GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Galbibacter marinus ck-I2-15

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_008990778.1 I215_RS04525 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000300875.1:WP_008990778.1
          Length = 395

 Score =  387 bits (994), Expect = e-112
 Identities = 203/399 (50%), Positives = 282/399 (70%), Gaps = 9/399 (2%)

Query: 2   RVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIER-ELPDHE 60
           ++LVIN+GSSSIK+QL+ M GE V+  G+ E IG+  +  +H    + ++ E  E+ +H+
Sbjct: 3   KILVINAGSSSIKFQLMRMPGEIVIASGLVESIGLSNAA-IHYKSKKMNISETVEIENHQ 61

Query: 61  EALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAP 120
             L+ I   L+D + G IK + EID VGHRVVHGG+ F  +V +D++V   I+ +  LAP
Sbjct: 62  VGLERIAALLMDSERGAIKSVDEIDVVGHRVVHGGKDFSSTVFIDDKVKATIKRLFSLAP 121

Query: 121 LHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHG 180
           LHNP N  GI+ A K+ P    VAVFDTAFHQTIP++AY YAIP  + ++  IR YGFHG
Sbjct: 122 LHNPHNYTGIEVAEKVFPNAKKVAVFDTAFHQTIPERAYKYAIPDSFLKENYIRLYGFHG 181

Query: 181 TSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTR 240
           TSH+YVS +A + + KK  + K+I+ H+GNG S+ AV+ GK VD SMGF P+ GL+MGTR
Sbjct: 182 TSHKYVSTKAKDFISKK--KSKLISIHLGNGCSITAVQNGKSVDHSMGFGPVNGLIMGTR 239

Query: 241 SGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKL 300
           SGD+D ++ F+++   G +  E+ +IL+KKSG+ G++ GF SD+R+IE+ A KGD  C+L
Sbjct: 240 SGDIDQSVIFYMVNTLGYTLDEVSEILHKKSGMIGMT-GF-SDLREIEDRAEKGDRRCQL 297

Query: 301 VLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNE 360
            LE+  YRI KYIG+YAAAMNGVD IVFTAG+GENS + R  +C  +++LG++L+  KN 
Sbjct: 298 ALEMNAYRIKKYIGSYAAAMNGVDVIVFTAGIGENSSVLRRMICDDMDYLGIELEDYKN- 356

Query: 361 ETIRGKEG-IISTPDSRVKVLVVPTNEELMIARDTKEIV 398
             +R  E  IIS   S+V VLVVPTNEEL IA+D  E++
Sbjct: 357 -NVRSTENRIISKESSKVLVLVVPTNEELEIAKDCYEMI 394


Lambda     K      H
   0.318    0.138    0.391 

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: 424
Number of extensions: 19
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: 403
Length of database: 395
Length adjustment: 31
Effective length of query: 372
Effective length of database: 364
Effective search space:   135408
Effective search space used:   135408
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_008990778.1 I215_RS04525 (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.72243.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-150  487.3   7.1   1.7e-150  487.2   7.1    1.0  1  NCBI__GCF_000300875.1:WP_008990778.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000300875.1:WP_008990778.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.2   7.1  1.7e-150  1.7e-150       4     404 ..       2     394 ..       1     395 [] 0.97

  Alignments for each domain:
  == domain 1  score: 487.2 bits;  conditional E-value: 1.7e-150
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           kkilv+naGsss+kf+l+ +  +e v++sglve i l++a i  +++ + + +e+++ie+h+ ++++++  l+
  NCBI__GCF_000300875.1:WP_008990778.1   2 KKILVINAGSSSIKFQLMRMP-GEIVIASGLVESIGLSNAAIHYKSK-KMNISETVEIENHQVGLERIAALLM 72 
                                           89*******************.7*****************8886554.5788999*****************9 PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                           + ++  +k+ +ei+++GHRvvhGg++f+++v ++d+v + ik++ +lAPlHnp + +gie +   kv ++ak+
  NCBI__GCF_000300875.1:WP_008990778.1  73 DsERGAIKSVDEIDVVGHRVVHGGKDFSSTVFIDDKVKATIKRLFSLAPLHNPHNYTGIEVAE--KVFPNAKK 143
                                           98999**********************************************************..899999** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtafHqtipe+ay Ya+P s+ ke+ +R YGfHGtshkyv+ +a++ + k  ++++li++HlGnG s++
  NCBI__GCF_000300875.1:WP_008990778.1 144 VAVFDTAFHQTIPERAYKYAIPDSFLKENYIRLYGFHGTSHKYVSTKAKDFISK--KKSKLISIHLGNGCSIT 214
                                           ******************************************************..999************** PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           av+nGks+d smG+ P++Gl+mGtRsGdiD ++i+y+ +tlg +lde+ e+l kksG++g++g  sDlR+i+d
  NCBI__GCF_000300875.1:WP_008990778.1 215 AVQNGKSVDHSMGFGPVNGLIMGTRSGDIDQSVIFYMVNTLGYTLDEVSEILHKKSGMIGMTG-FSDLREIED 286
                                           ***************************************************************.68******* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           + e+g+ +++lAl++ ++Ri+kyig+y+a+++g +D ivFt+GiGen++ +r++++++++ lG++l+  +nn 
  NCBI__GCF_000300875.1:WP_008990778.1 287 RAEKGDRRCQLALEMNAYRIKKYIGSYAAAMNG-VDVIVFTAGIGENSSVLRRMICDDMDYLGIELEDYKNN- 357
                                           *******************************88.**********************************9999. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404
                                            rs+++++is+e skv vlv+ptneel ia+D+++++
  NCBI__GCF_000300875.1:WP_008990778.1 358 VRSTENRIISKESSKVLVLVVPTNEELEIAKDCYEMI 394
                                           89*******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (395 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.24
//
[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:

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