Alignments for a candidate for ackA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Halomonas desiderata SP1

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate WP_086510347.1 BZY95_RS12985 acetate/propionate family kinase

Query= SwissProt::P74879
         (404 letters)



>NCBI__GCF_002151265.1:WP_086510347.1
          Length = 406

 Score =  244 bits (622), Expect = 4e-69
 Identities = 163/404 (40%), Positives = 224/404 (55%), Gaps = 27/404 (6%)

Query: 1   MSYKIMAINAGSSSLKFQLLEMPQ--GDMLCQ--------GLIERIGMADAQVTIKTHSQ 50
           MS +I+A+N+GSSSLKF L +       M  Q        GL  R+   + Q    T   
Sbjct: 1   MSGEILAVNSGSSSLKFALFDAASTASPMAMQVRYRGQFSGLGSRV-RTELQAGFGTELN 59

Query: 51  KWQET----VPVA-DHRDAVTLLLEKLLGYQIIN-SLRDIDGVGHRVAHGGEFFKDSTLV 104
           + Q+     VP A DH  A    LE+LL +   N +L DI  VGHR+ HGG  +++   +
Sbjct: 60  EEQDAALYDVPAALDHAGA----LERLLQWVEDNPALGDIRAVGHRIVHGGARYREPLRL 115

Query: 105 TDETLAQIERLAELAPLHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLP 164
             ++ A +E L ELAPLH P     +     L P  P  A FDTAFH T    A  +PLP
Sbjct: 116 DADSFAALEALNELAPLHQPHGLAPVRSLTGLRPGLPQYACFDTAFHATQPAVAQTFPLP 175

Query: 165 WHYYAELGIRRYGFHGTSHKYVSGVLAEKL--GVPLSALRVICCHLGNGSSICAIKNGRS 222
              + E G+ RYGFHG S  YVS  L+ +   G  L   RV+  HLGNG+S+CA+++G+S
Sbjct: 176 -RRFREQGVIRYGFHGLSFDYVSRALSAERQHGQALPGGRVVIAHLGNGASLCALRDGKS 234

Query: 223 VNTSMGFTPQSGVMMGTRSGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSD 282
           V  + GFT   G+MMGTRSG +DP ++  +   E  + + + +LL  ESGLLGVSG+S D
Sbjct: 235 VAATTGFTAVEGLMMGTRSGSLDPGLVLHLILHEGMSAEAVQRLLYKESGLLGVSGISGD 294

Query: 283 YRDVEQAANTGNRQAKLALTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAV 342
            R++  +      +A  A+ LF  RI   IGS    +GGLD LVFT GIGE +A  R+AV
Sbjct: 295 MRELLASEVP---EAAEAIALFVYRIVREIGSLAAALGGLDHLVFTAGIGERAAPIRAAV 351

Query: 343 CHNLQFLGLAVDEEKNQRNATFIQTENALVKVAVINTNEELMIA 386
               ++LG  +D+  N  NA  I   ++ + + VI T+EE MIA
Sbjct: 352 AQGCEWLGARLDDAANAANALDIAGPDSRLGLWVIPTDEERMIA 395


Lambda     K      H
   0.319    0.135    0.392 

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: 373
Number of extensions: 15
Number of successful extensions: 5
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: 404
Length of database: 406
Length adjustment: 31
Effective length of query: 373
Effective length of database: 375
Effective search space:   139875
Effective search space used:   139875
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_086510347.1 BZY95_RS12985 (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.2249601.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-101  326.3   0.0   1.5e-101  326.0   0.0    1.0  1  NCBI__GCF_002151265.1:WP_086510347.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002151265.1:WP_086510347.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.0   0.0  1.5e-101  1.5e-101       5     397 ..       4     395 ..       1     402 [. 0.91

  Alignments for each domain:
  == domain 1  score: 326.0 bits;  conditional E-value: 1.5e-101
                             TIGR00016   5 kilvlnaGssslkfalldaen.....sekv......llsglverikleeariktvedgekkeeeklaie...d 63 
                                            il +n+Gssslkfal+da++     +  +       +sgl  r+  e +  +  e +e+++++  +++   d
  NCBI__GCF_002151265.1:WP_086510347.1   4 EILAVNSGSSSLKFALFDAAStaspmA--MqvryrgQFSGLGSRVRTELQAGFGTELNEEQDAALYDVPaalD 74 
                                           79****************997544332..1445666789******9999999999999999988776543338 PP

                             TIGR00016  64 heeavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegiea 136
                                           h+ a+++ll+ +++       l +i+++GHR+vhGg ++ e   +++++ ++++ + elAPlH p  l  +++
  NCBI__GCF_002151265.1:WP_086510347.1  75 HAGALERLLQWVED----NPALGDIRAVGHRIVHGGARYREPLRLDADSFAALEALNELAPLHQPHGLAPVRS 143
                                           ************96....5799*************************************************** PP

                             TIGR00016 137 vlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqr..aakllnkplddl 207
                                           ++     +  ++ a+FDtafH t p  a  ++lP + ++e+gv rYGfHG+s+ yv++   a++  +++l   
  NCBI__GCF_002151265.1:WP_086510347.1 144 LT--GLRPGLPQYACFDTAFHATQPAVAQTFPLP-RRFREQGVIRYGFHGLSFDYVSRAlsAERQHGQALPGG 213
                                           **..5666778***********************.667889999*************972256789999**** PP

                             TIGR00016 208 nlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGll 280
                                           +++++HlGnGas++a+++Gks+  + G+t +eGl+mGtRsG++Dp+++ +l  ++g+s+++++++l k+sGll
  NCBI__GCF_002151265.1:WP_086510347.1 214 RVVIAHLGNGASLCALRDGKSVAATTGFTAVEGLMMGTRSGSLDPGLVLHLILHEGMSAEAVQRLLYKESGLL 286
                                           ************************************************************************* PP

                             TIGR00016 281 gisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvlekl 353
                                           g+sg+s D+R++l+       ea+ A+ ++v+Ri + ig+ +a+l g lD +vFt+GiGe aa +r+ v ++ 
  NCBI__GCF_002151265.1:WP_086510347.1 287 GVSGISGDMRELLASE---VPEAAEAIALFVYRIVREIGSLAAALGG-LDHLVFTAGIGERAAPIRAAVAQGC 355
                                           ************9876...568999********************76.************************* PP

                             TIGR00016 354 evlGlkldlelnnaarsgkesvisteeskvkvlviptneelvia 397
                                           e lG +ld + n      +   i+ ++s++ + vipt+ee +ia
  NCBI__GCF_002151265.1:WP_086510347.1 356 EWLGARLDDAANA----ANALDIAGPDSRLGLWVIPTDEERMIA 395
                                           *********9999....45566999******************8 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.58
//
[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