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.31306.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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 3.38
//
[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:

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:

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:

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:

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