Alignments for a candidate for ackA in Gracilibacillus halophilus YIM-C55.5

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Gracilibacillus halophilus YIM-C55.5

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_003467979.1 J416_RS07685 acetate kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000359605.1:WP_003467979.1
          Length = 399

 Score =  631 bits (1627), Expect = 0.0
 Identities = 303/395 (76%), Positives = 354/395 (89%)

Query: 1   MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60
           M  I+AINAGSSSLKFQL +MP+ETV  KGL+ERIGI+DSVFT+  N  +     DIPDH
Sbjct: 1   MQNILAINAGSSSLKFQLIQMPAETVKAKGLIERIGISDSVFTLEYNDNEQEWQQDIPDH 60

Query: 61  AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120
             AVK+LL+KLT  G+I  L+EIDGIGHRVVHGGEKFSDSVL+T+E I++IE++SELAPL
Sbjct: 61  EQAVKLLLDKLTSVGVIDSLDEIDGIGHRVVHGGEKFSDSVLITEEVIQQIEEVSELAPL 120

Query: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 180
           HNPAN+ GI+AF+E+LPNVP+VAVFDTAFHQTMPEQ+YLYSLPYEYYEK+GIRKYGFHGT
Sbjct: 121 HNPANLTGIRAFREILPNVPSVAVFDTAFHQTMPEQAYLYSLPYEYYEKYGIRKYGFHGT 180

Query: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 240
           SHKYV++RA+EL+G P   LRL+SCHLGNGASIAA+E GKSIDTSMGFTPLAGV MGTRS
Sbjct: 181 SHKYVSQRASELMGVPQDQLRLLSCHLGNGASIAAIENGKSIDTSMGFTPLAGVTMGTRS 240

Query: 241 GNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETAL 300
           GNIDPALIPYIM+KTGQ+A EV+N LNKKSG+L +SGFSSDLRDI E +KEG+ERAE AL
Sbjct: 241 GNIDPALIPYIMDKTGQSAQEVMNILNKKSGMLALSGFSSDLRDIEEKSKEGDERAELAL 300

Query: 301 EVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVR 360
           +VFA RIHKY+GSYAARM GVDAI+FTAG+GENSV +RERVL+GLEFMGVYWDP LN VR
Sbjct: 301 QVFAERIHKYVGSYAARMHGVDAIVFTAGVGENSVAIRERVLKGLEFMGVYWDPKLNEVR 360

Query: 361 GEEAFISYPHSPVKVMIIPTDEEVMIARDVVRLAK 395
           G+E F++YPHSPVKV+IIPT+EEVM+ARD VRL++
Sbjct: 361 GKERFVNYPHSPVKVIIIPTNEEVMLARDTVRLSQ 395


Lambda     K      H
   0.317    0.136    0.381 

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: 523
Number of extensions: 12
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: 395
Length of database: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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_003467979.1 J416_RS07685 (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.996241.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-180  586.3   0.0   1.5e-180  586.2   0.0    1.0  1  NCBI__GCF_000359605.1:WP_003467979.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359605.1:WP_003467979.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.2   0.0  1.5e-180  1.5e-180       4     404 ..       2     394 ..       1     395 [. 0.99

  Alignments for each domain:
  == domain 1  score: 586.2 bits;  conditional E-value: 1.5e-180
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           + il +naGssslkf+l+++  +e+v ++gl+eri ++++ ++t+e +++++e +++i+dhe+avk ll++l+
  NCBI__GCF_000359605.1:WP_003467979.1   2 QNILAINAGSSSLKFQLIQMP-AETVKAKGLIERIGISDS-VFTLEYNDNEQEWQQDIPDHEQAVKLLLDKLT 72 
                                           689******************.79999*************.999***************************** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                               ++++l+ei+ iGHRvvhGgekf++sv++t+ev+++i+++selAPlHnpa+l+gi+a+   ++l++++ v
  NCBI__GCF_000359605.1:WP_003467979.1  73 -SVGVIDSLDEIDGIGHRVVHGGEKFSDSVLITEEVIQQIEEVSELAPLHNPANLTGIRAFR--EILPNVPSV 142
                                           .699**********************************************************..99******* PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDtafHqt+pe+aylY+lPy++y+++g+R+YGfHGtshkyv+qra++l++ p d+l+l++cHlGnGas++a
  NCBI__GCF_000359605.1:WP_003467979.1 143 AVFDTAFHQTMPEQAYLYSLPYEYYEKYGIRKYGFHGTSHKYVSQRASELMGVPQDQLRLLSCHLGNGASIAA 215
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           ++nGksidtsmG+tPL+G+ mGtRsG+iDpa+i y+++++g+s++e+ ++lnkksG+l++sg+ssDlRdi++k
  NCBI__GCF_000359605.1:WP_003467979.1 216 IENGKSIDTSMGFTPLAGVTMGTRSGNIDPALIPYIMDKTGQSAQEVMNILNKKSGMLALSGFSSDLRDIEEK 288
                                           ************************************************************************* PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                            +eg+e+a+lAl+v+++Ri+ky+g+y+a+++g +DaivFt+G+Gen++ +re+vl++le++G+++d++ln+  
  NCBI__GCF_000359605.1:WP_003467979.1 289 SKEGDERAELALQVFAERIHKYVGSYAARMHG-VDAIVFTAGVGENSVAIRERVLKGLEFMGVYWDPKLNE-- 358
                                           ******************************88.**************************************.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404
                                            +gke+++++++s vkv++iptnee+++a+D++rl+
  NCBI__GCF_000359605.1:WP_003467979.1 359 VRGKERFVNYPHSPVKVIIIPTNEEVMLARDTVRLS 394
                                           9*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (399 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: 15.83
//
[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 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