Alignments for a candidate for ackA in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Polaromonas naphthalenivorans CJ2

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011802935.1 PNAP_RS17810 acetate/propionate family kinase

Query= BRENDA::P38502
         (408 letters)



>NCBI__GCF_000015505.1:WP_011802935.1
          Length = 411

 Score =  267 bits (682), Expect = 5e-76
 Identities = 165/402 (41%), Positives = 242/402 (60%), Gaps = 14/402 (3%)

Query: 3   VLVINAGSSSLKYQLIDMTN-ESALAV---GLCERIGIDNSIITQKKFDGKKLEKLTDLP 58
           +LVIN+GSSS+K+   D+   +SALA    G  E IG    ++   + DG  LE      
Sbjct: 5   LLVINSGSSSVKFAAYDVARPDSALARIANGRIEGIGGKPRLLVWGQ-DGALLEDSRISV 63

Query: 59  THKDAL--EEVVKALTDDEFGVIKDMGEINAVGHRVVHGGEKFTTSALYDEGVEKAIKDC 116
           +    L  EE  +AL D   G       + AVGHRVVHGGE+F   A     +   +   
Sbjct: 64  SADPVLGPEEAFEALFD-WLGRHAAGRTLLAVGHRVVHGGERFARPARVTPEILAQLDGF 122

Query: 117 FELAPLHNPPNMMGISACAEIMPGTPMVIVFDTAFHQTMPPYAYMYALPYDLYEKHGVRK 176
             LAPLH P N+  I A A ++P    V  FDT FH T P  A   ALP  + E  GV++
Sbjct: 123 TPLAPLHQPHNLSAIRAIASLLPELAQVACFDTEFHATQPWVAQACALPRHITEA-GVKR 181

Query: 177 YGFHGTSHKYVAERAALMLGKPAEETKIITCHLGNGSSITAVEGGKSVETSMGFTPLEGL 236
           YGFHG S++Y+A      LG  A   +++  HLGNG+S+ A++  +SV ++MGFT L+GL
Sbjct: 182 YGFHGLSYEYIASVLPGHLGAAANG-RVVVAHLGNGASLCAMQDRRSVASTMGFTALDGL 240

Query: 237 AMGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEAASKGNR 296
            MGTRCGS+DP +V +LM   G++ + ++ L+ ++SG+LGVSG+S D R ++   +    
Sbjct: 241 MMGTRCGSLDPGVVLYLMSGLGMSVQAVEKLLYEQSGLLGVSGISGDMRTVE---ASDTP 297

Query: 297 KAELALEIFAYKVKKFIGEYSAVLNGADAVVFTAGIGENSASIRKRILTGLDGIGIKIDD 356
           +A  A+E++ Y+V + +G  +A L G DA+VFTAGIGENSAS+R+R+      +G+ +D+
Sbjct: 298 EARQAIELYVYRVGQQLGSLAAPLGGLDALVFTAGIGENSASLRRRVCEDAAWLGVALDE 357

Query: 357 EKNKIRGQ-EIDISTPDAKVRVFVIPTNEELAIARETKEIVE 397
           + N+ +      ISTP ++V V+VIPTNEEL IAR T+ +++
Sbjct: 358 DANQAQASGPRCISTPGSRVAVWVIPTNEELMIARHTQAVLQ 399


Lambda     K      H
   0.316    0.135    0.380 

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: 374
Number of extensions: 13
Number of successful extensions: 6
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: 411
Length adjustment: 31
Effective length of query: 377
Effective length of database: 380
Effective search space:   143260
Effective search space used:   143260
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_011802935.1 PNAP_RS17810 (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.14399.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-112  360.2   0.0   7.1e-112  360.0   0.0    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011802935.1  PNAP_RS17810 acetate/propionate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802935.1  PNAP_RS17810 acetate/propionate family kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.0   0.0  7.1e-112  7.1e-112       3     401 ..       2     395 ..       1     399 [. 0.92

  Alignments for each domain:
  == domain 1  score: 360.0 bits;  conditional E-value: 7.1e-112
                                 TIGR00016   3 skkilvlnaGssslkfalldaensekv...llsglverikleeariktvedgekkeeeklaiedh.... 64 
                                               ++ +lv+n+Gsss+kfa +d + +++    +++g +e i  +   + + +dg   e     +++     
  lcl|NCBI__GCF_000015505.1:WP_011802935.1   2 KQALLVINSGSSSVKFAAYDVARPDSAlarIANGRIEGIGGKPRLLVWGQDGALLEDSRISVSADpvlg 70 
                                               5679******************98877556789*********999999999987666655554432222 PP

                                 TIGR00016  65 .eeavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaele 132
                                                eea ++l++ l +    +     + ++GHRvvhGge+f+  + vt e+l+++  +++lAPlH p +l+
  lcl|NCBI__GCF_000015505.1:WP_011802935.1  71 pEEAFEALFDWLGR----HAAGRTLLAVGHRVVHGGERFARPARVTPEILAQLDGFTPLAPLHQPHNLS 135
                                               27788888888885....567788999****************************************** PP

                                 TIGR00016 133 gieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraaklln 201
                                               +i+a+     l++  +va+FDt fH t p  a   alP +  +e gv+rYGfHG+s++y++  +  +l+
  lcl|NCBI__GCF_000015505.1:WP_011802935.1 136 AIRAIA--SLLPELAQVACFDTEFHATQPWVAQACALP-RHITEAGVKRYGFHGLSYEYIASVLPGHLG 201
                                               ******..7778888***********************.67789************************* PP

                                 TIGR00016 202 kplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeie 270
                                                 +++ +++v+HlGnGas++a+++ +s+  +mG+t L+Gl+mGtR+G++Dp+++ yl++ lg+s++++e
  lcl|NCBI__GCF_000015505.1:WP_011802935.1 202 A-AANGRVVVAHLGNGASLCAMQDRRSVASTMGFTALDGLMMGTRCGSLDPGVVLYLMSGLGMSVQAVE 269
                                               9.8899*************************************************************** PP

                                 TIGR00016 271 etlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiG 339
                                               ++l  +sGllg+sg+s D+R++++       ea+ A+++yv+R+ + +g+ +a l g lDa+vFt+GiG
  lcl|NCBI__GCF_000015505.1:WP_011802935.1 270 KLLYEQSGLLGVSGISGDMRTVEASD---TPEARQAIELYVYRVGQQLGSLAAPLGG-LDALVFTAGIG 334
                                               **********************9877...6789**********************76.*********** PP

                                 TIGR00016 340 enaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401
                                               en+a++r++v+e+ + lG++ld++ n+ a+    + ist+ s+v v viptneel+ia+ + 
  lcl|NCBI__GCF_000015505.1:WP_011802935.1 335 ENSASLRRRVCEDAAWLGVALDEDANQ-AQASGPRCISTPGSRVAVWVIPTNEELMIARHTQ 395
                                               **************************9.8899999***********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (411 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: 10.95
//
[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