Alignments for a candidate for ackA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Paraburkholderia bryophila 376MFSha3.1

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate H281DRAFT_02796 H281DRAFT_02796 acetate kinase

Query= SwissProt::P74879
         (404 letters)



>FitnessBrowser__Burk376:H281DRAFT_02796
          Length = 385

 Score =  242 bits (618), Expect = 1e-68
 Identities = 157/389 (40%), Positives = 207/389 (53%), Gaps = 28/389 (7%)

Query: 3   YKIMAINAGSSSLKFQLLEMPQGD--MLCQGLIERIGMADAQVTIKTHSQKW--QETVPV 58
           + I+ +N+GSSSLKF L E    D  +L +G  + IG  D ++ I     +   QE   +
Sbjct: 10  HTILVLNSGSSSLKFGLFEHSGDDESLLLEGSAQGIGRRDGRLRIAAPDGRVLVQEEHVL 69

Query: 59  ADHRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAEL 118
               DA    L+KL              VGHRV HGG   +    +T E   +++     
Sbjct: 70  ESQTDA----LQKLSTVLAQQHHEQPTAVGHRVVHGGPHLRSHQRLTPEVRRRLQDAVHF 125

Query: 119 APLHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGF 178
           APLH P     I   +++   A   A FDTAFH TL   A    LP   Y+E G+ RYGF
Sbjct: 126 APLHIPPALDLIDEAQKIFGGAQHFACFDTAFHATLPPRAAQLALP-RRYSEAGVIRYGF 184

Query: 179 HGTSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMG 238
           HG S++     L  +LG  L A RV+C HLGNGSS+CA+++GRSV+TSMG TP  GV MG
Sbjct: 185 HGLSYES----LVAQLGATLPA-RVVCAHLGNGSSVCALRDGRSVDTSMGMTPTGGVPMG 239

Query: 239 TRSGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDVEQAANTGNRQAK 298
           TR GD+DP +L ++ + E      L  LLN  SGL G +   SD + +EQ A  G+  A 
Sbjct: 240 TRCGDLDPGVLLYLMRVEKLDANGLETLLNRHSGLAGYADGESDMQALEQRAAAGDPHAS 299

Query: 299 LALTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEKN 358
           LAL  FA  +R TIG Y   +GG+D LVFTGGIGE+S + R  +C  L FLGL       
Sbjct: 300 LALDAFATAVRKTIGGYAALLGGIDLLVFTGGIGEHSVQMRKRICEGLSFLGL------- 352

Query: 359 QRNATFIQTENALVKVAVINTNEELMIAQ 387
                     +A  KV V++T EE  IA+
Sbjct: 353 -------HEGDASGKVRVLHTEEEKQIAR 374


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: 363
Number of extensions: 15
Number of successful extensions: 4
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: 385
Length adjustment: 31
Effective length of query: 373
Effective length of database: 354
Effective search space:   132042
Effective search space used:   132042
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 H281DRAFT_02796 H281DRAFT_02796 (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.29681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
      3e-96  308.5   0.0    8.3e-96  307.1   0.0    1.6  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02796  H281DRAFT_02796 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02796  H281DRAFT_02796 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.1   0.0   8.3e-96   8.3e-96       4     360 ..      10     354 ..       7     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 307.1 bits;  conditional E-value: 8.3e-96
                                    TIGR00016   4 kkilvlnaGssslkfalldaen.sekvllsglverikleeariktv.edgekkeeeklaiedheea 67 
                                                  + ilvln+Gssslkf l+++++  e++ll+g ++ i   + r+ +   dg    +e+   e+++ a
  lcl|FitnessBrowser__Burk376:H281DRAFT_02796  10 HTILVLNSGSSSLKFGLFEHSGdDESLLLEGSAQGIGRRDGRLRIAaPDGRVLVQEEHVLESQTDA 75 
                                                  689****************997467779*********999988877356666778888899999** PP

                                    TIGR00016  68 vkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaeleg 133
                                                  ++kl + l +     +++++ +++GHRvvhGg ++ +   +t ev ++++d++++APlH p++l+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02796  76 LQKLSTVLAQ-----QHHEQPTAVGHRVVHGGPHLRSHQRLTPEVRRRLQDAVHFAPLHIPPALDL 136
                                                  ***9999995.....778999********************************************* PP

                                    TIGR00016 134 ieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakl 199
                                                  i++++  k+   a++ a+FDtafH t+p +a+  alP + y e gv rYGfHG+s++ +  ++  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_02796 137 IDEAQ--KIFGGAQHFACFDTAFHATLPPRAAQLALP-RRYSEAGVIRYGFHGLSYESLVAQLGAT 199
                                                  *****..7778888***********************.678999************9777776666 PP

                                    TIGR00016 200 lnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls 265
                                                  l       +++ +HlGnG+sv+a+++G+s+dtsmG+tP  G+ mGtR+Gd+Dp+++ yl+  ++l 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02796 200 LPA-----RVVCAHLGNGSSVCALRDGRSVDTSMGMTPTGGVPMGTRCGDLDPGVLLYLMRVEKLD 260
                                                  655.....89******************************************************** PP

                                    TIGR00016 266 ldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDa 331
                                                  ++ +e++ln++sGl g ++  sD+  ++++ ++g+ +a+lAl+ ++  ++k ig y+a l g +D 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02796 261 ANGLETLLNRHSGLAGYADGESDMQALEQRAAAGDPHASLALDAFATAVRKTIGGYAALLGG-IDL 325
                                                  ************************************************************66.*** PP

                                    TIGR00016 332 ivFtgGiGenaaevrelvleklevlGlkl 360
                                                  +vFtgGiGe ++++r++++e+l +lGl+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02796 326 LVFTGGIGEHSVQMRKRICEGLSFLGLHE 354
                                                  **************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (385 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 4.09
//
[ok]

This GapMind analysis is from Sep 17 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