97

  Alignments for each domain:
  == domain 1  score: 554.6 bits;  conditional E-value: 6e-171
                             TIGR00016   1 mkskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                           m+sk++lvln+Gssslkfa+ldae++++  lsg++e++ l+++rik+  dg+k+++   a ++h++a++++++
  NCBI__GCF_002936955.1:WP_104486274.1   1 MTSKLVLVLNCGSSSLKFAILDAESGNER-LSGIAECFYLPDTRIKWTLDGHKGSASLGAGAAHQQALDFIVD 72 
                                           56899*******************99999.9****************************************** PP

                             TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           +l  ++    +++++ ++GHRvvhGge+ft+sv+++++v+++i+d ++lAPlHnpa+l gi ++      ++ 
  NCBI__GCF_002936955.1:WP_104486274.1  73 KLLMQN--PVLMANLCAVGHRVVHGGEQFTQSVLIDESVIQGIEDCASLAPLHNPAHLVGIASAR--RSFPEL 141
                                           ***877..557899**************************************************9..667788 PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                           ++vavFDtafHq +pe+aylYa+Py+ly+e+g+RrYG+HGtsh++++q+aa+ lnkpl++ln+i+cHlGnGas
  NCBI__GCF_002936955.1:WP_104486274.1 142 PQVAVFDTAFHQSMPEPAYLYAIPYHLYREHGIRRYGMHGTSHYFIAQQAAERLNKPLAELNIISCHLGNGAS 214
                                           9************************************************************************ PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292
                                           v+a+knG+s+dtsmGltPLeGlvmGtRsGdiDpaii++l++tlg s+d i+++l+k+sGllg+++ ssD+R  
  NCBI__GCF_002936955.1:WP_104486274.1 215 VCAIKNGESVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDTLGYSTDRINTMLTKESGLLGLTEHSSDCRFA 287
                                           ************************************************************************* PP

                             TIGR00016 293 ldkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldleln 365
                                           ++++ ++  eak+Al+++++R+akyi+ y  +l+g+lDaivFtgGiGen+  vrel+l+kl +lG+kld+e n
  NCBI__GCF_002936955.1:WP_104486274.1 288 EENY-DQLPEAKRALDIFCYRLAKYIAGYGCALDGRLDAIVFTGGIGENSGLVRELTLSKLSLLGVKLDPEAN 359
                                           ****.55669*************************************************************** PP

                             TIGR00016 366 naarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                            aar+gk + i+t +s+  + viptnee+via+Dal l
  NCBI__GCF_002936955.1:WP_104486274.1 360 LAARFGKAGRITTADST-PAWVIPTNEEWVIAQDALAL 396
                                           *************9996.6899************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (406 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.25
//
[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